9sw5

Structure of the MvhAGD-HdrABC dimer of M. marburgensis under state 1 substate b (composite structure)

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） F420-non-reducing hydrogenase subunit A × 2 （P60227） F420-non-reducing hydrogenase subunit G × 2 （P60239） F420-non-reducing hydrogenase iron-sulfur subunit D × 2 （P60238） IRON/SULFUR CLUSTER × 22 FLAVIN-ADENINE DINUCLEOTIDE × 2 Non-cubane [4Fe-4S]-cluster × 4 formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDRA_METTM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–659； UniProt 1–659

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

OrganismNot specified

UniProt Q50755

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） F420-non-reducing hydrogenase subunit A × 2 （P60227） F420-non-reducing hydrogenase subunit G × 2 （P60239） F420-non-reducing hydrogenase iron-sulfur subunit D × 2 （P60238） IRON/SULFUR CLUSTER × 22 FLAVIN-ADENINE DINUCLEOTIDE × 2 Non-cubane [4Fe-4S]-cluster × 4 formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDRB_METTM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–302； UniProt 1–302

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

OrganismNot specified

UniProt Q50754

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） F420-non-reducing hydrogenase subunit A × 2 （P60227） F420-non-reducing hydrogenase subunit G × 2 （P60239） F420-non-reducing hydrogenase iron-sulfur subunit D × 2 （P60238） IRON/SULFUR CLUSTER × 22 FLAVIN-ADENINE DINUCLEOTIDE × 2 Non-cubane [4Fe-4S]-cluster × 4 formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDRC_METTM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–185； UniProt 1–185

F420-non-reducing hydrogenase subunit A

OrganismNot specified

UniProt P60227

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） F420-non-reducing hydrogenase subunit G × 2 （P60239） F420-non-reducing hydrogenase iron-sulfur subunit D × 2 （P60238） IRON/SULFUR CLUSTER × 22 FLAVIN-ADENINE DINUCLEOTIDE × 2 Non-cubane [4Fe-4S]-cluster × 4 formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MVHA_METTM
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–472； UniProt 1–472

F420-non-reducing hydrogenase subunit G

OrganismNot specified

UniProt P60239

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） F420-non-reducing hydrogenase subunit A × 2 （P60227） F420-non-reducing hydrogenase iron-sulfur subunit D × 2 （P60238） IRON/SULFUR CLUSTER × 22 FLAVIN-ADENINE DINUCLEOTIDE × 2 Non-cubane [4Fe-4S]-cluster × 4 formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MVHG_METTM
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–308； UniProt 1–308

F420-non-reducing hydrogenase iron-sulfur subunit D

OrganismNot specified

UniProt P60238

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） F420-non-reducing hydrogenase subunit A × 2 （P60227） F420-non-reducing hydrogenase subunit G × 2 （P60239） IRON/SULFUR CLUSTER × 22 FLAVIN-ADENINE DINUCLEOTIDE × 2 Non-cubane [4Fe-4S]-cluster × 4 formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MVHD_METTM
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–141； UniProt 1–141

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9sw5
Deposition date deposition_date	2025-10-04
Structure title title	Structure of the MvhAGD-HdrABC dimer of M. marburgensis under state 1 substate b (composite structure)
Keywords keywords	Oxidoreductase, hydrogenase, dehydrogenase, polyferredoxin; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9sw5__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9sw5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9sw5__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	61.68 Å
Rg (electron density)	63.01 Å
Total Rg	62.07 Å
Atom count	61800
Residues	4008
Excluded volume	560990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9sw5__assembly_1__model_1`	12-meric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
Molecular weight formula_weight	72265.0 kDa
EC 编号 ec_number	1.8.98.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	30901

MAEEKKETMEEPKIGVYVCHCGVNIGGVVDVEAVRDYAAKLPNVVIAKDYKYYCSDPGQLEIQKDIKELGINRVVVAACSPRLHEPTFRRCVEEAGLNQFLFEFANIREHDSWVHMDNPEGATEKAKDLVRMAVAKARLLEPLEASKVSVDDKALVIGGGVAGIQAALDLADMGFKTYMVEKRPSISGRMGQLDKTFPTLDCSMCILAPKMVDVGKHDNIELITYAEVKEVDGYIGNFKVKIEKKPRYIDEELCTGCGSCVEVCPIEMPNYFDEGIGMTKAVYIPFPQAVPLCATIDKDYCIECMLCDEVCERGAVKHDQEPEEIEIEVGTIIVATGYDAYDPTEKLEYGYGRHTNVITGLELERMINASGPTDGKVLKPSDGEKPKRVAFIHCVGSRDEQIGKPYCSRVCCMYIMKNAQLIKDKMPDTEVTLYYMDIRAFGKGFEEFYKRSQEKYGIKFIRGRPAEVIENPDLTLTVRSEDTLLGKVTEYDYDMVVLGVGLVPPEGAETLRQTIGLSKSADGFLMEAHPKLRPVDTLTDGVYLAGVAQGPKDIPDAVAQASGAAARAAIPMVKGEVEIEPIIAVTDSDVCGGCEVCIELCPFGAISIEEGHANVNVALCKGCGTCVAACPSGAMDQQHFKTEQIMAQIEAALNEPASK

