8rvy

CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (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 9	Formate dehydrogenase, beta subunit × 1 （D9PY03） Formate dehydrogenase, alpha subunit × 1 （D9PY04） Methyl viologen-reducing hydrogenase, subunit D-related protein × 1 （D9PY02） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） IRON/SULFUR CLUSTER × 18 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 1 Non-cubane [4Fe-4S]-cluster × 4 water × 5	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 Author chain a； PDBConstruct 1–659； UniProt 1–659

Formate dehydrogenase, beta subunit

OrganismNot specified

UniProt D9PY03

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） Formate dehydrogenase, alpha subunit × 1 （D9PY04） Methyl viologen-reducing hydrogenase, subunit D-related protein × 1 （D9PY02） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） IRON/SULFUR CLUSTER × 18 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 1 Non-cubane [4Fe-4S]-cluster × 4 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D9PY03_METTM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–380； UniProt 1–380

Formate dehydrogenase, alpha subunit

OrganismNot specified

UniProt D9PY04

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） Formate dehydrogenase, beta subunit × 1 （D9PY03） Methyl viologen-reducing hydrogenase, subunit D-related protein × 1 （D9PY02） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） IRON/SULFUR CLUSTER × 18 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 1 Non-cubane [4Fe-4S]-cluster × 4 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D9PY04_METTM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–342； UniProt 1–342

Methyl viologen-reducing hydrogenase, subunit D-related protein

OrganismNot specified

UniProt D9PY02

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） Formate dehydrogenase, beta subunit × 1 （D9PY03） Formate dehydrogenase, alpha subunit × 1 （D9PY04） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） IRON/SULFUR CLUSTER × 18 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 1 Non-cubane [4Fe-4S]-cluster × 4 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D9PY02_METTM
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–136； UniProt 1–136

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 9	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） Formate dehydrogenase, beta subunit × 1 （D9PY03） Formate dehydrogenase, alpha subunit × 1 （D9PY04） Methyl viologen-reducing hydrogenase, subunit D-related protein × 1 （D9PY02） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C × 2 （Q50754） IRON/SULFUR CLUSTER × 18 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 1 Non-cubane [4Fe-4S]-cluster × 4 water × 5	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	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–302； UniProt 1–302 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 9	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A × 2 （Q50756） Formate dehydrogenase, beta subunit × 1 （D9PY03） Formate dehydrogenase, alpha subunit × 1 （D9PY04） Methyl viologen-reducing hydrogenase, subunit D-related protein × 1 （D9PY02） H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B × 2 （Q50755） IRON/SULFUR CLUSTER × 18 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 1 Non-cubane [4Fe-4S]-cluster × 4 water × 5	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	6
Chains and sequence ranges	Author chain C； PDBConstruct 1–185； UniProt 1–185 Author chain c； PDBConstruct 1–185； UniProt 1–185

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	8rvy
Deposition date deposition_date	2024-02-02
Structure title title	CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (composite structure)
Keywords keywords	Redox, Flavin-based electron bifurcation, methanogenesis, heterodisulfide reductase, F420-H2 oxidase, Oxidoreductase; 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.

8rvy__assembly_1__model_1

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

Download this curve (.dat)

8rvy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rvy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.88 Å
Rg (electron density)	49.15 Å
Total Rg	48.89 Å
Atom count	44198
Residues	2857
Excluded volume	401080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rvy__assembly_1__model_1`	nonameric （9）	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 (11)

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,a
Atom count atom_count	44212

MAEEKKETMEEPKIGVYVCHCGVNIGGVVDVEAVRDYAAKLPNVVIAKDYKYYCSDPGQLEIQKDIKELGINRVVVAACSPRLHEPTFRRCVEEAGLNQFLFEFANIREHDSWVHMDNPEGATEKAKDLVRMAVAKARLLEPLEASKVSVDDKALVIGGGVAGIQAALDLADMGFKTYMVEKRPSISGRMGQLDKTFPTLDCSMCILAPKMVDVGKHDNIELITYAEVKEVDGYIGNFKVKIEKKPRYIDEELCTGCGSCVEVCPIEMPNYFDEGIGMTKAVYIPFPQAVPLCATIDKDYCIECMLCDEVCERGAVKHDQEPEEIEIEVGTIIVATGYDAYDPTEKLEYGYGRHTNVITGLELERMINASGPTDGKVLKPSDGEKPKRVAFIHCVGSRDEQIGKPYCSRVCCMYIMKNAQLIKDKMPDTEVTLYYMDIRAFGKGFEEFYKRSQEKYGIKFIRGRPAEVIENPDLTLTVRSEDTLLGKVTEYDYDMVVLGVGLVPPEGAETLRQTIGLSKSADGFLMEAHPKLRPVDTLTDGVYLAGVAQGPKDIPDAVAQASGAAARAAIPMVKGEVEIEPIIAVTDSDVCGGCEVCIELCPFGAISIEEGHANVNVALCKGCGTCVAACPSGAMDQQHFKTEQIMAQIEAALNEPASK

