3b3i

Citrullination-dependent differential presentation of a self-peptide by HLA-B27 subtypes

Method: X-RAY DIFFRACTION Dmax: 75.4 Å Quality: EXCELLENT

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

HLA class I histocompatibility antigen, B-27 alpha chain

Homo sapiens

UniProt P03989

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 25–300 Fragment:EXTRACELLUAR DOMAIN, RESIDUES 25-300 Beta-2-microglobulin × 1 (P61769) Vasoactive intestinal polypeptide receptor 1 × 1 (P32241) GOL GLYCEROL × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;291 K;0.1 M Tris, 25% PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.86 Å R-free 0.233

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.

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

View Construct and Data Evidence
UniProt name 1B27_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 21–119 Fragment:RESIDUES 21-119 HLA class I histocompatibility antigen, B-27 alpha chain × 1 (P03989) Vasoactive intestinal polypeptide receptor 1 × 1 (P32241) GOL GLYCEROL × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;291 K;0.1 M Tris, 25% PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.86 Å R-free 0.233

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 1998 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

Vasoactive intestinal polypeptide receptor 1

Homo sapiens

UniProt P32241

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 C; UniProt 400–408 Fragment:RESIDUES 400-408 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA class I histocompatibility antigen, B-27 alpha chain × 1 (P03989) Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;291 K;0.1 M Tris, 25% PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.86 Å R-free 0.233

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.

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VIPR1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 400–408

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 3b3i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3b3i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3b3i
Deposition date deposition_date2007-10-22
Structure title titleCitrullination-dependent differential presentation of a self-peptide by HLA-B27 subtypes
Keywords keywords;HLA-B2709, ankylosing spondylitis, Glycoprotein, Host-virus interaction, Immune response, Membrane, MHC I, Transmembrane, Disease mutation, Glycation, Immunoglobulin domain, Pyrrolidone carboxylic acid, Secreted, G-protein coupled receptor, Phosphorylation, Receptor, Transducer, PROTEIN BINDING, 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_guinier24.14
Radius of gyration Rg (electron density) rg_electron23.01
Forward intensity I(0) i038049800.00
Molecular weight molecular_weight45708.0 kDa
Excluded volume excluded_volume56363 ų
Envelope volume envelope_volume69222 ų
Hydration-shell volume shell_volume25067 ų
Envelope diameter envelope_diameter78.4
Shell Rg shell_rg30.04
Envelope Rg envelope_rg23.19
Shape Rg shape_rg23.00
Total Rg total_rg23.88
Total atoms total_atoms3227
Residues n_residues384
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 dmax75.4
Rg (real space) rg_real24.08
Rg uncertainty (real space) rg_real_error0.48
I(0) (real space) i0_real3.8050e+07
I(0) uncertainty (real space) i0_real_error5.7050e+05
Rg (reciprocal space) rg_reciprocal24.09
I(0) (reciprocal space) i0_reciprocal38050000.0000
Solution quality estimate total_estimate0.9109
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5
Skewness Skewness skewness0.251
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10330000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3b3ia1
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_idd3b3ia2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd3b3ib2
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_idd3b3ib3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id3b3iA01
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_id3b3iA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3b3iB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)