3sjv

Crystal structure of the RL42 TCR in complex with HLA-B8-FLR

Method: X-RAY DIFFRACTION Dmax: 173.3 Å Quality: GOOD

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

HLA class I histocompatibility antigen, B-8 alpha chain

Homo sapiens

UniProt P30460

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 25–301 Fragment:Extracellular domain residues 25-301 Beta-2-microglobulin × 1 (P61769) Epstein-Barr nuclear antigen 3 × 1 (Q3KST2) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 25–301 Fragment:Extracellular domain residues 25-301 Beta-2-microglobulin × 1 (P61769) Epstein-Barr nuclear antigen 3 × 1 (Q3KST2) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain K; UniProt 25–301 Fragment:Extracellular domain residues 25-301 Beta-2-microglobulin × 1 (P61769) Epstein-Barr nuclear antigen 3 × 1 (Q3KST2) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 25–301 Fragment:Extracellular domain residues 25-301 Beta-2-microglobulin × 1 (P61769) Epstein-Barr nuclear antigen 3 × 1 (Q3KST2) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321

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.

24 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1B08_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–277; UniProt 25–301 Author chain F; PDBConstruct 1–277; UniProt 25–301 Author chain K; PDBConstruct 1–277; UniProt 25–301 Author chain P; PDBConstruct 1–277; UniProt 25–301

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, B-8 alpha chain × 1 (P30460) Epstein-Barr nuclear antigen 3 × 1 (Q3KST2) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
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, B-8 alpha chain × 1 (P30460) Epstein-Barr nuclear antigen 3 × 1 (Q3KST2) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
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, B-8 alpha chain × 1 (P30460) Epstein-Barr nuclear antigen 3 × 1 (Q3KST2) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
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, B-8 alpha chain × 1 (P30460) Epstein-Barr nuclear antigen 3 × 1 (Q3KST2) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321

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

Epstein-Barr nuclear antigen 3

OrganismNot specified

UniProt Q3KST2

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 325–333 Fragment:sequence database residues 325-333 HLA class I histocompatibility antigen, B-8 alpha chain × 1 (P30460) Beta-2-microglobulin × 1 (P61769) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 325–333 Fragment:sequence database residues 325-333 HLA class I histocompatibility antigen, B-8 alpha chain × 1 (P30460) Beta-2-microglobulin × 1 (P61769) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain M; UniProt 325–333 Fragment:sequence database residues 325-333 HLA class I histocompatibility antigen, B-8 alpha chain × 1 (P30460) Beta-2-microglobulin × 1 (P61769) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 325–333 Fragment:sequence database residues 325-333 HLA class I histocompatibility antigen, B-8 alpha chain × 1 (P30460) Beta-2-microglobulin × 1 (P61769) RL42 T cell receptor, alpha chain × 1 RL42 T cell receptor, beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K Resolution 3.10 Å R-free 0.321

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EBNA3_EBVG
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 325–333 Author chain H; PDBConstruct 1–9; UniProt 325–333 Author chain M; PDBConstruct 1–9; UniProt 325–333 Author chain R; PDBConstruct 1–9; UniProt 325–333

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 3sjv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3sjv
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3sjv
Deposition date deposition_date2011-06-22
Structure title titleCrystal structure of the RL42 TCR in complex with HLA-B8-FLR
Keywords keywordsT cell, 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_guinier52.47
Radius of gyration Rg (electron density) rg_electron52.11
Forward intensity I(0) i02170980000.00
Molecular weight molecular_weight375020.0 kDa
Excluded volume excluded_volume462810 ų
Envelope volume envelope_volume685420 ų
Hydration-shell volume shell_volume108940 ų
Envelope diameter envelope_diameter173.4
Shell Rg shell_rg56.45
Envelope Rg envelope_rg51.23
Shape Rg shape_rg52.11
Total Rg total_rg52.22
Total atoms total_atoms26455
Residues n_residues3281
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 dmax173.3
Rg (real space) rg_real52.34
Rg uncertainty (real space) rg_real_error1.49
I(0) (real space) i0_real2.1710e+09
I(0) uncertainty (real space) i0_real_error3.8870e+07
Rg (reciprocal space) rg_reciprocal52.56
I(0) (reciprocal space) i0_reciprocal2172000000.0000
Solution quality estimate total_estimate0.8702
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.5
Skewness Skewness skewness0.264
Kurtosis Kurtosis kurtosis-0.345
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha142700000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.794

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id3sjvA01
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_id3sjvA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvF01
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_id3sjvF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvK01
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_id3sjvK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvN02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvO01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvO02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvP01
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_id3sjvP02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvQ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvS01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvS02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvT01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3sjvT02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)