2vr0

Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor

Method: X-RAY DIFFRACTION

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

CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA

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	NAPC/NIRT CYTOCHROME C FAMILY PROTEIN × 2 （Q72EF4） HEME C × 28 CALCIUM ION × 8 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72EF3_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–524； UniProt 1–524 Author chain B； PDBConstruct 1–524； UniProt 1–524 Author chain D； PDBConstruct 1–524； UniProt 1–524 Author chain E； PDBConstruct 1–524； UniProt 1–524

NAPC/NIRT CYTOCHROME C FAMILY PROTEIN

OrganismNot specified

UniProt Q72EF4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA × 4 （Q72EF3） HEME C × 28 CALCIUM ION × 8 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72EF4_DESVH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–159； UniProt 1–159 Author chain F； PDBConstruct 1–159； UniProt 1–159

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	2vr0
Deposition date deposition_date	2008-03-24
Structure title title	Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor
Keywords keywords	QUINOL DEHYDROGENASE, OXIDOREDUCTASE, HQNO, NRFH, NRFHA, MEMBRANE COMPLEX; OXIDOREDUCTASE
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.

2vr0__assembly_1__model_1

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

Download this curve (.dat)

2vr0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vr0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.17 Å
Rg (electron density)	43.04 Å
Total Rg	43.30 Å
Atom count	19467
Residues	2272
Excluded volume	346690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vr0__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 (6)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA
Molecular weight formula_weight	60090.3 kDa
EC 编号 ec_number	1.7.2.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	19601

MNNQKTFKGLRLAALGLVAVAAFTAGCSDVSTELKTPVYKTKLTAEEIRNSAFKPEFPKQYASYERNDETTVMTEYKGSVPFNKNDNVNPLPEGYRHAQPYLKNLWLGYPFMYEYREARGHTYAIQDFLHIDRINRYAEKGGLPATCWNCKTPKMMEWVKESGDGFWAKDVNEFRDKIDMKDHTIGCATCHDPQTMELRITSVPLTDYLVSQGKDPKKLPRNEMRALVCGQCHVEYYFNGPTMGVNKKPVFPWAEGFDPADMYRYYDKHGDLQVKGFEGKFADWTHPASKTPMIKAQHPEYETWINGTHGAAGVTCADCHMSYTRSDDKKKISSHWWTSPMKDPEMRACRQCHSDKTPDYLKSRVLFTQKRTFDLLLAAQEVSVKAHEAVRLANEYQGAKAAGYDDLMIQAREMVRKGQFFWDYVSAENSVGFHNPAKALDTLAQSQQFSQKAIDLAMEATQYGIGKDLSGDIKTIVPPILKMNRKLQQDPEFMKTHKWFQYLPVLPKADQVWDGQKRLVSAKQ

Entity 2 Entity 2 polymer

Description description	NAPC/NIRT CYTOCHROME C FAMILY PROTEIN
Molecular weight formula_weight	17290.1 kDa
EC 编号 ec_number	1.10.2.-
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MSEEKSRNGPARLKLVLGGATLGVVALATVAFGMKYTDQRPFCTSCHIMNPVGVTHKLSGHANISCNDCHAPHNLLAKLPFKAIAGARDVYMNTLGHPGDLILAGMETKEVVNANCKACHTMTNVEVASMEAKKYCTDCHRNVQHMRMKPISTREVADE

Entity 3 Entity 3 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
Molecular weight formula_weight	259.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2vr0a_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d2vr0b_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d2vr0d_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d2vr0e_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

CATH v4.4 (10 domains)

Domain ID domain_id	2vr0A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	2vr0A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2vr0B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	2vr0B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2vr0C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3820 — Multiheme cytochrome fold
Homologous superfamily homologous superfamily	10 — Di-heme elbow motif domain

Domain ID domain_id	2vr0D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	2vr0D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2vr0E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	2vr0E02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	2vr0F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3820 — Multiheme cytochrome fold
Homologous superfamily homologous superfamily	10 — Di-heme elbow motif domain

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Unit-cell length a length_a	80.102 Å
Unit-cell length b length_b	189.115 Å
Unit-cell length c length_c	263.460 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	154.300 Å
R factor r_factor	0.2210
R_work r_work	0.2200
R_free r_free	0.2610

Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor

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

CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA

State in the Current Structure

Other States of the Same Protein in the Database

NAPC/NIRT CYTOCHROME C FAMILY PROTEIN

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

2vr0__assembly_1__model_1

2vr0__assembly_1__model_1 | I(q)

2vr0__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor

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

CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NAPC/NIRT CYTOCHROME C FAMILY 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2vr0__assembly_1__model_1

2vr0__assembly_1__model_1 | I(q)

2vr0__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)