3ffc

Crystal Structure of CF34 TCR in complex with HLA-B8/FLR

Method: X-RAY DIFFRACTION Dmax: 168.3 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 Not recorded Beta-2-microglobulin × 1 (P61769) FLRGRAYGL peptide from an EBV protein × 1 CF34 alpha chain × 1 CF34 beta chain × 1 CD CADMIUM ION × 5 CL CHLORIDE ION × 6 NA SODIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.4;293 K;11% PEG 20000, 0.2M LiSO4, 0.1M Tris, 6mM CdCl, 4% ethylene glycol, 4% dioxane, pH 8.4, vapor diffusion, hanging drop, temperature 293K Resolution 2.80 Å R-free 0.268
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 25–301 Not recorded Beta-2-microglobulin × 1 (P61769) FLRGRAYGL peptide from an EBV protein × 1 CF34 alpha chain × 1 CF34 beta chain × 1 CD CADMIUM ION × 5 CL CHLORIDE ION × 5 NA SODIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.4;293 K;11% PEG 20000, 0.2M LiSO4, 0.1M Tris, 6mM CdCl, 4% ethylene glycol, 4% dioxane, pH 8.4, vapor diffusion, hanging drop, temperature 293K Resolution 2.80 Å R-free 0.268

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 30 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

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) FLRGRAYGL peptide from an EBV protein × 1 CF34 alpha chain × 1 CF34 beta chain × 1 CD CADMIUM ION × 5 CL CHLORIDE ION × 6 NA SODIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.4;293 K;11% PEG 20000, 0.2M LiSO4, 0.1M Tris, 6mM CdCl, 4% ethylene glycol, 4% dioxane, pH 8.4, vapor diffusion, hanging drop, temperature 293K Resolution 2.80 Å R-free 0.268
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) FLRGRAYGL peptide from an EBV protein × 1 CF34 alpha chain × 1 CF34 beta chain × 1 CD CADMIUM ION × 5 CL CHLORIDE ION × 5 NA SODIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.4;293 K;11% PEG 20000, 0.2M LiSO4, 0.1M Tris, 6mM CdCl, 4% ethylene glycol, 4% dioxane, pH 8.4, vapor diffusion, hanging drop, temperature 293K Resolution 2.80 Å R-free 0.268

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 1997 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

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 3ffc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3ffc
Deposition date deposition_date2008-12-03
Structure title titleCrystal Structure of CF34 TCR in complex with HLA-B8/FLR
Keywords keywords;TCR-peptide-MHC, Glycoprotein, Host-virus interaction, Immune response, Membrane, MHC I, Transmembrane, Disease mutation, Glycation, Immunoglobulin domain, Pyrrolidone carboxylic acid, Secreted, 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_guinier47.37
Radius of gyration Rg (electron density) rg_electron47.74
Forward intensity I(0) i0588773000.00
Molecular weight molecular_weight192020.0 kDa
Excluded volume excluded_volume236240 ų
Envelope volume envelope_volume328800 ų
Hydration-shell volume shell_volume60477 ų
Envelope diameter envelope_diameter181.4
Shell Rg shell_rg47.77
Envelope Rg envelope_rg47.79
Shape Rg shape_rg47.72
Total Rg total_rg47.81
Total atoms total_atoms13456
Residues n_residues1669
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 dmax168.3
Rg (real space) rg_real47.87
Rg uncertainty (real space) rg_real_error2.09
I(0) (real space) i0_real5.8880e+08
I(0) uncertainty (real space) i0_real_error1.3010e+07
Rg (reciprocal space) rg_reciprocal47.38
I(0) (reciprocal space) i0_reciprocal588400000.0000
Solution quality estimate total_estimate0.8261
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.9
Skewness Skewness skewness0.559
Kurtosis Kurtosis kurtosis-0.081
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42550000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.888; Smooth: 0.531

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3ffcb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3ffcb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3ffcg1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3ffcg2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (14 domains)

Domain ID domain_id3ffcA01
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_id3ffcA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcF01
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_id3ffcF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ffcJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)