SAXSdb — 5dhy

▼

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

Protein Rev

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–65	Not recorded	Anti-Rev Antibody Fab single-chain variable fragment, heavy chain × 1 Anti-Rev Antibody Fab single-chain variable fragment, light chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5	Resolution 3.10 Å R-free 0.300
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain M； UniProt 1–65	Not recorded	Anti-Rev Antibody Fab single-chain variable fragment, heavy chain × 1 Anti-Rev Antibody Fab single-chain variable fragment, light chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5	Resolution 3.10 Å R-free 0.300

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5DHY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11BC Human Nap1 in complex with HIV-1 Rev Deposited 2026-02-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–116（116 aa） Chain D 1–116（116 aa） Chain E 1–116（116 aa） Chain F 1–116（116 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
11BE HIV-1 Rev Filament Deposited 2026-02-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 155 PDB declaration: 155-meric	Chain A1 1–116（116 aa） Chain A4 1–116（116 aa） Chain A5 1–116（116 aa） Chain A9 1–116（116 aa） Chain B1 1–116（116 aa） Chain B4 1–116（116 aa） Chain B5 1–116（116 aa） Chain B9 1–116（116 aa） Chain C1 1–116（116 aa） Chain C5 1–116（116 aa） Chain C6 1–116（116 aa） Chain C9 1–116（116 aa） Chain D1 1–116（116 aa） Chain D5 1–116（116 aa） Chain D6 1–116（116 aa） Chain D9 1–116（116 aa） Chain E1 1–116（116 aa） Chain E5 1–116（116 aa） Chain E6 1–116（116 aa） Chain E9 1–116（116 aa） Chain F1 1–116（116 aa） Chain F5 1–116（116 aa） Chain F6 1–116（116 aa） Chain F9 1–116（116 aa） Chain G1 1–116（116 aa） Chain G5 1–116（116 aa） Chain G6 1–116（116 aa） Chain G9 1–116（116 aa） Chain H1 1–116（116 aa） Chain H5 1–116（116 aa） Chain H6 1–116（116 aa） Chain H9 1–116（116 aa） Chain I1 1–116（116 aa） Chain I4 1–116（116 aa） Chain I9 1–116（116 aa） Chain J1 1–116（116 aa） Chain J4 1–116（116 aa） Chain J9 1–116（116 aa） Chain K1 1–116（116 aa） Chain K4 1–116（116 aa） Chain K9 1–116（116 aa） Chain L1 1–116（116 aa） Chain L4 1–116（116 aa） Chain L9 1–116（116 aa） Chain M1 1–116（116 aa） Chain M4 1–116（116 aa） Chain M5 1–116（116 aa） Chain M9 1–116（116 aa） Chain N1 1–116（116 aa） Chain N4 1–116（116 aa） Chain N5 1–116（116 aa） Chain N9 1–116（116 aa） Chain O1 1–116（116 aa） Chain O4 1–116（116 aa） Chain O5 1–116（116 aa） Chain O9 1–116（116 aa） Chain P1 1–116（116 aa） Chain P5 1–116（116 aa） Chain P9 1–116（116 aa） Chain R1 1–116（116 aa） Chain R4 1–116（116 aa） Chain R9 1–116（116 aa） Chain S1 1–116（116 aa） Chain S4 1–116（116 aa） Chain S9 1–116（116 aa） Chain T1 1–116（116 aa） Chain T4 1–116（116 aa） Chain T5 1–116（116 aa） Chain T9 1–116（116 aa） Chain U1 1–116（116 aa） Chain U4 1–116（116 aa） Chain U5 1–116（116 aa） Chain U9 1–116（116 aa） Chain V1 1–116（116 aa） Chain V5 1–116（116 aa） Chain V6 1–116（116 aa） Chain V9 1–116（116 aa） Chain W1 1–116（116 aa） Chain W5 1–116（116 aa） Chain W6 1–116（116 aa） Chain W9 1–116（116 aa） Chain X1 1–116（116 aa） Chain X5 1–116（116 aa） Chain X6 1–116（116 aa） Chain X9 1–116（116 aa） Chain Y1 1–116（116 aa） Chain Y5 1–116（116 aa） Chain Y6 1–116（116 aa） Chain Y9 1–116（116 aa） Chain a3 1–116（116 aa） Chain a7 1–116（116 aa） Chain a8 1–116（116 aa） Chain b3 1–116（116 aa） Chain b7 1–116（116 aa） Chain b8 1–116（116 aa） Chain c2 1–116（116 aa） Chain c7 1–116（116 aa） Chain c8 1–116（116 aa） Chain d2 1–116（116 aa） Chain d7 1–116（116 aa） Chain d8 1–116（116 aa） Chain e2 1–116（116 aa） Chain e7 1–116（116 aa） Chain e8 1–116（116 aa） Chain f2 1–116（116 aa） Chain f7 1–116（116 aa） Chain f8 1–116（116 aa） Chain g2 1–116（116 aa） Chain g7 1–116（116 aa） Chain g8 1–116（116 aa） Chain h2 1–116（116 aa） Chain h7 1–116（116 aa） Chain h8 1–116（116 aa） Chain i3 1–116（116 aa） Chain i7 1–116（116 aa） Chain j3 1–116（116 aa） Chain j7 1–116（116 aa） Chain k3 1–116（116 aa） Chain k7 1–116（116 aa） Chain l3 1–116（116 aa） Chain l7 1–116（116 aa） Chain m3 1–116（116 aa） Chain m7 1–116（116 aa） Chain m8 1–116（116 aa） Chain n3 1–116（116 aa） Chain n7 1–116（116 aa） Chain n8 1–116（116 aa） Chain o3 1–116（116 aa） Chain o7 1–116（116 aa） Chain o8 1–116（116 aa） Chain p3 1–116（116 aa） Chain p7 1–116（116 aa） Chain p8 1–116（116 aa） Chain r3 1–116（116 aa） Chain r7 1–116（116 aa） Chain s3 1–116（116 aa） Chain s7 1–116（116 aa） Chain t3 1–116（116 aa） Chain t7 1–116（116 aa） Chain t8 1–116（116 aa） Chain u3 1–116（116 aa） Chain u7 1–116（116 aa） Chain u8 1–116（116 aa） Chain v2 1–116（116 aa） Chain v7 1–116（116 aa） Chain v8 1–116（116 aa） Chain w2 1–116（116 aa） Chain w7 1–116（116 aa） Chain w8 1–116（116 aa） Chain x2 1–116（116 aa） Chain x7 1–116（116 aa） Chain x8 1–116（116 aa） Chain y2 1–116（116 aa） Chain y7 1–116（116 aa） Chain y8 1–116（116 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.30 Å
5DHV HIV-1 Rev NTD dimers with variable crossing angles Deposited 2015-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 1–65（65 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5.	Resolution 2.30 Å R-free 0.227
5DHV HIV-1 Rev NTD dimers with variable crossing angles Deposited 2015-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 1–65（65 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5.	Resolution 2.30 Å R-free 0.227
5DHZ HIV-1 Rev NTD dimers with variable crossing angles Deposited 2015-08-31	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 1–65（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5	Resolution 4.30 Å R-free 0.324
6BSY HIV-1 Rev assembly domain (residues 1-69) Deposited 2017-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–70（70 aa） Fragment：assembly domain (UNP residues 1-70) Chain B 1–70（70 aa） Fragment：assembly domain (UNP residues 1-70)	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；283.15 K；0.1 M sodium citrate, 25% MPD	Resolution 2.25 Å R-free 0.260
6CF2 Crystal structure of HIV-1 Rev (residues 1-93)-RNA aptamer complex Deposited 2018-02-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain F 1–93（93 aa） Fragment：UNP residues 1-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；2% v/v 1,4-dioxane, 0.1 M Tris, pH 8.0, 15% w/v PEG3350	Resolution 3.00 Å R-free 0.241

