5d2l

Crystal structure of TCR C7 in complex with HCMV NLV epitope presented by HLA-A2

Method: X-RAY DIFFRACTION Dmax: 199.5 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 25–299 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) C7 TCR alpha chain × 1 C7 TCR beta chain × 1 ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 Resolution 3.51 Å R-free 0.355
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 25–299 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) C7 TCR alpha chain × 1 C7 TCR beta chain × 1 ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 Resolution 3.51 Å R-free 0.355
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain M; UniProt 25–299 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) C7 TCR alpha chain × 1 C7 TCR beta chain × 1 ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 Resolution 3.51 Å R-free 0.355
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 25–299 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) C7 TCR alpha chain × 1 C7 TCR beta chain × 1 ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 Resolution 3.51 Å R-free 0.355

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 462 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 2–276; UniProt 25–299 Author chain C; PDBConstruct 2–276; UniProt 25–299 Author chain G; PDBConstruct 2–276; UniProt 25–299 Author chain M; PDBConstruct 2–276; UniProt 25–299

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 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) C7 TCR alpha chain × 1 C7 TCR beta chain × 1 ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 Resolution 3.51 Å R-free 0.355
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 21–119 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) C7 TCR alpha chain × 1 C7 TCR beta chain × 1 ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 Resolution 3.51 Å R-free 0.355
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain N; UniProt 21–119 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) C7 TCR alpha chain × 1 C7 TCR beta chain × 1 ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 Resolution 3.51 Å R-free 0.355
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 21–119 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) C7 TCR alpha chain × 1 C7 TCR beta chain × 1 ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 Resolution 3.51 Å R-free 0.355

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 D; PDBConstruct 2–100; UniProt 21–119 Author chain H; PDBConstruct 2–100; UniProt 21–119 Author chain N; 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 5d2l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5d2l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5d2l
Deposition date deposition_date2015-08-05
Structure title titleCrystal structure of TCR C7 in complex with HCMV NLV epitope presented by HLA-A2
Keywords keywordsTCR, HCMV, HLA-A2, 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_guinier55.86
Radius of gyration Rg (electron density) rg_electron55.65
Forward intensity I(0) i01961070000.00
Molecular weight molecular_weight357090.0 kDa
Excluded volume excluded_volume440420 ų
Envelope volume envelope_volume687030 ų
Hydration-shell volume shell_volume103770 ų
Envelope diameter envelope_diameter212.3
Shell Rg shell_rg57.44
Envelope Rg envelope_rg55.47
Shape Rg shape_rg55.64
Total Rg total_rg55.71
Total atoms total_atoms25218
Residues n_residues3198
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 dmax199.5
Rg (real space) rg_real56.00
Rg uncertainty (real space) rg_real_error2.27
I(0) (real space) i0_real1.9610e+09
I(0) uncertainty (real space) i0_real_error4.1680e+07
Rg (reciprocal space) rg_reciprocal55.74
I(0) (reciprocal space) i0_reciprocal1960000000.0000
Solution quality estimate total_estimate0.8518
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary64.1
Skewness Skewness skewness0.483
Kurtosis Kurtosis kurtosis0.041
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha124700000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.871

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id5d2lA01
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_id5d2lA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lC01
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_id5d2lC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lG01
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_id5d2lG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lK01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lM01
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_id5d2lM02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lN00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lO01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lO02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lP01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5d2lP02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)