6z9v

Human Class I Major Histocompatibility Complex, A02 allele, presenting IIGWMWIPV

Method: X-RAY DIFFRACTION Dmax: 100.9 Å Quality: REASONABLE

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

MHC class I antigen

Homo sapiens

UniProt A0A5B8RNS7

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 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL × 1 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 SO4 SULFATE ION × 3 NA SODIUM ION × 1 P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;295 K;PACT premier screen, condition G06: 0.2M Na Formate, 0.1M Bis-Tris Propane, 20% PEG 3350 Resolution 2.01 Å R-free 0.216
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL × 1 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 5 SO4 SULFATE ION × 1 P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;295 K;PACT premier screen, condition G06: 0.2M Na Formate, 0.1M Bis-Tris Propane, 20% PEG 3350 Resolution 2.01 Å R-free 0.216

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.

27 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A5B8RNS7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 25–300 Author chain D; PDBConstruct 1–276; UniProt 25–300

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 antigen × 1 (A0A5B8RNS7) ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL × 1 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 SO4 SULFATE ION × 3 NA SODIUM ION × 1 P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;295 K;PACT premier screen, condition G06: 0.2M Na Formate, 0.1M Bis-Tris Propane, 20% PEG 3350 Resolution 2.01 Å R-free 0.216
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Not recorded MHC class I antigen × 1 (A0A5B8RNS7) ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL × 1 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 5 SO4 SULFATE ION × 1 P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;295 K;PACT premier screen, condition G06: 0.2M Na Formate, 0.1M Bis-Tris Propane, 20% PEG 3350 Resolution 2.01 Å R-free 0.216

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 1997 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

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 6z9v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6z9v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6z9v
Deposition date deposition_date2020-06-04
Structure title titleHuman Class I Major Histocompatibility Complex, A02 allele, presenting IIGWMWIPV
Keywords keywordsMHC I, 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_guinier32.28
Radius of gyration Rg (electron density) rg_electron31.50
Forward intensity I(0) i0142724000.00
Molecular weight molecular_weight92062.0 kDa
Excluded volume excluded_volume113720 ų
Envelope volume envelope_volume150370 ų
Hydration-shell volume shell_volume39494 ų
Envelope diameter envelope_diameter107.0
Shell Rg shell_rg39.32
Envelope Rg envelope_rg30.55
Shape Rg shape_rg31.49
Total Rg total_rg32.15
Total atoms total_atoms6485
Residues n_residues770
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 dmax100.9
Rg (real space) rg_real32.20
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real1.4270e+08
I(0) uncertainty (real space) i0_real_error1.9920e+06
Rg (reciprocal space) rg_reciprocal32.24
I(0) (reciprocal space) i0_reciprocal142700000.0000
Solution quality estimate total_estimate0.7022
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.1
Skewness Skewness skewness0.207
Kurtosis Kurtosis kurtosis-0.600
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15610000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.999; Smooth: 0.946

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

8. Citations (1)

9. Files and Curves (10)