8fjb

CryoEM structure of HLA-A2 MAGEA4 (286-294) in complex with H2aM31345N Fab

Method: ELECTRON MICROSCOPY Dmax: 136.1 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt Q861F7

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–276 Not recorded Beta-2-microglobulin × 1 (P61769) Melanoma-associated antigen 4 peptide × 1 (P43361) H2aM31345N Fab heavy chain × 1 H2aM31345N Fab light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.06 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.

31 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q861F7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–277; UniProt 1–276

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded MHC class I antigen × 1 (Q861F7) Melanoma-associated antigen 4 peptide × 1 (P43361) H2aM31345N Fab heavy chain × 1 H2aM31345N Fab light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.06 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 2
Chains and sequence ranges Author chain B; PDBConstruct 2–100; UniProt 21–119

Melanoma-associated antigen 4 peptide

OrganismNot specified

UniProt P43361

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 288–296 Not recorded MHC class I antigen × 1 (Q861F7) Beta-2-microglobulin × 1 (P61769) H2aM31345N Fab heavy chain × 1 H2aM31345N Fab light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.06 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 MAGA8_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 288–296

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 8fjb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8fjb
Deposition date deposition_date2022-12-19
Structure title titleCryoEM structure of HLA-A2 MAGEA4 (286-294) in complex with H2aM31345N Fab
Keywords keywordsHLA, MHC, IMMUNE SYSTEM, antibody; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.80
Radius of gyration Rg (electron density) rg_electron38.37
Forward intensity I(0) i0130379000.00
Molecular weight molecular_weight89746.0 kDa
Excluded volume excluded_volume111320 ų
Envelope volume envelope_volume155390 ų
Hydration-shell volume shell_volume37428 ų
Envelope diameter envelope_diameter145.6
Shell Rg shell_rg39.27
Envelope Rg envelope_rg38.68
Shape Rg shape_rg38.34
Total Rg total_rg38.54
Total atoms total_atoms6330
Residues n_residues802
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 dmax136.1
Rg (real space) rg_real38.48
Rg uncertainty (real space) rg_real_error1.38
I(0) (real space) i0_real1.3040e+08
I(0) uncertainty (real space) i0_real_error2.4460e+06
Rg (reciprocal space) rg_reciprocal38.06
I(0) (reciprocal space) i0_reciprocal130300000.0000
Solution quality estimate total_estimate0.7697
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.4
Skewness Skewness skewness0.708
Kurtosis Kurtosis kurtosis-0.024
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15680000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.564; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.670; Smooth: 0.640

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)