9nig

PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide

Method: X-RAY DIFFRACTION Dmax: 197.4 Å Quality: REASONABLE

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

HLA class II histocompatibility antigen, DR alpha chain

Homo sapiens

UniProt P01903

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 30–206 Fragment:UNP residues 30-206 HLA class II histocompatibility antigen DR beta chain × 1 (A0A1V1IGJ9) PB TCR alpha chain × 1 PB TCR beta chain × 1 Tenascin × 1 (P24821) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 30–206 Fragment:UNP residues 30-206 HLA class II histocompatibility antigen DR beta chain × 1 (A0A1V1IGJ9) PB TCR alpha chain × 1 PB TCR beta chain × 1 Tenascin × 1 (P24821) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260
3 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 30–206 Fragment:UNP residues 30-206 HLA class II histocompatibility antigen DR beta chain × 1 (A0A1V1IGJ9) PB TCR alpha chain × 1 PB TCR beta chain × 1 Tenascin × 1 (P24821) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260

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.

139 other PDB entries and 217 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DRA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–181; UniProt 30–206 Author chain C; PDBConstruct 5–181; UniProt 30–206 Author chain H; PDBConstruct 5–181; UniProt 30–206

HLA class II histocompatibility antigen DR beta chain

Homo sapiens

UniProt A0A1V1IGJ9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 31–220 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) PB TCR alpha chain × 1 PB TCR beta chain × 1 Tenascin × 1 (P24821) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 31–220 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) PB TCR alpha chain × 1 PB TCR beta chain × 1 Tenascin × 1 (P24821) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260
3 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain I; UniProt 31–220 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) PB TCR alpha chain × 1 PB TCR beta chain × 1 Tenascin × 1 (P24821) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260

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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A1V1IGJ9_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–190; UniProt 31–220 Author chain D; PDBConstruct 1–190; UniProt 31–220 Author chain I; PDBConstruct 1–190; UniProt 31–220

Tenascin

OrganismNot specified

UniProt P24821

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 1013–1024 Fragment:residues 1013-1024 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen DR beta chain × 1 (A0A1V1IGJ9) PB TCR alpha chain × 1 PB TCR beta chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1013–1024 Fragment:residues 1013-1024 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen DR beta chain × 1 (A0A1V1IGJ9) PB TCR alpha chain × 1 PB TCR beta chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260
3 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain L; UniProt 1013–1024 Fragment:residues 1013-1024 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen DR beta chain × 1 (A0A1V1IGJ9) PB TCR alpha chain × 1 PB TCR beta chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350 Resolution 3.20 Å R-free 0.260

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.

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TENA_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain G; PDBConstruct 1–12; UniProt 1013–1024 Author chain L; PDBConstruct 1–12; UniProt 1013–1024 Author chain P; PDBConstruct 1–12; UniProt 1013–1024

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 9nig

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9nig
Deposition date deposition_date2025-02-26
Structure title titlePB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide
Keywords keywordsHuman Leukocyte Antigen, T cell receptor, citrullinated epitope, rheumatoid arthritis., 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_guinier50.75
Radius of gyration Rg (electron density) rg_electron50.98
Forward intensity I(0) i01057620000.00
Molecular weight molecular_weight265500.0 kDa
Excluded volume excluded_volume329700 ų
Envelope volume envelope_volume479490 ų
Hydration-shell volume shell_volume81824 ų
Envelope diameter envelope_diameter215.0
Shell Rg shell_rg51.14
Envelope Rg envelope_rg51.26
Shape Rg shape_rg50.99
Total Rg total_rg50.92
Total atoms total_atoms18764
Residues n_residues2411
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 dmax197.4
Rg (real space) rg_real51.01
Rg uncertainty (real space) rg_real_error2.57
I(0) (real space) i0_real1.0580e+09
I(0) uncertainty (real space) i0_real_error2.2350e+07
Rg (reciprocal space) rg_reciprocal50.55
I(0) (reciprocal space) i0_reciprocal1057000000.0000
Solution quality estimate total_estimate0.5668
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary57.3
Skewness Skewness skewness0.647
Kurtosis Kurtosis kurtosis0.446
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha64580000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.515; Stabil: 1.000; Sysdev: 0.003; Positv: 1.000; Valcen: 0.865; Smooth: 0.945

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)