9qqt

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture

Method: X-RAY DIFFRACTION

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

Methyl-coenzyme M reductase subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Methyl-coenzyme M reductase subunit beta × 2 （A0A822J4Y5） Methyl-coenzyme M reductase subunit gamma × 2 POTASSIUM ION × 1 FACTOR 430 × 2 1,2-ETHANEDIOL × 22 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2 O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A822J3V5_9EURY
Isoform	—
PDB entities	1, 4
Chains and sequence ranges	Author chain A； PDBConstruct 1–566； UniProt 1–566 Author chain D； PDBConstruct 1–566； UniProt 1–566

Methyl-coenzyme M reductase subunit beta

OrganismNot specified

UniProt A0A822J4Y5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Methyl-coenzyme M reductase subunit alpha × 1 （A0A822J3V5） Methyl-coenzyme M reductase subunit gamma × 2 Methyl-coenzyme M reductase subunit alpha × 1 （A0A822J3V5） POTASSIUM ION × 1 FACTOR 430 × 2 1,2-ETHANEDIOL × 22 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2 O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A822J4Y5_9EURY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–434； UniProt 1–434 Author chain E； PDBConstruct 1–434； UniProt 1–434

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	9qqt
Deposition date deposition_date	2025-04-02
Structure title title	Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture
Keywords keywords	;methanotrophy, anaerobic methanotrophic archaea, methane oxidation, methyl-coenzyme M reductase, ANME, MCR, reverse methanogenesis, nickel-dependent enzyme, coenzyme M, coenzyme B, F430 cofactor, post-translational modification, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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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.

9qqt__assembly_1__model_1

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

Download this curve (.dat)

9qqt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qqt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.06 Å
Rg (electron density)	37.38 Å
Total Rg	37.86 Å
Atom count	37826
Residues	2474
Excluded volume	340020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qqt__assembly_1__model_1`	hexameric （6）	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	Methyl-coenzyme M reductase subunit alpha
Molecular weight formula_weight	61873.8 kDa
EC 编号 ec_number	2.8.4.1
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	43046

MAEPRFKKSMETKYAKEWGSNKVGSTAKAKITDKKTKYLRLGYQQNPRKVEMAKCGAAITKKRGLQAYDPKLHLAGIPMGQRQLTPYTISGTDIVCDGDDLHFVNNAAMQQEWDDIRRTCVVGLDLAHETLEKRLGKEVTPETINYYLEVLNHAMPGAAIVQEHMVETHPALVDDCYVKIFTGDETLQDEVDKQFVINIDNEFPANQAKQIKAAVGKTSWQAVHIPTIVTRTEDGPGTSRWMAMQVGMTFISAYHMCAGEAAVGELAFTAKHAGLVEMGDMIPARRARGPNEPGGLSFGHMADIVQTNRKGPEDPVNVVLQTASAATMLYDQIWLGGYMSGGVGFTMYATPAYTNDIVDDFLYWGNDYAAKKYGGNGKAKATIDTVKDIATETTLYGLEAYEKYPTTLEDHFGGSQRATVISIAAGGATALATGHSQAGLSAWYLSMYLHKEAHGRLGFYGYDLQDQCGATNVFSIASDEGCIGECRGANYPNYAMNVGHQGGYTSVVAAAHAGKDAFCVNPLVKTCFADELINFDFADPRAAFGKAALREWDRCAGERAFVIPAK

Entity 2 Entity 2 polymer

Description description	Methyl-coenzyme M reductase subunit beta
Molecular weight formula_weight	45334.6 kDa
EC 编号 ec_number	2.8.4.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MADTIDLYSDRGAKLKSGVDINDISPMRNAAIKSIVTGIKRTAAVDLAGIEKTLATSAIGGKGRKIPGREMKLDIVKNAAAIQKAVNELVQVDSGDDTVVKALNGGKQLIVQVPSVRIDVAAEYVSSLTCTASAVTQALVSQFNIGMFDAPTIKSAVWGQYPQTLDMVGGNVKSIVDIPQKDEGFGYTLRNVMANHLAATCKKSAMNTAALCSILENTGVFEMGDAIGNQTRHRLLAFSHQGLNANNLVYGTTKALGKTGTIGSAVHACVEKAIADKVISADKKFASGYTTYKTNDVGKWNAYCAAGTLVATLINCGAQRAPQSVSAVLLYFNDLIEKETSLPGCDFGKVQGAAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSKGLAVPCVAAAVALDAGVQIYSPEKTSGLVGDVFSSVDEFREPIKAVAGAV

Entity 3 Entity 3 polymer

Description description	Methyl-coenzyme M reductase subunit gamma
Molecular weight formula_weight	28253.8 kDa
EC 编号 ec_number	2.8.4.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MAYKPQYYPGSTSVAKNRRKHMSDDVEKMRDISDEDLTALLGHRAPGSDYPSTHPPLSEIGEPACSVREVVEPTPGAAAGDRLRYVQWSDSMYNAPSVPYWRSYHAAINFRGVDPGTLSGRQVNEMRERDMEEYAKRQAETEMTDWGLAGMRGCTVHGXSLRLQEDGVMFDMLDRRRLEGGVIVSDKDQVGVPIDRKVNLGKPMSEAEAAKRTTFYRVDNVAFRSDKEVIEHVQKVWELRTKYGFVPKA

Entity 4 Entity 4 polymer

Description description	Methyl-coenzyme M reductase subunit alpha
Molecular weight formula_weight	61857.8 kDa
EC 编号 ec_number	2.8.4.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	FACTOR 430
Molecular weight formula_weight	906.6 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 8 Entity 8 non-polymer

Description description	Coenzyme B
Molecular weight formula_weight	343.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	1-THIOETHANESULFONIC ACID
Molecular weight formula_weight	142.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE
Molecular weight formula_weight	481.5 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3293

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Unit-cell length a length_a	81.621 Å
Unit-cell length b length_b	189.823 Å
Unit-cell length c length_c	83.930 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	0.980 Å
Low-resolution limit resolution_low	41.710 Å
R factor r_factor	0.1293
R_work r_work	0.1283
R_free r_free	0.1481

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture

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

Methyl-coenzyme M reductase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Methyl-coenzyme M reductase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qqt__assembly_1__model_1

9qqt__assembly_1__model_1 | I(q)

9qqt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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 non-polymer

Entity 6 Entity 6 non-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)

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture

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

Methyl-coenzyme M reductase subunit alpha

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-coenzyme M reductase subunit beta

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

9qqt__assembly_1__model_1

9qqt__assembly_1__model_1 | I(q)

9qqt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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 non-polymer

Entity 6 Entity 6 non-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)