6biz

HLA-DRB1 in complex with citrullinated Histone 2B peptide

Method: X-RAY DIFFRACTION Dmax: 85.7 Å Quality: GOOD

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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 26–206 Not recorded HLA class II DR-beta (HLA-DR B) × 1 (Q29890) Histone2B_73,81cit68-82 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.3;294 K;22-28% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3 Resolution 2.10 Å R-free 0.228

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 219 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 1–181; UniProt 26–206

HLA class II DR-beta (HLA-DR B)

Homo sapiens

UniProt Q29890

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 30–219 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) Histone2B_73,81cit68-82 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.3;294 K;22-28% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3 Resolution 2.10 Å R-free 0.228

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 Q29890_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 3–192; UniProt 30–219

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 6biz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6biz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6biz
Deposition date deposition_date2017-11-03
Structure title titleHLA-DRB1 in complex with citrullinated Histone 2B peptide
Keywords keywordsHLA, MHC, citrulline, 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_guinier24.67
Radius of gyration Rg (electron density) rg_electron23.78
Forward intensity I(0) i032804600.00
Molecular weight molecular_weight44480.0 kDa
Excluded volume excluded_volume55650 ų
Envelope volume envelope_volume67004 ų
Hydration-shell volume shell_volume23883 ų
Envelope diameter envelope_diameter83.7
Shell Rg shell_rg30.43
Envelope Rg envelope_rg24.10
Shape Rg shape_rg23.74
Total Rg total_rg24.66
Total atoms total_atoms3149
Residues n_residues379
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 dmax85.7
Rg (real space) rg_real24.70
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real3.2800e+07
I(0) uncertainty (real space) i0_real_error5.4840e+05
Rg (reciprocal space) rg_reciprocal24.70
I(0) (reciprocal space) i0_reciprocal32800000.0000
Solution quality estimate total_estimate0.7910
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary77.6
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.372
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7820000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.803; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.880; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6bizA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id6bizA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6bizB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id6bizB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)