SAXSdb — 3cyt

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

CYTOCHROME C

Thunnus alalunga

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	HEME C × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	HEME C × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYC_THUAA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain I； PDBConstruct 2–104； UniProt 1–103 Author chain O； PDBConstruct 2–104； UniProt 1–103

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	3cyt
Deposition date deposition_date	1980-07-01
Structure title title	REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C
Keywords keywords	ELECTRON TRANSPORT (HEME PROTEIN); ELECTRON TRANSPORT (HEME PROTEIN)
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.

3cyt__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3cyt__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cyt__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	13.77 Å
Rg (electron density)	12.39 Å
Total Rg	13.85 Å
Atom count	846
Residues	103
Excluded volume	15176 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cyt__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cyt__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME C
Molecular weight formula_weight	11416.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,I
Atom count atom_count	1743

XGDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNNDTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS

Source Source

Source organism organism	Thunnus alalunga
Common name common_name	albacore
NCBI taxonomy ID ncbi_taxonomy_id	8235

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3cyti_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d3cyto_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

CATH v4.4 (2 domains)

Domain ID domain_id	3cytI00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	3cytO00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

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7. Citations (10)

Redox conformation changes in refined tuna cytochrome c.

Proc.Natl.Acad.Sci.USA (1980)

PMID: 6256733 · DOI: 10.1073/pnas.77.11.6371 PRIMARY

Conformation Change of Cytochrome C. I. Ferrocytochrome C Structure Refined at 1.5 Angstroms Resolution

J.Mol.Biol. (1981)

;Conformation Change of Cytochrome C. II. Ferricytochrome C Refinement at 1.8 Angstroms and Comparison with the Ferrocytochrome Structure ;

J.Mol.Biol. (1981)

Cytochrome C and the Evolution of Energy Metabolism

Sci.Am. (1980)

Internal Mobility of Ferrocytochrome C

Nature (1980)

Tuna Cytochrome C at 2.0 Angstroms Resolution. II. Ferrocytochrome Structure Analysis

J.Biol.Chem. (1977)

Tuna Cytochrome C at 2.0 Angstroms Resolution. I. Ferricytochrome Structure Analysis

J.Biol.Chem. (1977)

Untitled

Atlas of Protein Sequence and Structure,Supplement 2 (1976)

The Structure of Ferrocytochrome C at 2.45 Angstroms Resolution

J.Biol.Chem. (1973)

The Structure and History of an Ancient Protein

Sci.Am. (1972)

Unit-cell length a length_a	74.420 Å
Unit-cell length b length_b	74.420 Å
Unit-cell length c length_c	36.300 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C

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

CYTOCHROME C

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

3cyt__assembly_2__model_1

3cyt__assembly_2__model_1 | I(q)

3cyt__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (10)

REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C

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

CYTOCHROME C

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

3cyt__assembly_2__model_1

3cyt__assembly_2__model_1 | I(q)

3cyt__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (10)