2j7a

Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME C NITRITE REDUCTASE NRFA

OrganismNot specified

UniProt Q72EF3

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 QUINOL DEHYDROGENASE NRFH × 2 (Q72EF4) HEME C × 28 CALCIUM ION × 8 DODECYL-BETA-D-MALTOSIDE × 2 ACETATE ION × 1 water × 6 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 CYTOCHROME C QUINOL DEHYDROGENASE NRFH × 2 (Q72EF4) HEME C × 28 CALCIUM ION × 8 DODECYL-BETA-D-MALTOSIDE × 2 ACETATE ION × 1 water × 6 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 CYTOCHROME C QUINOL DEHYDROGENASE NRFH × 2 (Q72EF4) HEME C × 28 CALCIUM ION × 8 DODECYL-BETA-D-MALTOSIDE × 2 ACETATE ION × 1 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 1–500; UniProt 25–524 Author chain B; PDBConstruct 1–500; UniProt 25–524 Author chain D; PDBConstruct 1–500; UniProt 25–524 Author chain E; PDBConstruct 1–500; UniProt 25–524 Author chain G; PDBConstruct 1–500; UniProt 25–524 Author chain H; PDBConstruct 1–500; UniProt 25–524 Author chain J; PDBConstruct 1–500; UniProt 25–524 Author chain K; PDBConstruct 1–500; UniProt 25–524 Author chain M; PDBConstruct 1–500; UniProt 25–524 Author chain N; PDBConstruct 1–500; UniProt 25–524 Author chain P; PDBConstruct 1–500; UniProt 25–524 Author chain Q; PDBConstruct 1–500; UniProt 25–524

CYTOCHROME C QUINOL DEHYDROGENASE NRFH

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 NRFA × 4 (Q72EF3) HEME C × 28 CALCIUM ION × 8 DODECYL-BETA-D-MALTOSIDE × 2 ACETATE ION × 1 water × 6 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 CYTOCHROME C NITRITE REDUCTASE NRFA × 4 (Q72EF3) HEME C × 28 CALCIUM ION × 8 DODECYL-BETA-D-MALTOSIDE × 2 ACETATE ION × 1 water × 6 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 CYTOCHROME C NITRITE REDUCTASE NRFA × 4 (Q72EF3) HEME C × 28 CALCIUM ION × 8 DODECYL-BETA-D-MALTOSIDE × 2 ACETATE ION × 1 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 Author chain I; PDBConstruct 1–159; UniProt 1–159 Author chain L; PDBConstruct 1–159; UniProt 1–159 Author chain O; PDBConstruct 1–159; UniProt 1–159 Author chain R; 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_id2j7a
Deposition date deposition_date2006-10-06
Structure title titleCrystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris
Keywords keywordsQUINOL DEHYDROGENASE, CYTOCHROME C NITRITE REDUCTASE, NRFA, NRFH, NAPC/NIRT FAMILY, MEMBRANE COMPLEX, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-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.

2j7a__assembly_1__model_1

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

Download this curve (.dat)

2j7a__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2j7a__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)43.12 Å
Rg (electron density)42.99 Å
Total Rg43.26 Å
Atom count19498
Residues2271
Excluded volume347380 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2j7a__assembly_1__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2j7a__assembly_2__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2j7a__assembly_3__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 (7)

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6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd2j7aa_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7ab_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7ad_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7ae_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7ag_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7ah_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7aj_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7ak_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7am_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7an_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7ap_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd2j7aq_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif

CATH v4.4 (30 domains)

Domain ID domain_id2j7aA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3820 — Multiheme cytochrome fold
Homologous superfamily homologous superfamily10 — Di-heme elbow motif domain
Domain ID domain_id2j7aD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aD02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aE02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3820 — Multiheme cytochrome fold
Homologous superfamily homologous superfamily10 — Di-heme elbow motif domain
Domain ID domain_id2j7aG01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aG02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aH01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aH02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aI00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3820 — Multiheme cytochrome fold
Homologous superfamily homologous superfamily10 — Di-heme elbow motif domain
Domain ID domain_id2j7aJ01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aJ02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aK01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aK02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aL00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3820 — Multiheme cytochrome fold
Homologous superfamily homologous superfamily10 — Di-heme elbow motif domain
Domain ID domain_id2j7aM01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aM02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aN01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aN02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aO00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3820 — Multiheme cytochrome fold
Homologous superfamily homologous superfamily10 — Di-heme elbow motif domain
Domain ID domain_id2j7aP01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aP02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aQ01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2j7aQ02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id2j7aR00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3820 — Multiheme cytochrome fold
Homologous superfamily homologous superfamily10 — Di-heme elbow motif domain
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7. Citations (2)