7bh8

3H4-Fab HLA-E-VL9 co-complex

Method: X-RAY DIFFRACTION Dmax: 209.2 Å Quality: REASONABLE

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

HLA class I histocompatibility antigen, alpha chain E

Homo sapiens

UniProt P13747

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 22–297 Chain C; UniProt 22–297 Not recorded Beta-2-microglobulin × 2 (P61769) 3H4 Fab heavy chain × 2 3H4 Fab light chain × 2 VL9 leader peptide × 2 GOL GLYCEROL × 10 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293.5 K;20% PEG 8000, 0.1 M NA HEPES Resolution 1.80 Å R-free 0.232

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.

28 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 22–297 Author chain C; PDBConstruct 1–276; UniProt 22–297

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain B; UniProt 21–119 Chain D; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, alpha chain E × 2 (P13747) 3H4 Fab heavy chain × 2 3H4 Fab light chain × 2 VL9 leader peptide × 2 GOL GLYCEROL × 10 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293.5 K;20% PEG 8000, 0.1 M NA HEPES Resolution 1.80 Å R-free 0.232

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 Author chain D; 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 7bh8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7bh8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7bh8
Deposition date deposition_date2021-01-10
Structure title title3H4-Fab HLA-E-VL9 co-complex
Keywords keywordsAntibody Fab Fragment MHC class I molecule Human leukocyte antigen E, 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_guinier58.16
Radius of gyration Rg (electron density) rg_electron60.14
Forward intensity I(0) i0506130000.00
Molecular weight molecular_weight182980.0 kDa
Excluded volume excluded_volume227390 ų
Envelope volume envelope_volume339700 ų
Hydration-shell volume shell_volume55153 ų
Envelope diameter envelope_diameter226.5
Shell Rg shell_rg49.03
Envelope Rg envelope_rg60.23
Shape Rg shape_rg60.03
Total Rg total_rg60.10
Total atoms total_atoms12900
Residues n_residues1604
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 dmax209.2
Rg (real space) rg_real59.45
Rg uncertainty (real space) rg_real_error2.49
I(0) (real space) i0_real5.0600e+08
I(0) uncertainty (real space) i0_real_error1.1850e+07
Rg (reciprocal space) rg_reciprocal57.07
I(0) (reciprocal space) i0_reciprocal504300000.0000
Solution quality estimate total_estimate0.7215
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.7
Skewness Skewness skewness0.749
Kurtosis Kurtosis kurtosis-0.004
Angular range angular_range— – 0.1350 −1
Current regularization parameter α current_alpha0.0007
Highest regularization parameter α highest_alpha21480000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.473; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.275; Smooth: 0.682

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7bh8A01
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_id7bh8A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7bh8C01
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_id7bh8C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)