9Q87 | pdb_00009q87

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8B0X


Literature

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angs. resolution bacterial ribosome structure - Part I: Mg2+.

Leonarski, F., Henning-Knechtel, A., Kirmizialtin, S., Ennifar, E., Auffinger, P.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkae1148
  • Primary Citation of Related Structures:  
    9Q87

  • PubMed Abstract: 

    The importance of Mg2+ ions for RNA structure and function cannot be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites as observed in a recent cryo-EM 1.55 Å Escherichia coli ribosome structure where incomplete ion assignments blurred our understanding of their binding patterns. We revisited this model to establish general binding principles applicable to any RNA of sufficient resolution. These principles rely on the 2.9 Å distance separating two water molecules bound in cis to Mg2+. By applying these rules, we could assign all Mg2+ ions bound with 2-4 non-water oxygens. We also uncovered unanticipated motifs where up to five adjacent nucleotides wrap around a single ion. The formation of such motifs involves a hierarchical Mg2+ ion dehydration process that plays a significant role in ribosome biogenesis and in the folding of large RNAs. Besides, we established a classification of the Mg2+…Mg2+ and Mg2+…K+ ion pairs observed in this ribosome. Overall, the uncovered binding principles enhance our understanding of the roles of ions in RNA structure and will help refining the solvation shell of other RNA systems.

    • Organizational Affiliation: 
    • Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI 5232, Switzerland.

