5nmf

868 TCR in complex with HLA A02 presenting SLYNTIATL

Method: X-RAY DIFFRACTION Dmax: 197.8 Å Quality: REASONABLE

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 (O11803) HUman T-cell receptor Alpha chain × 1 Human T-cell receptor Beta chain × 1 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 2 SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 6.0, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.89 Å R-free 0.255
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 (O11803) Human T-cell receptor Beta chain × 1 HUman T-cell receptor Alpha chain × 1 EDO 1,2-ETHANEDIOL × 14 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 6.0, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.89 Å R-free 0.255

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 (O11803) HUman T-cell receptor Alpha chain × 1 Human T-cell receptor Beta chain × 1 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 2 SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 6.0, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.89 Å R-free 0.255
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 (O11803) Human T-cell receptor Beta chain × 1 HUman T-cell receptor Alpha chain × 1 EDO 1,2-ETHANEDIOL × 14 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 6.0, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.89 Å R-free 0.255

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 O11803

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 7–15 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 × 5 GOL GLYCEROL × 2 SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 6.0, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.89 Å R-free 0.255
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 7–15 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Human T-cell receptor Beta chain × 1 HUman T-cell receptor Alpha chain × 1 EDO 1,2-ETHANEDIOL × 14 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.1 M Sodium Cacodylate, pH 6.0, 15% PEG 4000, 0.2 M Ammonium Sulphate Resolution 2.89 Å R-free 0.255

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name O11803_9HIV1
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 7–15 Author chain H; PDBConstruct 1–9; UniProt 7–15

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 5nmf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5nmf
Deposition date deposition_date2017-04-05
Structure title title868 TCR in complex with HLA A02 presenting SLYNTIATL
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_guinier63.31
Radius of gyration Rg (electron density) rg_electron64.56
Forward intensity I(0) i0564765000.00
Molecular weight molecular_weight190690.0 kDa
Excluded volume excluded_volume234930 ų
Envelope volume envelope_volume386470 ų
Hydration-shell volume shell_volume55197 ų
Envelope diameter envelope_diameter214.0
Shell Rg shell_rg55.96
Envelope Rg envelope_rg62.67
Shape Rg shape_rg64.52
Total Rg total_rg64.47
Total atoms total_atoms13434
Residues n_residues1649
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 dmax197.8
Rg (real space) rg_real64.32
Rg uncertainty (real space) rg_real_error2.00
I(0) (real space) i0_real5.6470e+08
I(0) uncertainty (real space) i0_real_error1.1930e+07
Rg (reciprocal space) rg_reciprocal62.35
I(0) (reciprocal space) i0_reciprocal562800000.0000
Solution quality estimate total_estimate0.7374
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.6
Skewness Skewness skewness0.419
Kurtosis Kurtosis kurtosis-0.773
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14500000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.681; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.542; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id5nmfA01
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_id5nmfA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfF01
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_id5nmfF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nmfJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)