4z78

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

Method: X-RAY DIFFRACTION Dmax: 124.9 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) EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 Å R-free 0.233
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) EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 Å R-free 0.233
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 22–296 Fragment:UNP residues 22-296 Beta-2-microglobulin × 1 (P61769) Insulin × 1 (P01308) EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 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.

13 other PDB entries and 20 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 Author chain G; 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) EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 Å R-free 0.233
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) EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 Å R-free 0.233
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 21–119 Fragment:UNP residues 21-119 H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) Insulin × 1 (P01308) EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 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 1996 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 Author chain H; 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 39–48 Fragment:UNP residues 39-48 H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) Beta-2-microglobulin × 1 (P61769) EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 Å R-free 0.233
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 39–48 Fragment:UNP residues 39-48 H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) Beta-2-microglobulin × 1 (P61769) EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 Å R-free 0.233
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 39–48 Fragment:UNP residues 39-48 H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) Beta-2-microglobulin × 1 (P61769) EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;4% PEG 4000, 0.1 M sodium acetate pH 4.6 Resolution 2.30 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.

369 other PDB entries and 581 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 1–10; UniProt 39–48 Author chain F; PDBConstruct 1–10; UniProt 39–48 Author chain I; PDBConstruct 1–10; UniProt 39–48

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 4z78

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4z78
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4z78
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_guinier39.22
Radius of gyration Rg (electron density) rg_electron38.62
Forward intensity I(0) i0303626000.00
Molecular weight molecular_weight137690.0 kDa
Excluded volume excluded_volume170430 ų
Envelope volume envelope_volume244310 ų
Hydration-shell volume shell_volume52850 ų
Envelope diameter envelope_diameter129.8
Shell Rg shell_rg44.96
Envelope Rg envelope_rg37.04
Shape Rg shape_rg38.62
Total Rg total_rg39.00
Total atoms total_atoms9716
Residues n_residues1161
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 dmax124.9
Rg (real space) rg_real39.06
Rg uncertainty (real space) rg_real_error0.86
I(0) (real space) i0_real3.0360e+08
I(0) uncertainty (real space) i0_real_error4.7790e+06
Rg (reciprocal space) rg_reciprocal39.16
I(0) (reciprocal space) i0_reciprocal303700000.0000
Solution quality estimate total_estimate0.9059
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.0
Skewness Skewness skewness0.124
Kurtosis Kurtosis kurtosis-0.618
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19600000.0000
Real-space data points n_real_points41
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: 1.000; Smooth: 0.927

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (15 domains)

Domain ID domain_idd4z78a1
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_idd4z78a2
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_idd4z78a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4z78b1
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_idd4z78b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4z78d1
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_idd4z78d2
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_idd4z78d3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4z78e1
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_idd4z78e2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4z78g1
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_idd4z78g2
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_idd4z78g3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4z78h1
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_idd4z78h2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (9 domains)

Domain ID domain_id4z78A01
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_id4z78A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4z78B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4z78D01
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_id4z78D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4z78E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4z78G01
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_id4z78G02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4z78H00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)