9mda

Conformational flexibility in HLA-B8: peptide tuning structural and dynamical changes

Method: X-RAY DIFFRACTION Dmax: 75.5 Å Quality: EXCELLENT

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

MHC class I protein

Homo sapiens

UniProt A0A3G6II09

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 25–299 Mutation:E76C Beta-2-microglobulin × 1 (P61769) ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-PHE-ALA-GLY-LYS-LYS-TYR-CYS-LEU × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;12.5-16% PEG 4000,100mM citrate acid pH5.5 ,100mM ammonium acetate Resolution 1.60 Å R-free 0.239

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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A3G6II09_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–275; UniProt 25–299

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 Not recorded MHC class I protein × 1 (A0A3G6II09) ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-PHE-ALA-GLY-LYS-LYS-TYR-CYS-LEU × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;12.5-16% PEG 4000,100mM citrate acid pH5.5 ,100mM ammonium acetate Resolution 1.60 Å R-free 0.239

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 1–99; 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 9mda

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9mda
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9mda
Deposition date deposition_date2024-12-05
Structure title titleConformational flexibility in HLA-B8: peptide tuning structural and dynamical changes
Keywords keywordsHLA-B8 Long MHC I peptides MHC I intermediate forms, 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_guinier24.09
Radius of gyration Rg (electron density) rg_electron22.95
Forward intensity I(0) i036594000.00
Molecular weight molecular_weight44466.0 kDa
Excluded volume excluded_volume54695 ų
Envelope volume envelope_volume67505 ų
Hydration-shell volume shell_volume24620 ų
Envelope diameter envelope_diameter78.5
Shell Rg shell_rg29.80
Envelope Rg envelope_rg23.03
Shape Rg shape_rg22.93
Total Rg total_rg23.82
Total atoms total_atoms3140
Residues n_residues383
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 dmax75.5
Rg (real space) rg_real24.02
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real3.6590e+07
I(0) uncertainty (real space) i0_real_error4.9650e+05
Rg (reciprocal space) rg_reciprocal24.03
I(0) (reciprocal space) i0_reciprocal36590000.0000
Solution quality estimate total_estimate0.9101
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.481
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8963000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.991

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)