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Entity ID: 2
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Small ribosomal subunit protein uS2233Escherichia coli BMutation(s): 0 
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Small ribosomal subunit protein bS6, fully modified isoform135Escherichia coli BMutation(s): 0 
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Small ribosomal subunit protein bS2087Escherichia coli BMutation(s): 0 
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Large ribosomal subunit protein uL2FA [auth c]273Escherichia coli BMutation(s): 0 
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Large ribosomal subunit protein uL13LA [auth i]142Escherichia coli BMutation(s): 0 
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Large ribosomal subunit protein uL14MA [auth j]123Escherichia coli BMutation(s): 0 
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Large ribosomal subunit protein bL20SA [auth p]118Escherichia coli BMutation(s): 0 
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Large ribosomal subunit protein bL25XA [auth u]94Escherichia coli BMutation(s): 0 
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Large ribosomal subunit protein bL28ZA [auth w]78Escherichia coli BMutation(s): 0 
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UniProt GroupP0A7M2
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29AB [auth x]63Escherichia coli BMutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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UniProt GroupP0A7M6
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30BB [auth y]59Escherichia coli BMutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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UniProt GroupP0AG51
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32CB [auth z]57Escherichia coli BMutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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UniProt GroupP0A7N4
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Entity ID: 1
MoleculeChains LengthOrganismImage
30S1,554Escherichia coli B
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Entity ID: 22
MoleculeChains LengthOrganismImage
mRNAV [auth X]6Escherichia coli B
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Entity ID: 23
MoleculeChains LengthOrganismImage
P-site tRNAW [auth Z]77Escherichia coli B
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Entity ID: 29
MoleculeChains LengthOrganismImage
A-site tRNACA [auth 6]2Escherichia coli B
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Entity ID: 30
MoleculeChains LengthOrganismImage
23S rRNADA [auth a]2,907Escherichia coli B
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Entity ID: 31
MoleculeChains LengthOrganismImage
5S rRNAEA [auth b]120Escherichia coli B
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TKW (Subject of Investigation/LOI)
Query on TKW
Download Ideal Coordinates CCD File 
YY [auth a]5-hydroxycytidine 5'-(dihydrogen phosphate)
C9 H14 N3 O9 P
QONOHPMEMVHOPP-UAKXSSHOSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
IH [auth 3]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU1
Query on CU1
Download Ideal Coordinates CCD File 
AH [auth A],
IAA [auth w],
IZ [auth a],
QX [auth a],
XY [auth a]		COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
AAA [auth c]
AD [auth A]
AF [auth A]
AG [auth A]
AL [auth a]
AAA [auth c],
AD [auth A],
AF [auth A],
AG [auth A],
AL [auth a],
AM [auth a],
AN [auth a],
AR [auth a],
AV [auth a],
AZ [auth a],
BAA [auth c],
BD [auth A],
BF [auth A],
BG [auth A],
BL [auth a],
BM [auth a],
BQ [auth a],
BR [auth a],
BV [auth a],
BW [auth a],
BY [auth a],
BZ [auth a],
CD [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
CJ [auth a],
CL [auth a],
CM [auth a],
CQ [auth a],
CR [auth a],
CU [auth a],
CV [auth a],
CZ [auth a],
DAA [auth d],
DB [auth A],
DD [auth A],
DF [auth A],
DJ [auth a],
DL [auth a],
DM [auth a],
DQ [auth a],
DR [auth a],
DV [auth a],
EAA [auth e],
EB [auth A],
ED [auth A],
EF [auth A],
EG [auth A],
EH [auth D],
