1u7k

Structure of a hexameric N-terminal domain from murine leukemia virus capsid

Method: X-RAY DIFFRACTION

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

Gag polyprotein

AKR (endogenous) murine leukemia virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GAG_MLVAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 215–345 Author chain B； PDBConstruct 1–131； UniProt 215–345 Author chain C； PDBConstruct 1–131； UniProt 215–345 Author chain D； PDBConstruct 1–131； UniProt 215–345 Author chain E； PDBConstruct 1–131； UniProt 215–345 Author chain F； PDBConstruct 1–131； UniProt 215–345

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	1u7k
Deposition date deposition_date	2004-08-04
Structure title title	Structure of a hexameric N-terminal domain from murine leukemia virus capsid
Keywords keywords	capsid, Viral protein; VIRAL 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.

1u7k__assembly_1__model_1

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

Download this curve (.dat)

1u7k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u7k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.43 Å
Rg (electron density)	29.41 Å
Total Rg	30.17 Å
Atom count	6300
Residues	774
Excluded volume	110590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u7k__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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1u7ka_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

Domain ID domain_id	d1u7kb_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

Domain ID domain_id	d1u7kc_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

Domain ID domain_id	d1u7kd_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

Domain ID domain_id	d1u7ke_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

Domain ID domain_id	d1u7kf_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

CATH v4.4 (6 domains)

Domain ID domain_id	1u7kA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

Domain ID domain_id	1u7kB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

Domain ID domain_id	1u7kC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

Domain ID domain_id	1u7kD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

Domain ID domain_id	1u7kE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

Domain ID domain_id	1u7kF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

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Unit-cell length a length_a	85.995 Å
Unit-cell length b length_b	78.340 Å
Unit-cell length c length_c	85.766 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2113
R_work r_work	0.2096
R_free r_free	0.2421

Description description	Gag polyprotein
Molecular weight formula_weight	15004.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6731

Structure of a hexameric N-terminal domain from murine leukemia virus capsid

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

Gag polyprotein

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

1u7k__assembly_1__model_1

1u7k__assembly_1__model_1 | I(q)

1u7k__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	AKR (endogenous) murine leukemia virus
NCBI taxonomy ID ncbi_taxonomy_id	11791
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	431

Structure of a hexameric N-terminal domain from murine leukemia virus capsid

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

Gag polyprotein

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

1u7k__assembly_1__model_1

1u7k__assembly_1__model_1 | I(q)

1u7k__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)