4gup

Structure of MHC-class I related molecule MR1

Method: X-RAY DIFFRACTION Dmax: 117.7 Å Quality: GOOD

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

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 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 23–292 Fragment:extracellular domain, residues 23-292 Mutation:C261S Beta-2-microglobulin × 1 (P61769) 6FP 2-amino-4-oxo-3,4-dihydropteridine-6-carbaldehyde × 1 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;0.02M MgCl2, 0.1M HEPES, 22% polyacrylic acid 5100 sodium salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.20 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 23–292 Fragment:extracellular domain, residues 23-292 Mutation:C261S Beta-2-microglobulin × 1 (P61769) 6FP 2-amino-4-oxo-3,4-dihydropteridine-6-carbaldehyde × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;0.02M MgCl2, 0.1M HEPES, 22% polyacrylic acid 5100 sodium salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.20 Å R-free 0.260

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 2–271; UniProt 23–292 Author chain C; PDBConstruct 2–271; UniProt 23–292

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q95460) 6FP 2-amino-4-oxo-3,4-dihydropteridine-6-carbaldehyde × 1 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;0.02M MgCl2, 0.1M HEPES, 22% polyacrylic acid 5100 sodium salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.20 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 21–119 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q95460) 6FP 2-amino-4-oxo-3,4-dihydropteridine-6-carbaldehyde × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;0.02M MgCl2, 0.1M HEPES, 22% polyacrylic acid 5100 sodium salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.20 Å R-free 0.260

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 1–99; UniProt 21–119 Author chain D; 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 4gup

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gup
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gup
Deposition date deposition_date2012-08-29
Structure title titleStructure of MHC-class I related molecule MR1
Keywords keywordsMHC Class I-related protein, 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_guinier34.33
Radius of gyration Rg (electron density) rg_electron34.23
Forward intensity I(0) i0107489000.00
Molecular weight molecular_weight81826.0 kDa
Excluded volume excluded_volume101730 ų
Envelope volume envelope_volume136570 ų
Hydration-shell volume shell_volume35899 ų
Envelope diameter envelope_diameter120.2
Shell Rg shell_rg37.74
Envelope Rg envelope_rg33.70
Shape Rg shape_rg34.23
Total Rg total_rg34.51
Total atoms total_atoms5794
Residues n_residues718
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 dmax117.7
Rg (real space) rg_real34.59
Rg uncertainty (real space) rg_real_error1.23
I(0) (real space) i0_real1.0750e+08
I(0) uncertainty (real space) i0_real_error2.0440e+06
Rg (reciprocal space) rg_reciprocal34.43
I(0) (reciprocal space) i0_reciprocal107500000.0000
Solution quality estimate total_estimate0.8349
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.8
Skewness Skewness skewness0.576
Kurtosis Kurtosis kurtosis-0.157
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15610000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.608

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4gupA01
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_id4gupA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4gupB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4gupC01
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_id4gupC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4gupD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)