[English] 日本語
Yorodumi
- PDB-9e1j: Alpha-Delta heterodimeric form of soluble hydrogenase I from Pyro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e1j
TitleAlpha-Delta heterodimeric form of soluble hydrogenase I from Pyrococcus furiosus. Data processed and model refined in P21221
Components(Sulfhydrogenase 1 subunit ...) x 2
KeywordsLYASE / Ni-Fe hydrogenase
Function / homology
Function and homology information


hydrogen dehydrogenase (NADP+) / hydrogen dehydrogenase (NADP+) activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit
Similarity search - Domain/homology
CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / IRON/SULFUR CLUSTER / Sulfhydrogenase 1 subunit delta / Sulfhydrogenase 1 subunit alpha
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLanzilotta, W.N. / Adams, M.W.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural insights into the biotechnologically relevant reversible NADPH-oxidizing NiFe-hydrogenase from P.furiosus.
Authors: Xiansha Xiao / Gerrit J Schut / Xiang Feng / Patrick M McTernan / Dominik K Haja / William N Lanzilotta / Michael W W Adams / Huilin Li /
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 ...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 production. These structures will guide the adaptation of this unique enzyme for biotechnological applications.
History
DepositionOct 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfhydrogenase 1 subunit delta
B: Sulfhydrogenase 1 subunit alpha
C: Sulfhydrogenase 1 subunit delta
D: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,92716
Polymers151,8264
Non-polymers3,10212
Water1,09961
1
A: Sulfhydrogenase 1 subunit delta
B: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1988
Polymers75,9132
Non-polymers1,2856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-111 kcal/mol
Surface area24100 Å2
MethodPISA
2
C: Sulfhydrogenase 1 subunit delta
D: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7308
Polymers75,9132
Non-polymers1,8176
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-96 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.291, 111.188, 141.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

-
Sulfhydrogenase 1 subunit ... , 2 types, 4 molecules ACBD

#1: Protein Sulfhydrogenase 1 subunit delta / Hydrogenase I small subunit / NADP-reducing hydrogenase subunit HydD / Sulfhydrogenase I subunit delta


Mass: 28650.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: hydD, PF0893 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: E7FHU4, hydrogen dehydrogenase (NADP+)
#2: Protein Sulfhydrogenase 1 subunit alpha / Hydrogenase I large subunit / NADP-reducing hydrogenase subunit HydA / Sulfhydrogenase I subunit alpha


Mass: 47262.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: hydA, PF0894 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: E7FI44, hydrogen dehydrogenase (NADP+)

-
Non-polymers , 5 types, 73 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 50 mM potassium phosphate pH 7.5, 150 mM NaCl, and 30% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.34 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Jan 15, 2018
RadiationMonochromator: 1.34 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 87815 / % possible obs: 98.9 % / Redundancy: 14.5 % / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 4457 / CC1/2: 0.555

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→35.91 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3128 3832 4.36 %
Rwork0.2559 --
obs0.2584 87815 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10639 0 74 61 10774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110981
X-RAY DIFFRACTIONf_angle_d1.25714884
X-RAY DIFFRACTIONf_dihedral_angle_d7.9161473
X-RAY DIFFRACTIONf_chiral_restr0.0711639
X-RAY DIFFRACTIONf_plane_restr0.0111885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.32071390.29633039X-RAY DIFFRACTION98
2.63-2.670.31081410.28443075X-RAY DIFFRACTION99
2.67-2.70.34861440.29923142X-RAY DIFFRACTION99
2.7-2.740.30071420.30273099X-RAY DIFFRACTION99
2.74-2.780.40641400.29773064X-RAY DIFFRACTION99
2.78-2.830.36971420.28963058X-RAY DIFFRACTION99
2.83-2.870.33711430.28563144X-RAY DIFFRACTION100
2.87-2.920.3131380.27513155X-RAY DIFFRACTION100
2.92-2.980.3361420.26663086X-RAY DIFFRACTION100
2.98-3.030.33921420.27333105X-RAY DIFFRACTION100
3.03-3.10.33271460.28373124X-RAY DIFFRACTION100
3.1-3.160.32871450.2853084X-RAY DIFFRACTION100
3.16-3.240.35511380.28063111X-RAY DIFFRACTION100
3.24-3.320.36311420.27493159X-RAY DIFFRACTION100
3.32-3.410.27951410.25563079X-RAY DIFFRACTION100
3.41-3.510.31171460.25623141X-RAY DIFFRACTION100
3.51-3.620.28511450.2523124X-RAY DIFFRACTION100
3.62-3.750.32141420.24773099X-RAY DIFFRACTION100
3.75-3.90.26911420.24613143X-RAY DIFFRACTION100
3.9-4.080.30361400.24693110X-RAY DIFFRACTION100
4.08-4.290.28971420.2253143X-RAY DIFFRACTION100
4.29-4.560.29881410.21723104X-RAY DIFFRACTION100
4.56-4.910.30551430.22563116X-RAY DIFFRACTION100
4.91-5.40.29341440.24223119X-RAY DIFFRACTION100
5.4-6.180.33611360.26743137X-RAY DIFFRACTION100
6.18-7.770.3031440.25873121X-RAY DIFFRACTION100
7.78-35.910.30171420.24053102X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more