9d95

TRAV35/TRBV20 TCR - HLA-B38 complex

Method: X-RAY DIFFRACTION Dmax: 244.3 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt E5FQ58

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) Epstein-Barr nuclear antigen 2 × 1 (P12978) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
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) Epstein-Barr nuclear antigen 2 × 1 (P12978) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain K; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Epstein-Barr nuclear antigen 2 × 1 (P12978) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Epstein-Barr nuclear antigen 2 × 1 (P12978) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235

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 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name E5FQ58_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 Author chain K; PDBConstruct 1–276; UniProt 25–300 Author chain P; 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 Fragment:UNP residues 21-119 MHC class I antigen × 1 (E5FQ58) Epstein-Barr nuclear antigen 2 × 1 (P12978) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (E5FQ58) Epstein-Barr nuclear antigen 2 × 1 (P12978) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain L; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (E5FQ58) Epstein-Barr nuclear antigen 2 × 1 (P12978) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain Q; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (E5FQ58) Epstein-Barr nuclear antigen 2 × 1 (P12978) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235

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 2

human gammaherpesvirus 4

UniProt P12978

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 14–23 Not recorded MHC class I antigen × 1 (E5FQ58) Beta-2-microglobulin × 1 (P61769) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 14–23 Not recorded MHC class I antigen × 1 (E5FQ58) Beta-2-microglobulin × 1 (P61769) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain M; UniProt 14–23 Not recorded MHC class I antigen × 1 (E5FQ58) Beta-2-microglobulin × 1 (P61769) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 14–23 Not recorded MHC class I antigen × 1 (E5FQ58) Beta-2-microglobulin × 1 (P61769) T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4 Resolution 2.80 Å R-free 0.235

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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EBNA2_EBVB9
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 14–23 Author chain H; PDBConstruct 1–10; UniProt 14–23 Author chain M; PDBConstruct 1–10; UniProt 14–23 Author chain R; PDBConstruct 1–10; UniProt 14–23

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 9d95

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9d95
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9d95
Deposition date deposition_date2024-08-21
最后修订 last_revision2025-09-03
Structure title titleTRAV35/TRBV20 TCR - HLA-B38 complex
Keywords keywordsTCR - peptide - HLA complex T cell Human Leucocyte Antigen Epstein Barr virus, 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_guinier69.50
Radius of gyration Rg (electron density) rg_electron69.92
Forward intensity I(0) i01935280000.00
Molecular weight molecular_weight360920.0 kDa
Excluded volume excluded_volume446800 ų
Envelope volume envelope_volume729460 ų
Hydration-shell volume shell_volume93183 ų
Envelope diameter envelope_diameter240.0
Shell Rg shell_rg61.01
Envelope Rg envelope_rg68.11
Shape Rg shape_rg69.93
Total Rg total_rg69.71
Total atoms total_atoms25472
Residues n_residues3250
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 dmax244.3
Rg (real space) rg_real69.62
Rg uncertainty (real space) rg_real_error3.51
I(0) (real space) i0_real1.9350e+09
I(0) uncertainty (real space) i0_real_error4.8770e+07
Rg (reciprocal space) rg_reciprocal68.98
I(0) (reciprocal space) i0_reciprocal1933000000.0000
Solution quality estimate total_estimate0.8637
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary85.0
Skewness Skewness skewness0.293
Kurtosis Kurtosis kurtosis-0.431
Angular range angular_range— – 0.1150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha47290000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.667

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)