4pj8

Structure of human MR1-5-OP-RU in complex with human MAIT TRBV20 TCR

Method: X-RAY DIFFRACTION Dmax: 129.5 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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 23–292 Fragment:UNP residues 23-292 Mutation:C262S Beta-2-microglobulin × 1 (P61769) TCR-alpha × 1 TCR-beta × 1 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;PEG 3350, Bis-tris propane, sodium acetate Resolution 3.30 Å R-free 0.213

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 144 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

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q95460) TCR-alpha × 1 TCR-beta × 1 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;PEG 3350, Bis-tris propane, sodium acetate Resolution 3.30 Å R-free 0.213

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 4pj8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4pj8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4pj8
Deposition date deposition_date2014-05-12
Structure title titleStructure of human MR1-5-OP-RU in complex with human MAIT TRBV20 TCR
Keywords keywordsMR1, TCR, Immune complex, 5-OP-RU, 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_guinier36.74
Radius of gyration Rg (electron density) rg_electron36.99
Forward intensity I(0) i0124171000.00
Molecular weight molecular_weight88305.0 kDa
Excluded volume excluded_volume109650 ų
Envelope volume envelope_volume148870 ų
Hydration-shell volume shell_volume36700 ų
Envelope diameter envelope_diameter134.1
Shell Rg shell_rg38.84
Envelope Rg envelope_rg37.53
Shape Rg shape_rg37.00
Total Rg total_rg37.11
Total atoms total_atoms6241
Residues n_residues798
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 dmax129.5
Rg (real space) rg_real37.28
Rg uncertainty (real space) rg_real_error1.67
I(0) (real space) i0_real1.2420e+08
I(0) uncertainty (real space) i0_real_error2.4720e+06
Rg (reciprocal space) rg_reciprocal36.95
I(0) (reciprocal space) i0_reciprocal124100000.0000
Solution quality estimate total_estimate0.7767
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.1
Skewness Skewness skewness0.643
Kurtosis Kurtosis kurtosis-0.195
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15550000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.642; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.525; Smooth: 0.646

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id4pj8A01
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_id4pj8A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4pj8B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4pj8C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4pj8C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4pj8D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4pj8D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)