5w1v

Structure of the HLA-E-VMAPRTLIL/GF4 TCR complex

Method: X-RAY DIFFRACTION Dmax: 242.5 Å Quality: GOOD

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

HLA class I histocompatibility antigen, alpha chain E

Homo sapiens

UniProt P13747

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 22–299 Not recorded Beta-2-microglobulin × 1 (P61769) VMAPRTLIL peptide from CMV gpUL40 × 1 GF4 T cell receptor alpha chain × 1 GF4 T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M K, Na tartrate, 20% PEG 3350 Resolution 3.31 Å R-free 0.268
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 22–299 Not recorded Beta-2-microglobulin × 1 (P61769) VMAPRTLIL peptide from CMV gpUL40 × 1 GF4 T cell receptor alpha chain × 1 GF4 T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M K, Na tartrate, 20% PEG 3350 Resolution 3.31 Å R-free 0.268
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain K; UniProt 22–299 Not recorded Beta-2-microglobulin × 1 (P61769) VMAPRTLIL peptide from CMV gpUL40 × 1 GF4 T cell receptor alpha chain × 1 GF4 T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M K, Na tartrate, 20% PEG 3350 Resolution 3.31 Å R-free 0.268
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 22–299 Not recorded Beta-2-microglobulin × 1 (P61769) VMAPRTLIL peptide from CMV gpUL40 × 1 GF4 T cell receptor alpha chain × 1 GF4 T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M K, Na tartrate, 20% PEG 3350 Resolution 3.31 Å R-free 0.268

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 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–278; UniProt 22–299 Author chain F; PDBConstruct 1–278; UniProt 22–299 Author chain K; PDBConstruct 1–278; UniProt 22–299 Author chain P; PDBConstruct 1–278; UniProt 22–299

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, alpha chain E × 1 (P13747) VMAPRTLIL peptide from CMV gpUL40 × 1 GF4 T cell receptor alpha chain × 1 GF4 T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M K, Na tartrate, 20% PEG 3350 Resolution 3.31 Å R-free 0.268
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, alpha chain E × 1 (P13747) VMAPRTLIL peptide from CMV gpUL40 × 1 GF4 T cell receptor alpha chain × 1 GF4 T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M K, Na tartrate, 20% PEG 3350 Resolution 3.31 Å R-free 0.268
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain L; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) VMAPRTLIL peptide from CMV gpUL40 × 1 GF4 T cell receptor alpha chain × 1 GF4 T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M K, Na tartrate, 20% PEG 3350 Resolution 3.31 Å R-free 0.268
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain Q; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) VMAPRTLIL peptide from CMV gpUL40 × 1 GF4 T cell receptor alpha chain × 1 GF4 T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M K, Na tartrate, 20% PEG 3350 Resolution 3.31 Å R-free 0.268

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 G; PDBConstruct 2–100; UniProt 21–119 Author chain L; PDBConstruct 2–100; UniProt 21–119 Author chain Q; PDBConstruct 2–100; UniProt 21–119

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 5w1v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5w1v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5w1v
Deposition date deposition_date2017-06-04
Structure title titleStructure of the HLA-E-VMAPRTLIL/GF4 TCR complex
Keywords keywordsT-cell receptor, TCR, HLA-E, CMV, pMHC-TCR complex, 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_guinier66.47
Radius of gyration Rg (electron density) rg_electron66.93
Forward intensity I(0) i02086690000.00
Molecular weight molecular_weight374480.0 kDa
Excluded volume excluded_volume463710 ų
Envelope volume envelope_volume754940 ų
Hydration-shell volume shell_volume97180 ų
Envelope diameter envelope_diameter236.5
Shell Rg shell_rg61.99
Envelope Rg envelope_rg65.71
Shape Rg shape_rg66.94
Total Rg total_rg66.80
Total atoms total_atoms26433
Residues n_residues3302
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 dmax242.5
Rg (real space) rg_real67.00
Rg uncertainty (real space) rg_real_error2.66
I(0) (real space) i0_real2.0870e+09
I(0) uncertainty (real space) i0_real_error4.8080e+07
Rg (reciprocal space) rg_reciprocal66.00
I(0) (reciprocal space) i0_reciprocal2083000000.0000
Solution quality estimate total_estimate0.8590
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.7
Skewness Skewness skewness0.407
Kurtosis Kurtosis kurtosis-0.425
Angular range angular_range— – 0.1200 −1
Current regularization parameter α current_alpha0.0096
Highest regularization parameter α highest_alpha77590000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.824

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id5w1vA01
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_id5w1vA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vF01
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_id5w1vF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vK01
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_id5w1vK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vO01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vO02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vP01
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_id5w1vP02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vQ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vS01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vT01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w1vT02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)