4z77

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

Method: X-RAY DIFFRACTION Dmax: 94.6 Å Quality: EXCELLENT

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

H-2 class I histocompatibility antigen, K-D alpha chain

Mus musculus

UniProt P01902

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 22–296 Fragment:UNP residues 22-296 Beta-2-microglobulin × 1 (P61769) Insulin × 1 (P01308) GOL GLYCEROL × 4 15P POLYETHYLENE GLYCOL (N=34) × 1 EDO 1,2-ETHANEDIOL × 7 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;20% PEG 6000, 0.2 M calcium chloride, 0.1 M Tris propane pH 8.0 Resolution 1.85 Å R-free 0.253
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 22–296 Fragment:UNP residues 22-296 Beta-2-microglobulin × 1 (P61769) Insulin × 1 (P01308) GOL GLYCEROL × 3 15P POLYETHYLENE GLYCOL (N=34) × 2 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;20% PEG 6000, 0.2 M calcium chloride, 0.1 M Tris propane pH 8.0 Resolution 1.85 Å R-free 0.253

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.

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HA1D_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–276; UniProt 22–296 Author chain D; PDBConstruct 2–276; UniProt 22–296

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:UNP residues 21-119 H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) Insulin × 1 (P01308) GOL GLYCEROL × 4 15P POLYETHYLENE GLYCOL (N=34) × 1 EDO 1,2-ETHANEDIOL × 7 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;20% PEG 6000, 0.2 M calcium chloride, 0.1 M Tris propane pH 8.0 Resolution 1.85 Å R-free 0.253
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Fragment:UNP residues 21-119 H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) Insulin × 1 (P01308) GOL GLYCEROL × 3 15P POLYETHYLENE GLYCOL (N=34) × 2 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;20% PEG 6000, 0.2 M calcium chloride, 0.1 M Tris propane pH 8.0 Resolution 1.85 Å R-free 0.253

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 E; PDBConstruct 2–100; UniProt 21–119

Insulin

Homo sapiens

UniProt P01308

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 39–47 Fragment:UNP residues 39-47 H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 4 15P POLYETHYLENE GLYCOL (N=34) × 1 EDO 1,2-ETHANEDIOL × 7 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;20% PEG 6000, 0.2 M calcium chloride, 0.1 M Tris propane pH 8.0 Resolution 1.85 Å R-free 0.253
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 39–47 Fragment:UNP residues 39-47 H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 3 15P POLYETHYLENE GLYCOL (N=34) × 2 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;20% PEG 6000, 0.2 M calcium chloride, 0.1 M Tris propane pH 8.0 Resolution 1.85 Å R-free 0.253

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.

369 other PDB entries and 582 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INS_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 39–47 Author chain F; PDBConstruct 1–9; UniProt 39–47

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 4z77

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4z77
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4z77
Deposition date deposition_date2015-04-06
Structure title titleWeak TCR binding to an unstable insulin epitope drives type 1 diabetes
Keywords keywordsImmunoglobulin, H-2Kd, Type 1 Diabetes, 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_guinier30.81
Radius of gyration Rg (electron density) rg_electron29.85
Forward intensity I(0) i0144289000.00
Molecular weight molecular_weight92847.0 kDa
Excluded volume excluded_volume115030 ų
Envelope volume envelope_volume145470 ų
Hydration-shell volume shell_volume39817 ų
Envelope diameter envelope_diameter102.6
Shell Rg shell_rg37.84
Envelope Rg envelope_rg29.51
Shape Rg shape_rg29.82
Total Rg total_rg30.62
Total atoms total_atoms6544
Residues n_residues772
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 dmax94.6
Rg (real space) rg_real30.66
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real1.4430e+08
I(0) uncertainty (real space) i0_real_error2.0630e+06
Rg (reciprocal space) rg_reciprocal30.73
I(0) (reciprocal space) i0_reciprocal144300000.0000
Solution quality estimate total_estimate0.9089
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary92.8
Skewness Skewness skewness0.153
Kurtosis Kurtosis kurtosis-0.541
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20620000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.936

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd4z77a1
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_idd4z77a2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4z77a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4z77b1
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_idd4z77b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4z77d1
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_idd4z77d2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4z77d3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4z77e1
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_idd4z77e2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id4z77A01
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_id4z77A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4z77B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4z77D01
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_id4z77D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4z77E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)