8t6m

Human leukocyte antigen bound by two alloreactive antibody Fabs

Method: ELECTRON MICROSCOPY Dmax: 102.9 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt I3QHR3

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain E; UniProt 1–180 Not recorded JTK191b_M07_Light × 1 JTK191b_M07_Fab × 1 JTK191b_L02_Light × 1 JTK191b_L02_Fab × 1 Beta-2-microglobulin × 1 (P61769) HLA_A0101_peptide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.14 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name I3QHR3_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 2–181; UniProt 1–180

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain F; UniProt 21–119 Fragment:UNP residues 21-119 JTK191b_M07_Light × 1 JTK191b_M07_Fab × 1 JTK191b_L02_Light × 1 JTK191b_L02_Fab × 1 MHC class I antigen × 1 (I3QHR3) HLA_A0101_peptide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.14 Å

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 6
Chains and sequence ranges Author chain F; PDBConstruct 2–100; UniProt 21–119

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 8t6m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8t6m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8t6m
Deposition date deposition_date2023-06-16
Structure title titleHuman leukocyte antigen bound by two alloreactive antibody Fabs
Keywords keywordsantibody, human leukocyte antigen, graft rejection, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.71
Radius of gyration Rg (electron density) rg_electron30.30
Forward intensity I(0) i0114009000.00
Molecular weight molecular_weight83644.0 kDa
Excluded volume excluded_volume104130 ų
Envelope volume envelope_volume124440 ų
Hydration-shell volume shell_volume35218 ų
Envelope diameter envelope_diameter113.9
Shell Rg shell_rg36.18
Envelope Rg envelope_rg30.42
Shape Rg shape_rg30.24
Total Rg total_rg30.99
Total atoms total_atoms5903
Residues n_residues746
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 dmax102.9
Rg (real space) rg_real30.67
Rg uncertainty (real space) rg_real_error0.80
I(0) (real space) i0_real1.1400e+08
I(0) uncertainty (real space) i0_real_error2.0040e+06
Rg (reciprocal space) rg_reciprocal30.69
I(0) (reciprocal space) i0_reciprocal114000000.0000
Solution quality estimate total_estimate0.8917
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.6
Skewness Skewness skewness0.263
Kurtosis Kurtosis kurtosis-0.449
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16790000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.945

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)