6ewc

Crystal structure of non-phosphorylated form of RLS PHOSPHOPEPTIDE BOUND TO HLA-A2 in complex with LILRB1

Method: X-RAY DIFFRACTION Dmax: 120.8 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A-2 alpha chain

Homo sapiens

UniProt P01892

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 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Reticulophagy regulator 2 × 1 (Q8NC44) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (A0A0G2JQ44) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide Resolution 3.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Reticulophagy regulator 2 × 1 (Q8NC44) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (A0A0G2JQ44) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide Resolution 3.20 Å R-free 0.246

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.

271 other PDB entries and 464 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A02_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 25–300 Author chain E; 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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Reticulophagy regulator 2 × 1 (Q8NC44) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (A0A0G2JQ44) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide Resolution 3.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Reticulophagy regulator 2 × 1 (Q8NC44) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (A0A0G2JQ44) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide Resolution 3.20 Å R-free 0.246

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 F; PDBConstruct 1–99; UniProt 21–119

Reticulophagy regulator 2

OrganismNot specified

UniProt Q8NC44

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 400–408 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (A0A0G2JQ44) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide Resolution 3.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 400–408 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (A0A0G2JQ44) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide Resolution 3.20 Å R-free 0.246

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 RETR2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 400–408 Author chain G; PDBConstruct 1–9; UniProt 400–408

Leukocyte immunoglobulin-like receptor subfamily B member 1

Homo sapiens

UniProt A0A0G2JQ44

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 27–221 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Reticulophagy regulator 2 × 1 (Q8NC44) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide Resolution 3.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain H; UniProt 27–221 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Reticulophagy regulator 2 × 1 (Q8NC44) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide Resolution 3.20 Å R-free 0.246

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.

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0G2JQ44_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–195; UniProt 27–221 Author chain H; PDBConstruct 1–195; UniProt 27–221

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 6ewc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6ewc
Deposition date deposition_date2017-11-03
Structure title titleCrystal structure of non-phosphorylated form of RLS PHOSPHOPEPTIDE BOUND TO HLA-A2 in complex with LILRB1
Keywords keywordsLILRB1, NONPHOSPHOPEPTIDE, peptide-MHC complex, HLA-A2, tumour antigen, crystallisation chaperone, 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_guinier35.89
Radius of gyration Rg (electron density) rg_electron35.47
Forward intensity I(0) i0277592000.00
Molecular weight molecular_weight130600.0 kDa
Excluded volume excluded_volume161760 ų
Envelope volume envelope_volume214930 ų
Hydration-shell volume shell_volume50854 ų
Envelope diameter envelope_diameter129.4
Shell Rg shell_rg41.41
Envelope Rg envelope_rg35.18
Shape Rg shape_rg35.45
Total Rg total_rg35.97
Total atoms total_atoms9226
Residues n_residues1140
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 dmax120.8
Rg (real space) rg_real35.87
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real2.7760e+08
I(0) uncertainty (real space) i0_real_error4.9880e+06
Rg (reciprocal space) rg_reciprocal35.89
I(0) (reciprocal space) i0_reciprocal277600000.0000
Solution quality estimate total_estimate0.8791
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.2
Skewness Skewness skewness0.350
Kurtosis Kurtosis kurtosis-0.276
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28560000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id6ewcA01
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_id6ewcA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ewcB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ewcD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ewcD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ewcE01
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_id6ewcE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ewcF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ewcH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ewcH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)