5hgb

HLA*A2402 complexed with HIV nef138 8mer epitope

Method: X-RAY DIFFRACTION Dmax: 131.6 Å Quality: EXCELLENT

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

HLA class I histocompatibility antigen, A-24 alpha chain

Homo sapiens

UniProt P05534

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 A; UniProt 25–298 Fragment:UNP RESIDUES 25-298 Beta-2-microglobulin × 1 (P61769) Protein Nef × 1 (P18801) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–298 Fragment:UNP RESIDUES 25-298 Beta-2-microglobulin × 1 (P61769) Protein Nef × 1 (P18801) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 25–298 Fragment:UNP RESIDUES 25-298 Beta-2-microglobulin × 1 (P61769) Protein Nef × 1 (P18801) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 25–298 Fragment:UNP RESIDUES 25-298 Beta-2-microglobulin × 1 (P61769) Protein Nef × 1 (P18801) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218

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.

28 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A24_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–275; UniProt 25–298 Author chain D; PDBConstruct 2–275; UniProt 25–298 Author chain G; PDBConstruct 2–275; UniProt 25–298 Author chain J; PDBConstruct 2–275; UniProt 25–298

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 B; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Protein Nef × 1 (P18801) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Protein Nef × 1 (P18801) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Protein Nef × 1 (P18801) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain K; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Protein Nef × 1 (P18801) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218

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.

1313 other PDB entries and 1995 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–100; UniProt 21–119 Author chain E; PDBConstruct 2–100; UniProt 21–119 Author chain H; PDBConstruct 2–100; UniProt 21–119 Author chain K; PDBConstruct 2–100; UniProt 21–119

Protein Nef

OrganismNot specified

UniProt P18801

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 135–142 Fragment:UNP RESIDUES 135-142 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 135–142 Fragment:UNP RESIDUES 135-142 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 135–142 Fragment:UNP RESIDUES 135-142 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain L; UniProt 135–142 Fragment:UNP RESIDUES 135-142 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;291 K;0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 Resolution 2.40 Å R-free 0.218

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.

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEF_HV1ND
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–8; UniProt 135–142 Author chain F; PDBConstruct 1–8; UniProt 135–142 Author chain I; PDBConstruct 1–8; UniProt 135–142 Author chain L; PDBConstruct 1–8; UniProt 135–142

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5hgb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5hgb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5hgb
Deposition date deposition_date2016-01-08
Structure title titleHLA*A2402 complexed with HIV nef138 8mer epitope
Keywords keywordsHLA, Antigen presentation, HIV, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.18
Radius of gyration Rg (electron density) rg_electron40.59
Forward intensity I(0) i0509133000.00
Molecular weight molecular_weight177460.0 kDa
Excluded volume excluded_volume218840 ų
Envelope volume envelope_volume305250 ų
Hydration-shell volume shell_volume62554 ų
Envelope diameter envelope_diameter138.4
Shell Rg shell_rg46.03
Envelope Rg envelope_rg40.04
Shape Rg shape_rg40.58
Total Rg total_rg40.92
Total atoms total_atoms12528
Residues n_residues1528
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax131.6
Rg (real space) rg_real41.04
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real5.0910e+08
I(0) uncertainty (real space) i0_real_error9.0570e+06
Rg (reciprocal space) rg_reciprocal41.18
I(0) (reciprocal space) i0_reciprocal509200000.0000
Solution quality estimate total_estimate0.9009
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.4
Skewness Skewness skewness0.155
Kurtosis Kurtosis kurtosis-0.501
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha46100000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.929

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id5hgbA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5hgbA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hgbB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hgbD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5hgbD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hgbE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hgbG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5hgbG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hgbH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hgbJ01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5hgbJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hgbK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)