7lli

Stimulatory immune receptor protein complex

Method: X-RAY DIFFRACTION Dmax: 144.7 Å Quality: EXCELLENT

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 C; UniProt 23–292 Not recorded Beta-2-microglobulin × 1 (P61769) T cell receptor gamma variable 8 × 1 (A0A0C4DH27) T cell receptor delta variable 3 × 1 (A0JD37) 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 Resolution 3.20 Å R-free 0.263
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 23–292 Not recorded Beta-2-microglobulin × 1 (P61769) T cell receptor gamma variable 8 × 1 (A0A0C4DH27) T cell receptor delta variable 3 × 1 (A0JD37) 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 Resolution 3.20 Å R-free 0.263

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 21–119 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q95460) T cell receptor gamma variable 8 × 1 (A0A0C4DH27) T cell receptor delta variable 3 × 1 (A0JD37) 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 Resolution 3.20 Å R-free 0.263
2 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) T cell receptor gamma variable 8 × 1 (A0A0C4DH27) T cell receptor delta variable 3 × 1 (A0JD37) 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 Resolution 3.20 Å R-free 0.263

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 D; PDBConstruct 2–100; UniProt 21–119

T cell receptor gamma variable 8

Homo sapiens

UniProt A0A0C4DH27

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 K; UniProt 19–117 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q95460) Beta-2-microglobulin × 1 (P61769) T cell receptor delta variable 3 × 1 (A0JD37) 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 Resolution 3.20 Å R-free 0.263
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 19–117 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q95460) Beta-2-microglobulin × 1 (P61769) T cell receptor delta variable 3 × 1 (A0JD37) 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 Resolution 3.20 Å R-free 0.263

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name TRGV8_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 3–101; UniProt 19–117 Author chain K; PDBConstruct 3–101; UniProt 19–117

T cell receptor delta variable 3

Homo sapiens

UniProt A0JD37

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 L; UniProt 19–112 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q95460) Beta-2-microglobulin × 1 (P61769) T cell receptor gamma variable 8 × 1 (A0A0C4DH27) 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 Resolution 3.20 Å R-free 0.263
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 19–112 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q95460) Beta-2-microglobulin × 1 (P61769) T cell receptor gamma variable 8 × 1 (A0A0C4DH27) 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 Resolution 3.20 Å R-free 0.263

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name TRDV3_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain F; PDBConstruct 2–95; UniProt 19–112 Author chain L; PDBConstruct 2–95; UniProt 19–112

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 7lli

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7lli
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7lli
Deposition date deposition_date2021-02-04
Structure title titleStimulatory immune receptor protein complex
Keywords keywordsImmune receptor complex, metabolite immunity, 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_guinier45.54
Radius of gyration Rg (electron density) rg_electron44.94
Forward intensity I(0) i0527604000.00
Molecular weight molecular_weight186800.0 kDa
Excluded volume excluded_volume232460 ų
Envelope volume envelope_volume336890 ų
Hydration-shell volume shell_volume63376 ų
Envelope diameter envelope_diameter147.4
Shell Rg shell_rg48.17
Envelope Rg envelope_rg44.62
Shape Rg shape_rg44.89
Total Rg total_rg45.26
Total atoms total_atoms13201
Residues n_residues1619
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 dmax144.7
Rg (real space) rg_real45.39
Rg uncertainty (real space) rg_real_error1.21
I(0) (real space) i0_real5.2760e+08
I(0) uncertainty (real space) i0_real_error9.2150e+06
Rg (reciprocal space) rg_reciprocal45.54
I(0) (reciprocal space) i0_reciprocal527700000.0000
Solution quality estimate total_estimate0.9054
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary57.9
Skewness Skewness skewness0.082
Kurtosis Kurtosis kurtosis-0.769
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha47810000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.929

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)