9NF0 | pdb_00009nf0

Structure of the NADPH-bound Pyrococcus furiosus SHI complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the biotechnologically relevant reversible NADPH-oxidizing NiFe-hydrogenase from P.furiosus.

Xiao, X.Schut, G.J.Feng, X.McTernan, P.M.Haja, D.K.Lanzilotta, W.N.Adams, M.W.W.Li, H.

(2025) Structure 33: 1470

  • DOI: https://doi.org/10.1016/j.str.2025.05.017
  • Primary Citation of Related Structures:  
    9E15, 9E1J, 9NEZ, 9NF0

  • PubMed Abstract: 

    The cytoplasmic hydrogenase I (SHI) from the hyperthermophilic archaeon Pyrococcus furiosus belongs to the group III hydrogenase family. SHI oxidizes NADPH rather than NADH to reduce protons and evolve hydrogen gas, and because of this property, coupled with its high thermal stability, the enzyme holds great potential for economical hydrogen production. Despite decades of efforts, the SHI structure has remained unknown. Here, we report the cryoelectron microscopic (cryo-EM) structures of the heterotetrameric SHI holoenzyme (αδβγ). SHI is a symmetric dimer of two individually functional heterotetramers. SHI-αδ resembles the standard [NiFe] hydrogenase, and SHI-βγ function as the NADPH oxidoreductase. SHI-β contains three [4Fe-4S] clusters that relay electrons from NADPH in SHI-γ to the catalytic [NiFe] cluster in SHI-αδ for H 2 production. These structures will guide the adaptation of this unique enzyme for biotechnological applications.


  • Organizational Affiliation
    • Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfhydrogenase 1 subunit delta
A, E
261Pyrococcus furiosusMutation(s): 0 
Gene Names: hydDPF0893
EC: 1.12.1.3
UniProt
Find proteins for E7FHU4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore E7FHU4 
Go to UniProtKB:  E7FHU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7FHU4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfhydrogenase 1 subunit beta
B, F
367Pyrococcus furiosusMutation(s): 0 
Gene Names: hydBPF0891
EC: 1.12.98.4
UniProt
Find proteins for Q8U2E5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U2E5 
Go to UniProtKB:  Q8U2E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U2E5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfhydrogenase 1 subunit gamma
C, G
292Pyrococcus furiosusMutation(s): 0 
Gene Names: hydGPF0892
EC: 1.12.98.4
UniProt
Find proteins for Q8U2E4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U2E4 
Go to UniProtKB:  Q8U2E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U2E4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfhydrogenase 1 subunit alpha
D, H
428Pyrococcus furiosusMutation(s): 0 
Gene Names: hydAPF0894
EC: 1.12.1.3
UniProt
Find proteins for E7FI44 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore E7FI44 
Go to UniProtKB:  E7FI44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7FI44
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
CA [auth G],
Q [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
DA [auth G],
R [auth C]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth F]
I [auth A]
J [auth A]
K [auth A]
L [auth B]
AA [auth F],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
U [auth E],
V [auth E],
W [auth E],
X [auth F],
Y [auth F],
Z [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
NFU (Subject of Investigation/LOI)
Query on NFU

Download Ideal Coordinates CCD File 
EA [auth H],
S [auth D]
formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
C3 H Fe N2 Ni O
QCZROEOIPZWDEO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
BA [auth G],
P [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
FA [auth H],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.2: 2025-09-17
    Changes: Data collection, Database references