SAXSdb — 5dhy

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

Protein Rev

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Anti-Rev Antibody Fab single-chain variable fragment, heavy chain × 1 Anti-Rev Antibody Fab single-chain variable fragment, light chain × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Anti-Rev Antibody Fab single-chain variable fragment, heavy chain × 1 Anti-Rev Antibody Fab single-chain variable fragment, light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q76PP8_9HIV1
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–65； UniProt 1–65 Author chain M； PDBConstruct 1–65； UniProt 1–65

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	5dhy
Deposition date deposition_date	2015-08-31
Structure title title	HIV-1 Rev NTD dimers with variable crossing angles
Keywords keywords	HIV, helical hairpin, RNA-binding, nuclear export, immune system; 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.

5dhy__assembly_1__model_1

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

Download this curve (.dat)

5dhy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dhy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.07 Å
Rg (electron density)	19.89 Å
Total Rg	20.98 Å
Atom count	2222
Residues	288
Excluded volume	39238 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dhy__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5dhy__assembly_2__model_1`	trimeric （3）	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	Anti-Rev Antibody Fab single-chain variable fragment, heavy chain
Molecular weight formula_weight	12579.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H
Atom count atom_count	4444

QEQLVESGGRLVTPGTALTLTCKVSGFSLSGFWLNWVRQAPGKGLEWVGAIYRGSGSEWYASWAKGRFTISDTSTTVTLKLTSPTTEDTATYFCAADTTDNGYFTIWGPGTLVTVSS

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	Rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Anti-Rev Antibody Fab single-chain variable fragment, light chain
Molecular weight formula_weight	11657.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,L

ELVMTQTPSSVSEPVGGTVTIKCQASQSISSWLSWYQQKPGQPPKLLIYDASNLASGVPSRFMGSGSGTEYTLTISGVQREDAATYYCLGGYPAASYRTAFGGGTELEII

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	Rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Protein Rev
Molecular weight formula_weight	7750.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAGRSGDSDEDLLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILSTYLG

Source Source

Source organism organism	Human immunodeficiency virus 1
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5dhya_
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.1.1.0 — automated matches

Domain ID domain_id	d5dhyb_
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.1.1.0 — automated matches

Domain ID domain_id	d5dhyh_
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.1.1.0 — automated matches

Domain ID domain_id	d5dhyl_
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.1.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	5dhyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dhyB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dhyC00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	630 —

Domain ID domain_id	5dhyH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dhyL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dhyM00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	630 —

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Unit-cell length a length_a	121.140 Å
Unit-cell length b length_b	121.140 Å
Unit-cell length c length_c	89.270 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	16

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	33.390 Å
R factor r_factor	0.2919
R_work r_work	0.2914
R_free r_free	0.3002

HIV-1 Rev NTD dimers with variable crossing angles

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

Protein Rev

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

5dhy__assembly_1__model_1

5dhy__assembly_1__model_1 | I(q)

5dhy__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 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

HIV-1 Rev NTD dimers with variable crossing angles

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

Protein Rev

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

5dhy__assembly_1__model_1

5dhy__assembly_1__model_1 | I(q)

5dhy__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 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)