4jry

Crystal Structure of SB47 TCR-HLA B*3505-LPEP complex

Method: X-RAY DIFFRACTION Dmax: 130.4 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt C5MK56

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 Fragment:UNP RESIDUES 25-300 Beta-2-microglobulin × 1 (P61769) Trans-activator protein BZLF1 × 1 (Q3KSS8) SB47 TCR alpha chain × 1 SB47 TCR beta chain × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;12% PEG 10K, 0.2M Na tartrate, 10mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.233

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.

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C5MK56_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; 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 MHC class I antigen × 1 (C5MK56) Trans-activator protein BZLF1 × 1 (Q3KSS8) SB47 TCR alpha chain × 1 SB47 TCR beta chain × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;12% PEG 10K, 0.2M Na tartrate, 10mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.233

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 1998 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

Trans-activator protein BZLF1

OrganismNot specified

UniProt Q3KSS8

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 52–64 Fragment:UNP RESIDUES 52-64 MHC class I antigen × 1 (C5MK56) Beta-2-microglobulin × 1 (P61769) SB47 TCR alpha chain × 1 SB47 TCR beta chain × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;12% PEG 10K, 0.2M Na tartrate, 10mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.233

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 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BZLF1_EBVG
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–13; UniProt 52–64

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 4jry

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4jry
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4jry
Deposition date deposition_date2013-03-22
Structure title titleCrystal Structure of SB47 TCR-HLA B*3505-LPEP complex
Keywords keywordsTCR, T cell, HLA B*3508, LPEP, EBV, alloreactivity, 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_guinier37.15
Radius of gyration Rg (electron density) rg_electron37.24
Forward intensity I(0) i0147826000.00
Molecular weight molecular_weight95017.0 kDa
Excluded volume excluded_volume117490 ų
Envelope volume envelope_volume155990 ų
Hydration-shell volume shell_volume37820 ų
Envelope diameter envelope_diameter137.4
Shell Rg shell_rg39.49
Envelope Rg envelope_rg37.52
Shape Rg shape_rg37.23
Total Rg total_rg37.42
Total atoms total_atoms6706
Residues n_residues832
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 dmax130.4
Rg (real space) rg_real37.63
Rg uncertainty (real space) rg_real_error1.34
I(0) (real space) i0_real1.4780e+08
I(0) uncertainty (real space) i0_real_error2.5890e+06
Rg (reciprocal space) rg_reciprocal37.34
I(0) (reciprocal space) i0_reciprocal147800000.0000
Solution quality estimate total_estimate0.7972
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.4
Skewness Skewness skewness0.596
Kurtosis Kurtosis kurtosis-0.273
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16750000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.684; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.560; Smooth: 0.747

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id4jryA01
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_id4jryA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4jryB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4jryD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4jryD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4jryE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4jryE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)