9GRX | pdb_00009grx

NDH-PSI-LHCI supercomplex from S. oleracea


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea.

Introini, B.Hahn, A.Kuhlbrandt, W.

(2025) Nat Struct Mol Biol 32: 968-978

  • DOI: https://doi.org/10.1038/s41594-024-01478-1
  • Primary Citation of Related Structures:  
    9GRX

  • PubMed Abstract: 

    The nicotinamide adenine dinucleotide phosphate (NADPH) dehydrogenase (NDH) complex is crucial for photosynthetic cyclic electron flow and respiration, transferring electrons from ferredoxin to plastoquinone while transporting H + across the chloroplast membrane. This process boosts adenosine triphosphate production, regardless of NADPH levels. In flowering plants, NDH forms a supercomplex with photosystem I, enhancing its stability under high light. We report the cryo-electron microscopy structure of the NDH supercomplex in Spinacia oleracea at a resolution of 3.0-3.3 Å. The supercomplex consists of 41 protein subunits, 154 chlorophylls and 38 carotenoids. Subunit interactions are reinforced by 46 distinct lipids. The structure of NDH resembles that of mitochondrial complex I closely, including the quinol-binding site and an extensive internal aqueous passage for proton translocation. A well-resolved catalytic plastoquinone (PQ) occupies the PQ channel. The pronounced structural similarity to complex I sheds light on electron transfer and proton translocation within the NDH supercomplex.


  • Organizational Affiliation
    • Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 1, chloroplasticA [auth 0]157Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 1, chloroplasticB [auth 1]403Spinacia oleraceaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 2, chloroplasticC [auth 2]372Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 3, chloroplasticD [auth 3]139Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 4, chloroplasticE [auth 4]93Spinacia oleraceaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 5, chloroplasticF [auth 5]154Spinacia oleraceaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 2, chloroplasticG [auth 6]125Spinacia oleraceaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 3, chloroplasticH [auth 7]144Spinacia oleraceaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
peptidylprolyl isomeraseI [auth 8]143Spinacia oleraceaMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseJ [auth 9]174Spinacia oleraceaMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 1, chloroplasticK [auth A]350Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplasticL [auth B]488Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 3, chloroplasticM [auth C]115Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase chain 4, chloroplasticN [auth D]498Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 4L, chloroplasticO [auth E]100Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 5, chloroplasticP [auth F]742Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 6, chloroplasticQ [auth G]176Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit H, chloroplasticR [auth H]389Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit I, chloroplasticS [auth I]163Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit J, chloroplasticT [auth J]158Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit K, chloroplasticU [auth K]202Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit L, chloroplasticV [auth L]109Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0JHB5 (Spinacia oleracea)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit M, chloroplasticW [auth M]141Spinacia oleraceaMutation(s): 0 
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Find proteins for A0A9R0JNY9 (Spinacia oleracea)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit N, chloroplasticX [auth N]165Spinacia oleraceaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit O, chloroplasticY [auth O]95Spinacia oleraceaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit U, chloroplasticZ [auth U]240Spinacia oleraceaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1AA [auth a]742Spinacia oleraceaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2BA [auth b]733Spinacia oleraceaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerCA [auth c]81Spinacia oleraceaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticDA [auth d]143Spinacia oleraceaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, chloroplasticEA [auth e]68Spinacia oleraceaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticFA [auth f]153Spinacia oleraceaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticGA [auth g]97Spinacia oleraceaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplasticHA [auth h]95Spinacia oleraceaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIIA [auth i]31Spinacia oleraceaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXJA [auth j]42Spinacia oleraceaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-KKA [auth k]130Spinacia oleraceaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplasticLA [auth l]160Spinacia oleraceaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticMA [auth w]215Spinacia oleraceaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticNA [auth x]198Spinacia oleraceaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticOA [auth y]221Spinacia oleraceaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticPA [auth z]193Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0J8B1 (Spinacia oleracea)
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Go to UniProtKB:  A0A9R0J8B1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9R0J8B1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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OI [auth x],
UE [auth b],
WB [auth a]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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CI [auth x]
HH [auth w]
II [auth x]
MH [auth w]
MJ [auth z]
CI [auth x],
HH [auth w],
II [auth x],
MH [auth w],
MJ [auth z],
OH [auth w],
QI [auth x],
UJ [auth z],
YH [auth x]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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AC [auth a]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AD [auth a]
AE [auth b]
AI [auth x]
AJ [auth y]
BC [auth a]
AD [auth a],
AE [auth b],
AI [auth x],
AJ [auth y],
BC [auth a],
BD [auth a],
BE [auth b],
BF [auth b],
BG [auth f],
BI [auth x],
BJ [auth y],
BK [auth z],
CD [auth a],
CE [auth b],
CG [auth f],
CH [auth l],
CJ [auth y],
DC [auth a],
DD [auth a],
DE [auth b],
DG [auth f],
DH [auth l],
DI [auth x],
DJ [auth y],
EC [auth a],
ED [auth a],
EE [auth b],
EI [auth x],
EJ [auth y],
FC [auth a],
FD [auth a],
FE [auth b],
FF [auth b],
FH [auth w],
FI [auth x],
FJ [auth y],
GC [auth a],
GD [auth a],
GE [auth b],
GF [auth b],
GH [auth w],
GI [auth x],
GJ [auth y],
HC [auth a],
HD [auth a],
HE [auth b],
HF [auth b],
HG [auth g],
HI [auth x],
IC [auth a],
ID [auth a],
IE [auth b],
IF [auth b],
IH [auth w],
JC [auth a],
JD [auth a],
JE [auth b],
JF [auth b],
JG [auth g],
JH [auth w],
JI [auth x],
KC [auth a],
KD [auth a],
KE [auth b],
KF [auth b],
KG [auth g],
KH [auth w],
KI [auth x],
KJ [auth z],
LC [auth a],
LD [auth a],
LE [auth b],
LF [auth b],
LG [auth h],
LH [auth w],
LJ [auth z],
MC [auth a],
MD [auth a],
ME [auth b],
MF [auth b],
NC [auth a],
ND [auth a],
NE [auth b],
NF [auth b],
NH [auth w],
NI [auth x],
NJ [auth z],
OC [auth a],
OD [auth a],
OE [auth b],
OF [auth b],
OG [auth j],
OJ [auth z],
PC [auth a],
PD [auth a],
PF [auth b],
PI [auth x],
PJ [auth z],
QC [auth a],
QD [auth a],
QF [auth b],
QJ [auth z],
RD [auth a],
RF [auth b],
RH [auth w],
RJ [auth z],
SC [auth a],
SD [auth a],
SF [auth b],
SH [auth w],
SJ [auth z],
TB [auth a],
TD [auth a],
TF [auth b],
TH [auth w],
TJ [auth z],
UB [auth a],
UD [auth a],
UF [auth b],
UI [auth y],
VD [auth a],
VE [auth b],
VF [auth b],
VG [auth k],
VI [auth y],
WD [auth a],
WE [auth b],
WF [auth b],
WG [auth k],
WI [auth y],
XD [auth a],
XE [auth b],
XG [auth k],
XI [auth y],
YD [auth a],
YE [auth b],
YF [auth b],
YG [auth l],
YI [auth y],
YJ [auth z],
ZC [auth a],
ZE [auth b],
ZH [auth x],
ZI [auth y]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

