3kxf

Crystal Structure of SB27 TCR in complex with the 'restriction triad' mutant HLA-B*3508-13mer

Method: X-RAY DIFFRACTION Dmax: 213.0 Å Quality: GOOD

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

HLA class I histocompatibility antigen, B-35 alpha chain

Homo sapiens

UniProt P30685

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:residues in UNP 25-300 Mutation:Q65A, T69A, Q155A Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 25–300 Fragment:residues in UNP 25-300 Mutation:Q65A, T69A, Q155A Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain K; UniProt 25–300 Fragment:residues in UNP 25-300 Mutation:Q65A, T69A, Q155A Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain I; UniProt 25–300 Fragment:residues in UNP 25-300 Mutation:Q65A, T69A, Q155A Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291

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.

33 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1B35_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 25–300 Author chain C; PDBConstruct 1–276; UniProt 25–300 Author chain I; PDBConstruct 1–276; UniProt 25–300 Author chain K; 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 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
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-35 alpha chain × 1 (P30685) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain J; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291

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 1–99; UniProt 21–119 Author chain F; PDBConstruct 1–99; UniProt 21–119 Author chain J; PDBConstruct 1–99; UniProt 21–119 Author chain L; PDBConstruct 1–99; UniProt 21–119

peptide from Trans-activator protein BZLF1

OrganismNot specified

UniProt P03206

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 Q; UniProt 52–64 Not recorded HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 52–64 Not recorded HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain T; UniProt 52–64 Not recorded HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain S; UniProt 52–64 Not recorded HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K Resolution 3.10 Å R-free 0.291

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.

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BZLF1_EBVB9
Isoform
PDB entities 5
Chains and sequence ranges Author chain Q; PDBConstruct 1–13; UniProt 52–64 Author chain R; PDBConstruct 1–13; UniProt 52–64 Author chain S; PDBConstruct 1–13; UniProt 52–64 Author chain T; 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 3kxf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3kxf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3kxf
Deposition date deposition_date2009-12-03
Structure title titleCrystal Structure of SB27 TCR in complex with the 'restriction triad' mutant HLA-B*3508-13mer
Keywords keywords;MHC, HLA, TCR, Disulfide bond, Host-virus interaction, Immune response, Membrane, MHC I, Transmembrane, Immunoglobulin domain, 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_guinier59.63
Radius of gyration Rg (electron density) rg_electron60.27
Forward intensity I(0) i02299950000.00
Molecular weight molecular_weight384180.0 kDa
Excluded volume excluded_volume471890 ų
Envelope volume envelope_volume717750 ų
Hydration-shell volume shell_volume104380 ų
Envelope diameter envelope_diameter238.8
Shell Rg shell_rg57.46
Envelope Rg envelope_rg59.69
Shape Rg shape_rg60.30
Total Rg total_rg60.09
Total atoms total_atoms26934
Residues n_residues3332
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 dmax213.0
Rg (real space) rg_real60.07
Rg uncertainty (real space) rg_real_error1.98
I(0) (real space) i0_real2.2990e+09
I(0) uncertainty (real space) i0_real_error4.7920e+07
Rg (reciprocal space) rg_reciprocal59.22
I(0) (reciprocal space) i0_reciprocal2297000000.0000
Solution quality estimate total_estimate0.8370
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary65.5
Skewness Skewness skewness0.639
Kurtosis Kurtosis kurtosis0.271
Angular range angular_range— – 0.1300 −1
Current regularization parameter α current_alpha0.0062
Highest regularization parameter α highest_alpha96600000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.680; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.838

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id3kxfA01
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_id3kxfA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfC01
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_id3kxfC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfG01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfI01
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_id3kxfI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfK01
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_id3kxfK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfM01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfM02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfN02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfO01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfO02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfP01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3kxfP02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)