8bp6

Structure of MHC-class I related molecule MR1 with bound M3Ade.

Method: X-RAY DIFFRACTION Dmax: 117.1 Å Quality: GOOD

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

Beta-2-microglobulin,Major histocompatibility complex class I-related gene protein

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 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 21–119 Not recorded R8F (1R,5S)-8-(9H-purin-6-yl)-2-oxa-8-azabicyclo[3.3.1]nona-3,6-diene-4,6-dicarbaldehyde × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;Morpheus-F9 Resolution 2.80 Å R-free 0.247
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded R8F (1R,5S)-8-(9H-purin-6-yl)-2-oxa-8-azabicyclo[3.3.1]nona-3,6-diene-4,6-dicarbaldehyde × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;Morpheus-F9 Resolution 2.80 Å R-free 0.247

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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–99; UniProt 21–119 Author chain B; PDBConstruct 1–99; UniProt 21–119

Beta-2-microglobulin,Major histocompatibility complex class I-related gene protein

Homo sapiens

UniProt Q95460

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 23–291 Not recorded R8F (1R,5S)-8-(9H-purin-6-yl)-2-oxa-8-azabicyclo[3.3.1]nona-3,6-diene-4,6-dicarbaldehyde × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;Morpheus-F9 Resolution 2.80 Å R-free 0.247
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 23–291 Not recorded R8F (1R,5S)-8-(9H-purin-6-yl)-2-oxa-8-azabicyclo[3.3.1]nona-3,6-diene-4,6-dicarbaldehyde × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;Morpheus-F9 Resolution 2.80 Å R-free 0.247

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.

82 other PDB entries and 143 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HMR1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 116–384; UniProt 23–291 Author chain B; PDBConstruct 116–384; UniProt 23–291

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 8bp6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8bp6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8bp6
Deposition date deposition_date2022-11-16
Structure title titleStructure of MHC-class I related molecule MR1 with bound M3Ade.
Keywords keywordsMajor histocompatibility complex class I-related gene protein, antigen, immnun system, 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_guinier33.98
Radius of gyration Rg (electron density) rg_electron33.83
Forward intensity I(0) i0120453000.00
Molecular weight molecular_weight86921.0 kDa
Excluded volume excluded_volume108290 ų
Envelope volume envelope_volume141350 ų
Hydration-shell volume shell_volume37317 ų
Envelope diameter envelope_diameter120.0
Shell Rg shell_rg37.66
Envelope Rg envelope_rg33.28
Shape Rg shape_rg33.85
Total Rg total_rg34.07
Total atoms total_atoms6148
Residues n_residues737
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 dmax117.1
Rg (real space) rg_real34.19
Rg uncertainty (real space) rg_real_error1.19
I(0) (real space) i0_real1.2050e+08
I(0) uncertainty (real space) i0_real_error2.0840e+06
Rg (reciprocal space) rg_reciprocal34.06
I(0) (reciprocal space) i0_reciprocal120400000.0000
Solution quality estimate total_estimate0.8391
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.9
Skewness Skewness skewness0.560
Kurtosis Kurtosis kurtosis-0.090
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17770000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.837; Smooth: 0.705

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)