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

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.

▼

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

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.60 Å
Radius of gyration Rg (electron density) rg_electron	27.93 Å
Forward intensity I(0) i0	66803100.00
Molecular weight molecular_weight	62991.0 kDa
Excluded volume excluded_volume	78475 Å³
Envelope volume envelope_volume	100300 Å³
Hydration-shell volume shell_volume	30232 Å³
Envelope diameter envelope_diameter	98.0 Å
Shell Rg shell_rg	34.89 Å
Envelope Rg envelope_rg	27.36 Å
Shape Rg shape_rg	27.89 Å
Total Rg total_rg	28.77 Å
Total atoms total_atoms	4444
Residues n_residues	576
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	95.0 Å
Rg (real space) rg_real	28.58 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	6.6800e+07
I(0) uncertainty (real space) i0_real_error	8.8150e+05
Rg (reciprocal space) rg_reciprocal	28.59 Å
I(0) (reciprocal space) i0_reciprocal	66800000.0000
Solution quality estimate total_estimate	0.8971
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.8 Å
Skewness Skewness skewness	0.277
Kurtosis Kurtosis kurtosis	-0.486
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8087000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.992

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. 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

来源 Source

来源生物 organism	Oryctolagus cuniculus
通用名 common_name	Rabbit
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 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

来源 Source

来源生物 organism	Oryctolagus cuniculus
通用名 common_name	Rabbit
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 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

来源 Source

来源生物 organism	Human immunodeficiency virus 1
通用名 common_name	HIV-1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

▼

7. 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 —

▶

8. Citations (1)

▶

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

fit	/app/data/saxs_computation/dh/5dhy/5dhy.fit
pddf	/app/data/pr_computation/dh/5dhy/5dhy.pr.out
profile	/app/data/saxs_computation/dh/5dhy/5dhy.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)