1qle

CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT

Method: X-RAY DIFFRACTION

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

CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA

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	CYTOCHROME C OXIDASE POLYPEPTIDE II × 1 （P08306） CYTOCHROME C OXIDASE POLYPEPTIDE III × 1 （P06030） CCYTOCHROME C OXIDASE × 1 （P77921） HEAVY CHAIN ANTIBODY FV FRAGMENT × 1 LIGHT CHAIN ANTIBODY FV FRAGMENT × 1 HEME-A × 2 COPPER (II) ION × 1 CALCIUM ION × 1 MANGANESE (II) ION × 1 DINUCLEAR COPPER ION × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CX1B_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–538； UniProt 17–554

CYTOCHROME C OXIDASE POLYPEPTIDE II

OrganismNot specified

UniProt P08306

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 OXIDASE POLYPEPTIDE I-BETA × 1 （P98002） CYTOCHROME C OXIDASE POLYPEPTIDE III × 1 （P06030） CCYTOCHROME C OXIDASE × 1 （P77921） HEAVY CHAIN ANTIBODY FV FRAGMENT × 1 LIGHT CHAIN ANTIBODY FV FRAGMENT × 1 HEME-A × 2 COPPER (II) ION × 1 CALCIUM ION × 1 MANGANESE (II) ION × 1 DINUCLEAR COPPER ION × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX2_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–252； UniProt 30–281

CYTOCHROME C OXIDASE POLYPEPTIDE III

OrganismNot specified

UniProt P06030

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 OXIDASE POLYPEPTIDE I-BETA × 1 （P98002） CYTOCHROME C OXIDASE POLYPEPTIDE II × 1 （P08306） CCYTOCHROME C OXIDASE × 1 （P77921） HEAVY CHAIN ANTIBODY FV FRAGMENT × 1 LIGHT CHAIN ANTIBODY FV FRAGMENT × 1 HEME-A × 2 COPPER (II) ION × 1 CALCIUM ION × 1 MANGANESE (II) ION × 1 DINUCLEAR COPPER ION × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX3_PARDE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–273； UniProt 1–273

CCYTOCHROME C OXIDASE

OrganismNot specified

UniProt P77921

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 OXIDASE POLYPEPTIDE I-BETA × 1 （P98002） CYTOCHROME C OXIDASE POLYPEPTIDE II × 1 （P08306） CYTOCHROME C OXIDASE POLYPEPTIDE III × 1 （P06030） HEAVY CHAIN ANTIBODY FV FRAGMENT × 1 LIGHT CHAIN ANTIBODY FV FRAGMENT × 1 HEME-A × 2 COPPER (II) ION × 1 CALCIUM ION × 1 MANGANESE (II) ION × 1 DINUCLEAR COPPER ION × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P77921
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–43； UniProt 8–50

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	1qle
Deposition date deposition_date	1999-08-30
Structure title title	CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT
Keywords keywords	;OXIDOREDUCTASE/IMMUNE SYSTEM, COMPLEX (OXIDOREDUCTASE-ANTIBODY), ELECTRON TRANSPORT, TRANSMEMBRANE, CYTOCHROME OXIDASE, ANTIBODY COMPLEX, OXIDOREDUCTASE-IMMUNE SYSTEM complex ;; OXIDOREDUCTASE/IMMUNE SYSTEM
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.

1qle__assembly_1__model_1

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

Download this curve (.dat)

1qle__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1qle__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.90 Å
Rg (electron density)	36.08 Å
Total Rg	36.53 Å
Atom count	10762
Residues	1333
Excluded volume	195180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1qle__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 (12)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA
Molecular weight formula_weight	60354.4 kDa
EC 编号 ec_number	1.9.3.1
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	10762

GFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFETLPKREDWDR

Entity 2 Entity 2 polymer

Description description	CYTOCHROME C OXIDASE POLYPEPTIDE II
Molecular weight formula_weight	27972.2 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAA

Entity 3 Entity 3 polymer

Description description	CYTOCHROME C OXIDASE POLYPEPTIDE III
Molecular weight formula_weight	30677.0 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

AHVKNHDYQILPPSIWPFFGAIGAFVMLTGAVAWMKGITFFGLPVEGPWMFLIGLVGVLYVMFGWWADVVNEGETGEHTPVVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLILLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFGLADTVYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWGR

Entity 4 Entity 4 polymer

Description description	CCYTOCHROME C OXIDASE
Molecular weight formula_weight	4701.4 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

TDHKHGEMDIRHQQATFAGFIKGATWVSILSIAVLVFLALANS

Entity 5 Entity 5 polymer

Description description	HEAVY CHAIN ANTIBODY FV FRAGMENT
Molecular weight formula_weight	13356.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVKLQESGGDLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVASINNGGGRTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHEYYYAMDYWGQGTTVTVSSA

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 6 Entity 6 polymer

Description description	LIGHT CHAIN ANTIBODY FV FRAGMENT
Molecular weight formula_weight	11786.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIELTQTPVSLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQFLVYNAKTLGEGVPSRFSGSGSGTQFSLKINSLLPEDFGSYYCQHHYGTPPLTFGGGTKLEIK

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 7 Entity 7 non-polymer

Description description	HEME-A
Molecular weight formula_weight	852.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	DINUCLEAR COPPER ION
Molecular weight formula_weight	127.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	790.1 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1qlea_
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	d1qleb1
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	d1qleb2
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	d1qlec_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.25 — Cytochrome c oxidase subunit III-like
Superfamily Superfamily superfamily	f.25.1 — Cytochrome c oxidase subunit III-like
Family Family family	f.25.1.1 — Cytochrome c oxidase subunit III-like

Domain ID domain_id	d1qled_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.8 — Bacterial aa3 type cytochrome c oxidase subunit IV
Family Family family	f.23.8.1 — Bacterial aa3 type cytochrome c oxidase subunit IV

Domain ID domain_id	d1qleh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1qlel_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id	1qleA00
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	1qleB01
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	1qleB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1qleC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	1qleC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

Domain ID domain_id	1qleD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	160 — Bacterial aa3 type cytochrome c oxidase subunit IV

Domain ID domain_id	1qleH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1qleL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	205.200 Å
Unit-cell length b length_b	205.200 Å
Unit-cell length c length_c	81.100 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	4

Space group space_group	P 4
Space-group number int_tables_number	75
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.3090

CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT

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

CYTOCHROME C OXIDASE POLYPEPTIDE I-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

CYTOCHROME C OXIDASE POLYPEPTIDE II

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 POLYPEPTIDE III

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CCYTOCHROME C OXIDASE

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

1qle__assembly_1__model_1

1qle__assembly_1__model_1 | I(q)

1qle__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

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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

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 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

CATH v4.4 (8 domains)

7. Citations (1)