EJ [auth a],
EL [auth a],
EM [auth a],
EQ [auth a],
ER [auth a],
EV [auth a],
FAA [auth f],
FB [auth A],
FD [auth A],
FF [auth A],
FH [auth F],
FJ [auth a],
FL [auth a],
FM [auth a],
FQ [auth a],
FR [auth a],
FV [auth a],
GB [auth A],
GD [auth A],
GF [auth A],
GJ [auth a],
GL [auth a],
GM [auth a],
GN [auth a],
GQ [auth a],
GR [auth a],
GU [auth a],
GV [auth a],
HB [auth A],
HC [auth A],
HD [auth A],
HF [auth A],
HJ [auth a],
HL [auth a],
HM [auth a],
HQ [auth a],
HR [auth a],
HV [auth a],
HX [auth a],
IC [auth A],
ID [auth A],
IF [auth A],
IG [auth A],
II [auth a],
IJ [auth a],
IL [auth a],
IM [auth a],
IQ [auth a],
IR [auth a],
IV [auth a],
JD [auth A],
JF [auth A],
JJ [auth a],
JL [auth a],
JM [auth a],
JQ [auth a],
JR [auth a],
JV [auth a],
JX [auth a],
JZ [auth a],
KF [auth A],
KG [auth A],
KI [auth a],
KJ [auth a],
KL [auth a],
KO [auth a],
KQ [auth a],
KR [auth a],
KV [auth a],
LB [auth A],
LC [auth A],
LF [auth A],
LI [auth a],
LJ [auth a],
LL [auth a],
LN [auth a],
LQ [auth a],
LR [auth a],
MF [auth A],
MJ [auth a],
ML [auth a],
MN [auth a],
MQ [auth a],
MT [auth a],
MX [auth a],
NF [auth A],
NH [auth a],
NJ [auth a],
NL [auth a],
NN [auth a],
NQ [auth a],
NT [auth a],
NU [auth a],
NY [auth a],
OC [auth A],
OL [auth a],
ON [auth a],
OQ [auth a],
OT [auth a],
PC [auth A],
PL [auth a],
PN [auth a],
PQ [auth a],
PT [auth a],
QC [auth A],
QL [auth a],
QQ [auth a],
QT [auth a],
QU [auth a],
QW [auth a],
QY [auth a],
RF [auth A],
RJ [auth a],
RK [auth a],
RL [auth a],
RQ [auth a],
RT [auth a],
RU [auth a],
SB [auth A],
SC [auth A],
SF [auth A],
SJ [auth a],
SK [auth a],
SL [auth a],
SQ [auth a],
ST [auth a],
SU [auth a],
TC [auth A],
TF [auth A],
TI [auth a],
TK [auth a],
TL [auth a],
TQ [auth a],
TT [auth a],
TU [auth a],
TZ [auth b],
UC [auth A],
UF [auth A],
UK [auth a],
UL [auth a],
UQ [auth a],
UT [auth a],
UU [auth a],
UV [auth a],
VC [auth A],
VE [auth A],
VF [auth A],
VI [auth a],
VK [auth a],
VL [auth a],
VQ [auth a],
VT [auth a],
VU [auth a],
WC [auth A],
WF [auth A],
WI [auth a],
WK [auth a],
WL [auth a],
WQ [auth a],
WU [auth a],
WZ [auth c],
XC [auth A],
XF [auth A],
XK [auth a],
XL [auth a],
XQ [auth a],
XU [auth a],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YK [auth a],
YL [auth a],
YQ [auth a],
YU [auth a],
YZ [auth c],
ZC [auth A],
ZE [auth A],
ZF [auth A],
ZH [auth a],
ZK [auth a],
ZL [auth a],
ZQ [auth a],
ZU [auth a]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth A]
AE [auth A]
AI [auth a]
AJ [auth a]
AK [auth a]
AC [auth A],
AE [auth A],
AI [auth a],
AJ [auth a],
AK [auth a],
AO [auth a],
AP [auth a],
AQ [auth a],
AS [auth a],
AT [auth a],
AU [auth a],
AW [auth a],
AX [auth a],
AY [auth a],
BC [auth A],
BE [auth A],
BH [auth A],
BI [auth a],
BJ [auth a],
BK [auth a],
BN [auth a],
BO [auth a],
BP [auth a],
BS [auth a],
BT [auth a],
BU [auth a],
BX [auth a],
CAA [auth d],
CC [auth A],
CE [auth A],
CI [auth a],
CK [auth a],
CN [auth a],
CO [auth a],
CP [auth a],
CS [auth a],
CT [auth a],
CW [auth a],
CX [auth a],
CY [auth a],
DC [auth A],
DE [auth A],
DG [auth A],
DH [auth B],
DI [auth a],
DK [auth a],
DN [auth a],
DO [auth a],
DP [auth a],
DS [auth a],
DT [auth a],
DU [auth a],
DW [auth a],
DX [auth a],
DY [auth a],
DZ [auth a],
EC [auth A],
EE [auth A],
EI [auth a],
EK [auth a],
EN [auth a],
EO [auth a],
EP [auth a],
ES [auth a],
ET [auth a],
EU [auth a],
EW [auth a],
EX [auth a],
EY [auth a],
EZ [auth a],
FC [auth A],
FE [auth A],
FG [auth A],
FI [auth a],
FK [auth a],
FN [auth a],
FO [auth a],
FP [auth a],
FS [auth a],
FT [auth a],
FU [auth a],
FW [auth a],
FX [auth a],
FY [auth a],
FZ [auth a],
GAA [auth k],
GC [auth A],
GE [auth A],
GG [auth A],
GH [auth M],
GI [auth a],
GK [auth a],
GO [auth a],
GP [auth a],
GS [auth a],
GT [auth a],
GW [auth a],
GX [auth a],
GY [auth a],
GZ [auth a],
HAA [auth p],
HE [auth A],
HG [auth A],
HH [auth Z],
HI [auth a],
HK [auth a],
HN [auth a],
HO [auth a],
HP [auth a],
HS [auth a],
HT [auth a],
HU [auth a],
HW [auth a],
HY [auth a],
HZ [auth a],
IB [auth A],
IE [auth A],
IK [auth a],
IN [auth a],
IO [auth a],
IP [auth a],
