SAXSdb — 4lqw

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

E3 SUMO-protein ligase RanBP2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Capsid protein p24 × 1 （P12497） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Capsid protein p24 × 1 （P12497） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–177； UniProt 3057–3224 Author chain B； PDBConstruct 10–177； UniProt 3057–3224

Capsid protein p24

Human immunodeficiency virus type 1

UniProt P12497

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	E3 SUMO-protein ligase RanBP2 × 1 （P49792） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	E3 SUMO-protein ligase RanBP2 × 1 （P49792） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1N5
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–146； UniProt 133–278 Author chain D； PDBConstruct 1–146； UniProt 133–278

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	4lqw
Deposition date deposition_date	2013-07-19
Structure title title	Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin
Keywords keywords	cyclophilin, isomerase, capsid; ISOMERASE
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.

4lqw__assembly_1__model_1

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

Download this curve (.dat)

4lqw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4lqw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.47 Å
Rg (electron density)	24.40 Å
Total Rg	25.16 Å
Atom count	2409
Residues	310
Excluded volume	42819 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4lqw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4lqw__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 (3)

Entity 1 Entity 1 polymer

Description description	E3 SUMO-protein ligase RanBP2
Molecular weight formula_weight	19713.3 kDa
EC 编号 ec_number	6.3.2.-, 5.2.1.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5271

MAHHHHHHMELSKETNPVVFFDVCADGEPLGRITMELFSNIVPRTAENFRALCTGEKGFGFKNSIFHRVIPDFVCQGGDITKHDGTGGQSIYGDKFEDENFDVKHTGPGLLSMANQGQNTNNSQFVITLKKAEHLDFKHVVFGFVKDGMDTVKKIESFGSPKGSVCRRITITECGQI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Capsid protein p24
Molecular weight formula_weight	16204.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS

Source Source

Source organism organism	Human immunodeficiency virus type 1
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11698
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	372

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4lqwa1
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d4lqwa2
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	d4lqwb1
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d4lqwb2
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	d4lqwc_
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	d4lqwd_
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 (4 domains)

Domain ID domain_id	4lqwA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	4lqwB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	4lqwC00
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	4lqwD00
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	142.180 Å
Unit-cell length b length_b	38.260 Å
Unit-cell length c length_c	123.810 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	33.040 Å
R factor r_factor	0.2071
R_work r_work	0.2050
R_free r_free	0.2465

Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin

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

E3 SUMO-protein ligase RanBP2

State in the Current Structure

Other States of the Same Protein in the Database

Capsid protein p24

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

4lqw__assembly_1__model_1

4lqw__assembly_1__model_1 | I(q)

4lqw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin

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

E3 SUMO-protein ligase RanBP2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Capsid protein p24

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

4lqw__assembly_1__model_1

4lqw__assembly_1__model_1 | I(q)

4lqw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)