SAXSdb — 2exf

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

Nucleocapsid protein* (NC*)

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(GPTPCPCPCPTPGPTPTPCPGPGPGPC)-3' × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1PV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 2–44； UniProt 389–431

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	2exf
Deposition date deposition_date	2005-11-08
Structure title title	Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site
Keywords keywords	protein-DNA complex, stem-loop, bulge, zinc-finger, Viral Protein-DNA COMPLEX; Viral Protein/DNA
Experimental Method method	SOLUTION NMR

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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.

2exf__assembly_1__model_1

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

Download this curve (.dat)

2exf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2exf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	13.74 Å
Rg (electron density)	13.04 Å
Total Rg	13.94 Å
Atom count	1122
Residues	58
Excluded volume	10182 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2exf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2exf__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2exf__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2exf__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2exf__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2exf__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2exf__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2exf__assembly_1__model_8`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2exf__assembly_1__model_9`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2exf__assembly_1__model_10`	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 (3)

Entity 1 Entity 1 polymer

Description description	5'-D(GPTPCPCPCPTPGPTPTPCPGPGPGPC)-3'
Molecular weight formula_weight	4263.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	11220

GTCCCTGTTCGGGC

Entity 2 Entity 2 polymer

Description description	Nucleocapsid protein* (NC*)
Molecular weight formula_weight	5022.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2exfa1
Class class	g — Small proteins
Fold Fold fold	g.40 — Retrovirus zinc finger-like domains
Superfamily Superfamily superfamily	g.40.1 — Retrovirus zinc finger-like domains
Family Family family	g.40.1.1 — Retrovirus zinc finger-like domains

Domain ID domain_id	d2exfa2
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 (1 domains)

Domain ID domain_id	2exfA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	60 — HIV-1 Nucleocapsid Protein
Homologous superfamily homologous superfamily	10 — Zinc finger, CCHC-type

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site

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

Nucleocapsid protein* (NC*)

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

2exf__assembly_1__model_1

2exf__assembly_1__model_1 | I(q)

2exf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site

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

Nucleocapsid protein* (NC*)

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

2exf__assembly_1__model_1

2exf__assembly_1__model_1 | I(q)

2exf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)