3d2u

Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor

Method: X-RAY DIFFRACTION Dmax: 140.4 Å Quality: REASONABLE

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

UL18 protein

OrganismNot specified

UniProt Q4A1U8

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 21–301 Fragment:sequence database residues 21-301 Beta-2-microglobulin × 1 (P61769) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (Q8NHL6) Actin × 1 (P60709) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1 FUC alpha-L-fucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.21 Å R-free 0.259
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 21–301 Fragment:sequence database residues 21-301 Beta-2-microglobulin × 1 (P61769) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (Q8NHL6) Actin × 1 (P60709) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.21 Å R-free 0.259

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 Q4A1U8_HCMV
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–281; UniProt 21–301 Author chain E; PDBConstruct 1–281; UniProt 21–301

Beta-2-microglobulin

OrganismNot specified

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 UL18 protein × 1 (Q4A1U8) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (Q8NHL6) Actin × 1 (P60709) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1 FUC alpha-L-fucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.21 Å R-free 0.259
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded UL18 protein × 1 (Q4A1U8) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (Q8NHL6) Actin × 1 (P60709) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.21 Å R-free 0.259

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

Leukocyte immunoglobulin-like receptor subfamily B member 1

OrganismNot specified

UniProt Q8NHL6

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 24–221 Fragment:Ig-like C2-type 1 and C2-type 2 domains UL18 protein × 1 (Q4A1U8) Beta-2-microglobulin × 1 (P61769) Actin × 1 (P60709) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1 FUC alpha-L-fucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.21 Å R-free 0.259
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain H; UniProt 24–221 Fragment:Ig-like C2-type 1 and C2-type 2 domains UL18 protein × 1 (Q4A1U8) Beta-2-microglobulin × 1 (P61769) Actin × 1 (P60709) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.21 Å R-free 0.259

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.

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LIRB1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–198; UniProt 24–221 Author chain H; PDBConstruct 1–198; UniProt 24–221

Actin

OrganismNot specified

UniProt P60709

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 170–178 Fragment:sequence database residues 170-178 UL18 protein × 1 (Q4A1U8) Beta-2-microglobulin × 1 (P61769) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (Q8NHL6) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1 FUC alpha-L-fucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.21 Å R-free 0.259
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 170–178 Fragment:sequence database residues 170-178 UL18 protein × 1 (Q4A1U8) Beta-2-microglobulin × 1 (P61769) Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 (Q8NHL6) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.21 Å R-free 0.259

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.

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

View Construct and Data Evidence
UniProt name ACTB_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 170–178 Author chain G; PDBConstruct 1–9; UniProt 170–178

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 3d2u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3d2u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3d2u
Deposition date deposition_date2008-05-08
Structure title titleStructure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor
Keywords keywords;MHC class I homolog, Disease mutation, Glycation, Glycoprotein, Immune response, Immunoglobulin domain, MHC I, Pyrrolidone carboxylic acid, Secreted, Membrane, Phosphoprotein, Receptor, Transmembrane, 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_guinier39.85
Radius of gyration Rg (electron density) rg_electron39.97
Forward intensity I(0) i0267450000.00
Molecular weight molecular_weight132050.0 kDa
Excluded volume excluded_volume164470 ų
Envelope volume envelope_volume220990 ų
Hydration-shell volume shell_volume47850 ų
Envelope diameter envelope_diameter153.1
Shell Rg shell_rg43.66
Envelope Rg envelope_rg39.52
Shape Rg shape_rg39.94
Total Rg total_rg40.28
Total atoms total_atoms9319
Residues n_residues1143
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 dmax140.4
Rg (real space) rg_real39.99
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real2.6740e+08
I(0) uncertainty (real space) i0_real_error4.9290e+06
Rg (reciprocal space) rg_reciprocal39.90
I(0) (reciprocal space) i0_reciprocal267400000.0000
Solution quality estimate total_estimate0.6480
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.6
Skewness Skewness skewness0.384
Kurtosis Kurtosis kurtosis-0.321
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24890000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.922; Smooth: 0.968

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3d2ub_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3d2ud1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd3d2ud2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd3d2uf_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3d2uh1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd3d2uh2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains

CATH v4.4 (10 domains)

Domain ID domain_id3d2uA01
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_id3d2uA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3d2uB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3d2uD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3d2uD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3d2uE01
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_id3d2uE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3d2uF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3d2uH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3d2uH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)