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CB [auth B]
HB [auth F]
LB [auth F]
SG [auth j]
UH [auth w]
CB [auth B],
HB [auth F],
LB [auth F],
SG [auth j],
UH [auth w],
VH [auth w],
ZD [auth a]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

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DB [auth B]
FB [auth D]
GG [auth f]
IB [auth F]
MB [auth H]
DB [auth B],
FB [auth D],
GG [auth f],
IB [auth F],
MB [auth H],
MI [auth x],
PH [auth w],
QG [auth j],
RG [auth j],
TA [auth 7],
WJ [auth z],
XJ [auth z]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PGT (Subject of Investigation/LOI)
Query on PGT

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AB [auth B]
BB [auth B]
CF [auth b]
DF [auth b]
EB [auth B]
AB [auth B],
BB [auth B],
CF [auth b],
DF [auth b],
EB [auth B],
FG [auth f],
GB [auth D],
JB [auth F],
JJ [auth z],
PB [auth I],
QH [auth w],
RA [auth 5],
RB [auth L],
SB [auth N],
UA [auth A],
VA [auth A],
VJ [auth z],
WA [auth A],
XA [auth A],
XB [auth a],
YB [auth a],
ZA [auth B],
ZB [auth a],
ZJ [auth z]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
PQ9 (Subject of Investigation/LOI)
Query on PQ9

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YA [auth A]5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
C43 H64 O2
JXUCGUASMMLSBH-HOHOQCMASA-N
LUT (Subject of Investigation/LOI)
Query on LUT

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CK [auth z]
DK [auth z]
HJ [auth y]
IJ [auth y]
RI [auth x]
CK [auth z],
DK [auth z],
HJ [auth y],
IJ [auth y],
RI [auth x],
SI [auth x],
WH [auth w],
XH [auth w]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
A1H1M (Subject of Investigation/LOI)
Query on A1H1M

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KB [auth F],
SA [auth 5]
4-trans-(4-trans-Propylcyclohexyl)-cyclohexyl alpha-maltoside
C27 H48 O11
ZESBUFKOCABQIP-YJUXXZBVSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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AH [auth l]
AK [auth z]
BH [auth l]
CC [auth a]
EF [auth b]
AH [auth l],
AK [auth z],
BH [auth l],
CC [auth a],
EF [auth b],
EG [auth f],
EH [auth w],
IG [auth g],
LI [auth x],
MG [auth i],
NG [auth j],
PE [auth b],
PG [auth j],
QA [auth 4],
QE [auth b],
RE [auth b],
SE [auth b],
TC [auth a],
TE [auth b],
TG [auth k],
TI [auth y],
UC [auth a],
UG [auth k],
VB [auth a],
VC [auth a],
WC [auth a],
XC [auth a],
XF [auth b],
ZG [auth l]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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AF [auth b],
RC [auth a]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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AG [auth c]
NB [auth I]
OB [auth I]
QB [auth K]
YC [auth a]
AG [auth c],
NB [auth I],
OB [auth I],
QB [auth K],
YC [auth a],
ZF [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection, Database references