Entity 2 Entity 2 polymer

Description description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
Molecular weight formula_weight	33496.4 kDa
EC 编号 ec_number	1.8.98.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEIAYFLGCIMNNRYPGIEKATRVLFDKLGIELKDMEGASCCPAPGVFGSFDKTTWAAIAARNITIAEDMGADIMTECNGCFGSLFETNHLLKEDEEMKAKINEILKETGREYKGEVNVRHFAEVLYNDVGLDKLSELVEKPLNLNVAVHYGCHFLKPSDEINIDNPERPTILDEIVEVTGAKSVEYKDKMMCCGAGGGVRSRDLDVALDFTREKLTNMKEAGVDAIVNVCPFCHLQFDVGQMEIKDKFGEEFDIPVLHLAQLLGLAMGLPKEDLVVDAHQVCVDECLEKLEELDRLAPGSG

Entity 3 Entity 3 polymer

Description description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
Molecular weight formula_weight	20548.7 kDa
EC 编号 ec_number	1.8.98.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MTLLQREENIIRKGNIDKEFSEKIKAAGGDSLEYCFQCGTCTGSCPSGRRTPYRVRQIIRKANVGLKDEIISDPTLWMCTTCYSCQERCPRKVKIVDVVKLARNEAAKAGFMAPAHKAVGSFVIKTGHGVPINDATMELRKAVGLGELPPTTHQFPEALEEVQKIIKATGFDQLIGYNWETGELE

Entity 4 Entity 4 polymer

Description description	F420-non-reducing hydrogenase subunit A
Molecular weight formula_weight	52905.1 kDa
EC 编号 ec_number	1.12.99.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MVKLTMEPVTRIEGHAKITVHLDDAGNVEDTRLHVMEFRGFEKFLQGRPIEEAPRIVPRICGICDVQHHLAAAKAVDACFGFEPDDVLPAAYKMREIMNWGSYMHSHGLHFYFLAAPDFIAGKDRKTRNVFQIIKDAPDVALQAIELRKNALEIVRATGGRPIHPTSSTPGGISTELDDETQKDLLQKAQRNVELAEATLELAVPIFEENIDLVNSLGNIETYHTGLVKNGVWDVYDGIVRIKDKEGNLFREFKPADYADTIAEHVKPYSWLKFPYIKDLGYPDGVYRVSPLSRLNVADKMPDAAPKAQDYFKEFQDKFGYAQQTLLYHWARLIEVLACAECAADALEGDLSGEKFPDSLERQAGDGVGIVEAPRGTLTHHYTCDENGLITKANIVVATIQNNPAMEMGIQKVAQDYIKPGVEVDDKIFNLMEMVIRAYDPCLSCATHTIDSQMRLATLEVYDSEGDLVKRI

Entity 5 Entity 5 polymer

Description description	F420-non-reducing hydrogenase subunit G
Molecular weight formula_weight	33786.6 kDa
EC 编号 ec_number	1.12.99.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MAEKIKIGTMWLGGCSGCHLSIADFHEKLLDVMEHADFEFSPVLMDTKYDEIPELDVVVIEGGIVNDENREFAEELREKAKFVISYGTCAVYGGIPGLRNLWDKDEVIEEAYINSITTPNEEGVIPSEDVPHLEGRVKPLGEVIDVDFEVPGCPPRSDVAAEVVMALLKGEEIELPSTNLCEVCPREKPPEGLAMDFIKRQFEVGKPEDDLCLIPQGLICMGPATVSICGAECPSIAIPCRGCYGPTARVEDQGAKMISAIASDYKVEEDKTVDPEEVAEQLDDIVGTFYTFTLPAALIPMKIKKEGK

Entity 6 Entity 6 polymer

Description description	F420-non-reducing hydrogenase iron-sulfur subunit D
Molecular weight formula_weight	15954.4 kDa
EC 编号 ec_number	1.12.99.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAEDDIKIVMFCCNWCSYGGADTAGTARMQYPTNIRVIRVMCSGRIEPQFVFKAFREGADGVLVTGCHHGDCHYDAGNYKLDRRMRLIYKLADELGIGRERIHHDWISASEGEKFAETVKMMVDRIRALGPSPIKKQLAEA

Entity 7 Entity 7 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 8 Entity 8 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	Non-cubane [4Fe-4S]-cluster
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
Molecular weight formula_weight	195.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.290 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.29 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	17398

Structure of the MvhAGD-HdrABC dimer of M. marburgensis under state 1 substate b (composite structure)

1. Protein Identity and Related Structures Protein Identity & Related Structures

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

F420-non-reducing hydrogenase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

F420-non-reducing hydrogenase subunit G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

F420-non-reducing hydrogenase iron-sulfur subunit D

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9sw5__assembly_1__model_1

9sw5__assembly_1__model_1 | I(q)

9sw5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)