3fyi

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide

Method: X-RAY DIFFRACTION

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

Cytochrome c oxidase subunit 1

Rhodobacter sphaeroides

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cytochrome c oxidase subunit 2 × 1 （Q03736） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 CYANIDE ION × 1 DECYL-BETA-D-MALTOPYRANOSIDE × 6 TRIDECANE × 6 HEPTANE-1,2,3-TRIOL × 1 CADMIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cytochrome c oxidase subunit 2 × 1 （Q03736） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 CYANIDE ION × 1 DECYL-BETA-D-MALTOPYRANOSIDE × 4 TRIDECANE × 6 CADMIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX1_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–566； UniProt 1–566 Author chain C； PDBConstruct 1–566； UniProt 1–566

Cytochrome c oxidase subunit 2

Rhodobacter sphaeroides

UniProt Q03736

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cytochrome c oxidase subunit 1 × 1 （P33517） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 CYANIDE ION × 1 DECYL-BETA-D-MALTOPYRANOSIDE × 6 TRIDECANE × 6 HEPTANE-1,2,3-TRIOL × 1 CADMIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cytochrome c oxidase subunit 1 × 1 （P33517） HEME-A × 2 COPPER (I) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 CYANIDE ION × 1 DECYL-BETA-D-MALTOPYRANOSIDE × 4 TRIDECANE × 6 CADMIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX2_RHOSH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–256； UniProt 26–281 Author chain D； PDBConstruct 1–256； UniProt 26–281

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	3fyi
Deposition date deposition_date	2009-01-22
Structure title title	Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide
Keywords keywords	;conformational changes, cyanide binding, Cell membrane, Electron transport, Heme, Hydrogen ion transport, Ion transport, Iron, Membrane, Metal-binding, Oxidoreductase, Respiratory chain, Transmembrane, Transport ;; 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.

3fyi__assembly_1__model_1

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

Download this curve (.dat)

3fyi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fyi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.55 Å
Rg (electron density)	27.24 Å
Total Rg	28.19 Å
Atom count	6619
Residues	791
Excluded volume	120990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fyi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fyi__assembly_2__model_1`	dimeric （2）	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	Cytochrome c oxidase subunit 1
Molecular weight formula_weight	63195.4 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	13601

MADAAIHGHEHDRRGFFTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTFEQLPKREDWERAPAH

Source Source

Source organism organism	Rhodobacter sphaeroides
Common name common_name	Rhodopseudomonas sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

Entity 2 Entity 2 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	29365.4 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QQQSLEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQHHHHHH

Source Source

Source organism organism	Rhodobacter sphaeroides
Common name common_name	Rhodopseudomonas sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

Entity 3 Entity 3 non-polymer

Description description	HEME-A
Molecular weight formula_weight	852.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	DECYL-BETA-D-MALTOPYRANOSIDE
Molecular weight formula_weight	482.6 kDa
Source method src_method	man
Copy count entity_count	10

Entity 9 Entity 9 non-polymer

Description description	TRIDECANE
Molecular weight formula_weight	184.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 10 Entity 10 non-polymer

Description description	HEPTANE-1,2,3-TRIOL
Molecular weight formula_weight	148.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	470

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3fyia_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.24 — Cytochrome c oxidase subunit I-like
Superfamily Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
Family Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

Domain ID domain_id	d3fyib1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

Domain ID domain_id	d3fyib2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d3fyib3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3fyic_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.24 — Cytochrome c oxidase subunit I-like
Superfamily Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
Family Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

Domain ID domain_id	d3fyid1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

Domain ID domain_id	d3fyid2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d3fyid3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	3fyiA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	3fyiB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3fyiB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3fyiC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	3fyiD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3fyiD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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Unit-cell length a length_a	124.344 Å
Unit-cell length b length_b	131.877 Å
Unit-cell length c length_c	176.160 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	8

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1950
R_work r_work	0.1943
R_free r_free	0.2191

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide

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

Cytochrome c oxidase subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome c oxidase subunit 2

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

3fyi__assembly_1__model_1

3fyi__assembly_1__model_1 | I(q)

3fyi__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-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 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide

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

Cytochrome c oxidase subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c oxidase subunit 2

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

3fyi__assembly_1__model_1

3fyi__assembly_1__model_1 | I(q)

3fyi__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-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 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)