Entity 2 Entity 2 polymer

Description description	Formate dehydrogenase, beta subunit
Molecular weight formula_weight	43387.1 kDa
EC 编号 ec_number	1.2.1.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MKYLLARATDEEIQRKGECGGAVTAIFKYMLDKEVVDAVLTLERGYDVYDGIPVLLEDSSGIESTCGSLHCAPTMFGDLISRYLSDMRLAVAVKPCDAMAIRELEKRHQIDPDKVYKIGLNCGGTLAPVSAREMIETFYEIDPDDVVSEEIDRGKFIVELRDGSHREISIDYLEEEGFGRRENCQRCEIMVPRNADLACGNWGADDGWTFIEVNTERGQEIIEGARSSGYIEAREPSEKMVKIREKIENAMISMARKFQDKYLDEEYPSLDEWDEYWKRCINCFACRDACPVCFCRECELEKDYLLESDEKAPDPLTFQGVRLSHMGFSCINCGQCEDVCPMDIPIARIYHRIQKKYRDRTGFTAGVSQELPPMYSGEKD

Entity 3 Entity 3 polymer

Description description	Formate dehydrogenase, alpha subunit
Molecular weight formula_weight	37682.7 kDa
EC 编号 ec_number	1.2.1.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MMVKHTLCPSCSAGCGVNIVEMGGAPVGTYPYRRHPVNEGKTCRAGRDCYEIPLMDRVTSPGVKKSGKLSGVNWDEALDKLTELLSSEDISILTTGTLTNEEALKLREIIENFNVKKSGLITVFPEFDYPEIDIRNIRDYDNIAVIGDAITCAPLIGRRIFHAMAAGAEVRSYDRRDETRMAVNSGFHITFSDEREVLNDLQQLPGGSLIIITPEIPEIIGPVLEFSSENEFDVLPIFEDFNTRGVMQHLPPVNEGEFDSVWLIDPGAAAEPVDVSGKFVLQSIRTEGLTPDIFLPVAAWCEKSGSYTSTAGYTMKLEPALQAPEGVLSDMEIFERILRAGD

Entity 4 Entity 4 polymer

Description description	Methyl viologen-reducing hydrogenase, subunit D-related protein
Molecular weight formula_weight	15550.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSFEPKIVGFCCNWCSYGGADTAGTARMQYPPNVRIIRVMCSGRVNASMILKAFSEGADGVFVGGCHIGDCHYDSGNYKWKRRARFIEDILPEFGIDKERFRWEWISASEGEKFQKTMQEFYETVKYLGPLKRAGK

Entity 5 Entity 5 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b,B

MEIAYFLGCIMNNRYPGIEKATRVLFDKLGIELKDMEGASCCPAPGVFGSFDKTTWAAIAARNITIAEDMGADIMTECNGCFGSLFETNHLLKEDEEMKAKINEILKETGREYKGEVNVRHFAEVLYNDVGLDKLSELVEKPLNLNVAVHYGCHFLKPSDEINIDNPERPTILDEIVEVTGAKSVEYKDKMMCCGAGGGVRSRDLDVALDFTREKLTNMKEAGVDAIVNVCPFCHLQFDVGQMEIKDKFGEEFDIPVLHLAQLLGLAMGLPKEDLVVDAHQVCVDECLEKLEELDRLAPGSG

Entity 6 Entity 6 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c,C

MTLLQREENIIRKGNIDKEFSEKIKAAGGDSLEYCFQCGTCTGSCPSGRRTPYRVRQIIRKANVGLKDEIISDPTLWMCTTCYSCQERCPRKVKIVDVVKLARNEAAKAGFMAPAHKAVGSFVIKTGHGVPINDATMELRKAVGLGELPPTTHQFPEALEEVQKIIKATGFDQLIGYNWETGELE

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	18

Entity 8 Entity 8 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 9 Entity 9 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 10 Entity 10 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	4

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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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	2.36 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	76528

CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (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

Formate dehydrogenase, beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Formate dehydrogenase, alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methyl viologen-reducing hydrogenase, subunit D-related protein

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8rvy__assembly_1__model_1

8rvy__assembly_1__model_1 | I(q)

8rvy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

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 water

7. Citations (1)