5nmg

868 TCR in complex with HLA A02 presenting SLYFNTIAVL

Method: X-RAY DIFFRACTION Dmax: 162.4 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A-2 alpha chain

Homo sapiens

UniProt P01892

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Gag protein × 1 (W0GUW4) Human T-cell receptor alpha chain × 1 Human T-cell Receptor beta chain × 1 EDO 1,2-ETHANEDIOL × 13 GOL GLYCEROL × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 5.5, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.75 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Gag protein × 1 (W0GUW4) Human T-cell receptor alpha chain × 1 Human T-cell Receptor beta chain × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 5.5, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.75 Å R-free 0.254

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.

271 other PDB entries and 464 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A02_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 25–300 Author chain F; PDBConstruct 1–276; UniProt 25–300

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Gag protein × 1 (W0GUW4) Human T-cell receptor alpha chain × 1 Human T-cell Receptor beta chain × 1 EDO 1,2-ETHANEDIOL × 13 GOL GLYCEROL × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 5.5, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.75 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Gag protein × 1 (W0GUW4) Human T-cell receptor alpha chain × 1 Human T-cell Receptor beta chain × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 5.5, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.75 Å R-free 0.254

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 1997 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 G; PDBConstruct 2–100; UniProt 21–119

Gag protein

OrganismNot specified

UniProt W0GUW4

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 67–75 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Human T-cell receptor alpha chain × 1 Human T-cell Receptor beta chain × 1 EDO 1,2-ETHANEDIOL × 13 GOL GLYCEROL × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 5.5, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.75 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 67–75 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Human T-cell receptor alpha chain × 1 Human T-cell Receptor beta chain × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 5.5, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.75 Å R-free 0.254

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name W0GUW4_9HIV1
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 67–75 Author chain H; PDBConstruct 1–9; UniProt 67–75

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 5nmg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5nmg
Deposition date deposition_date2017-04-05
Structure title title868 TCR in complex with HLA A02 presenting SLYFNTIAVL
Keywords keywordsMHC, TCR, CD8+, 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_guinier47.13
Radius of gyration Rg (electron density) rg_electron47.11
Forward intensity I(0) i0570245000.00
Molecular weight molecular_weight190090.0 kDa
Excluded volume excluded_volume234690 ų
Envelope volume envelope_volume335770 ų
Hydration-shell volume shell_volume61575 ų
Envelope diameter envelope_diameter173.2
Shell Rg shell_rg48.63
Envelope Rg envelope_rg47.21
Shape Rg shape_rg47.10
Total Rg total_rg47.19
Total atoms total_atoms13407
Residues n_residues1653
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 dmax162.4
Rg (real space) rg_real47.39
Rg uncertainty (real space) rg_real_error1.81
I(0) (real space) i0_real5.7020e+08
I(0) uncertainty (real space) i0_real_error1.2070e+07
Rg (reciprocal space) rg_reciprocal47.13
I(0) (reciprocal space) i0_reciprocal570100000.0000
Solution quality estimate total_estimate0.8628
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.1
Skewness Skewness skewness0.426
Kurtosis Kurtosis kurtosis-0.328
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41720000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.683

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id5nmgA01
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_id5nmgA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgF01
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_id5nmgF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmgJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)