IS [auth a],
IT [auth a],
IU [auth a],
IW [auth a],
IX [auth a],
IY [auth a],
JAA [auth z],
JB [auth A],
JC [auth A],
JE [auth A],
JG [auth A],
JH [auth a],
JI [auth a],
JK [auth a],
JN [auth a],
JO [auth a],
JP [auth a],
JS [auth a],
JT [auth a],
JU [auth a],
JW [auth a],
JY [auth a],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KH [auth a],
KK [auth a],
KM [auth a],
KN [auth a],
KP [auth a],
KS [auth a],
KT [auth a],
KU [auth a],
KW [auth a],
KX [auth a],
KY [auth a],
KZ [auth a],
LD [auth A],
LE [auth A],
LG [auth A],
LH [auth a],
LK [auth a],
LM [auth a],
LO [auth a],
LP [auth a],
LS [auth a],
LT [auth a],
LU [auth a],
LV [auth a],
LW [auth a],
LX [auth a],
LY [auth a],
LZ [auth a],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MG [auth A],
MH [auth a],
MI [auth a],
MK [auth a],
MM [auth a],
MO [auth a],
MP [auth a],
MR [auth a],
MS [auth a],
MU [auth a],
MV [auth a],
MW [auth a],
MY [auth a],
MZ [auth a],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NG [auth A],
NI [auth a],
NK [auth a],
NM [auth a],
NO [auth a],
NP [auth a],
NR [auth a],
NS [auth a],
NV [auth a],
NW [auth a],
NX [auth a],
NZ [auth a],
OB [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth a],
OI [auth a],
OJ [auth a],
OK [auth a],
OM [auth a],
OO [auth a],
OP [auth a],
OR [auth a],
OS [auth a],
OU [auth a],
OV [auth a],
OW [auth a],
OX [auth a],
OY [auth a],
OZ [auth a],
PB [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth a],
PI [auth a],
PJ [auth a],
PK [auth a],
PM [auth a],
PO [auth a],
PP [auth a],
PR [auth a],
PS [auth a],
PU [auth a],
PV [auth a],
PW [auth a],
PX [auth a],
PY [auth a],
PZ [auth b],
QB [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth a],
QI [auth a],
QJ [auth a],
QK [auth a],
QM [auth a],
QN [auth a],
QO [auth a],
QP [auth a],
QR [auth a],
QS [auth a],
QV [auth a],
QZ [auth b],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RG [auth A],
RH [auth a],
RI [auth a],
RM [auth a],
RN [auth a],
RO [auth a],
RP [auth a],
RR [auth a],
RS [auth a],
RV [auth a],
RW [auth a],
RX [auth a],
RY [auth a],
RZ [auth b],
SD [auth A],
SE [auth A],
SG [auth A],
SH [auth a],
SI [auth a],
SM [auth a],
SN [auth a],
SO [auth a],
SP [auth a],
SR [auth a],
SS [auth a],
SV [auth a],
SW [auth a],
SX [auth a],
SY [auth a],
SZ [auth b],
TB [auth A],
TD [auth A],
TE [auth A],
TG [auth A],
TH [auth a],
TJ [auth a],
TM [auth a],
TN [auth a],
TO [auth a],
TP [auth a],
TR [auth a],
TS [auth a],
TV [auth a],
TW [auth a],
TX [auth a],
TY [auth a],
UB [auth A],
UD [auth A],
UE [auth A],
UG [auth A],
UH [auth a],
UI [auth a],
UJ [auth a],
UM [auth a],
UN [auth a],
UO [auth a],
UP [auth a],
UR [auth a],
US [auth a],
UW [auth a],
UX [auth a],
UY [auth a],
UZ [auth b],
VB [auth A],
VD [auth A],
VG [auth A],
VH [auth a],
VJ [auth a],
VM [auth a],
VN [auth a],
VO [auth a],
VP [auth a],
VR [auth a],
VS [auth a],
VV [auth a],
VW [auth a],
VX [auth a],
VY [auth a],
VZ [auth b],
WB [auth A],
WD [auth A],
WE [auth A],
WG [auth A],
WH [auth a],
WJ [auth a],
WM [auth a],
WN [auth a],
WO [auth a],
WP [auth a],
WR [auth a],
WS [auth a],
WT [auth a],
WV [auth a],
WW [auth a],
WX [auth a],
WY [auth a],
XB [auth A],
XD [auth A],
XE [auth A],
XG [auth A],
XH [auth a],
XI [auth a],
XJ [auth a],
XM [auth a],
XN [auth a],
XO [auth a],
XP [auth a],
XR [auth a],
XS [auth a],
XT [auth a],
XV [auth a],
XW [auth a],
XX [auth a],
XZ [auth c],
YB [auth A],
YH [auth a],
YI [auth a],
YJ [auth a],
YM [auth a],
YN [auth a],
YO [auth a],
YP [auth a],
YR [auth a],
YS [auth a],
YT [auth a],
YV [auth a],
YW [auth a],
YX [auth a],
ZB [auth A],
ZD [auth A],
ZG [auth A],
ZI [auth a],
ZJ [auth a],
ZM [auth a],
ZN [auth a],
ZO [auth a],
ZP [auth a],
ZR [auth a],
ZS [auth a],
ZT [auth a],
ZV [auth a],
ZW [auth a],
ZX [auth a],
ZY [auth a],
ZZ [auth c]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ		GA [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		OA [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev_5505
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 2.0: 2025-11-12
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary