1kg0

Structure of the Epstein-Barr Virus gp42 Protein Bound to the MHC class II Receptor HLA-DR1

Method: X-RAY DIFFRACTION Dmax: 113.0 Å Quality: GOOD

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

MHC class II Receptor HLA-DR1

Homo sapiens

UniProt P01903

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 28–207 Fragment:ALPHA CHAIN, EXTRACELLULAR DOMAIN MHC class II Receptor HLA-DR1 × 1 (P04229) Hemagglutinin HA Peptide × 1 gp42 Protein × 1 (P03205) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;300 K;PEG 4000, Ammonium Acetate, Sodium Chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K Resolution 2.65 Å R-free 0.247

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.

139 other PDB entries and 219 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 2DRA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–180; UniProt 28–207

MHC class II Receptor HLA-DR1

Homo sapiens

UniProt P04229

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 32–219 Fragment:BETA CHAIN, EXTRACELLULAR DOMAIN MHC class II Receptor HLA-DR1 × 1 (P01903) Hemagglutinin HA Peptide × 1 gp42 Protein × 1 (P03205) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;300 K;PEG 4000, Ammonium Acetate, Sodium Chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K Resolution 2.65 Å R-free 0.247

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.

48 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 2B11_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–188; UniProt 32–219

gp42 Protein

Human herpesvirus 4

UniProt P03205

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 86–221 Fragment:Extracellular Domain MHC class II Receptor HLA-DR1 × 1 (P01903) MHC class II Receptor HLA-DR1 × 1 (P04229) Hemagglutinin HA Peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;300 K;PEG 4000, Ammonium Acetate, Sodium Chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K Resolution 2.65 Å R-free 0.247

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.

5 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name YZL2_EBV
Isoform
PDB entities 4
Chains and sequence ranges Author chain C; PDBConstruct 1–136; UniProt 86–221

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 1kg0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1kg0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1kg0
Deposition date deposition_date2001-11-25
Structure title titleStructure of the Epstein-Barr Virus gp42 Protein Bound to the MHC class II Receptor HLA-DR1
Keywords keywordsvirus, c-type lectin domain, membrane fusion, MHC, Viral protein-Immune system COMPLEX; Viral protein/Immune system
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.29
Radius of gyration Rg (electron density) rg_electron31.37
Forward intensity I(0) i057180300.00
Molecular weight molecular_weight59868.0 kDa
Excluded volume excluded_volume74843 ų
Envelope volume envelope_volume96011 ų
Hydration-shell volume shell_volume28090 ų
Envelope diameter envelope_diameter119.5
Shell Rg shell_rg34.88
Envelope Rg envelope_rg32.12
Shape Rg shape_rg31.37
Total Rg total_rg31.70
Total atoms total_atoms4228
Residues n_residues517
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 dmax113.0
Rg (real space) rg_real31.75
Rg uncertainty (real space) rg_real_error1.48
I(0) (real space) i0_real5.7180e+07
I(0) uncertainty (real space) i0_real_error1.0540e+06
Rg (reciprocal space) rg_reciprocal31.55
I(0) (reciprocal space) i0_reciprocal57170000.0000
Solution quality estimate total_estimate0.7767
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8
Skewness Skewness skewness0.647
Kurtosis Kurtosis kurtosis-0.083
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8647000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.620; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.464; Smooth: 0.800

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1kg0a1
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_idd1kg0a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1kg0b1
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_idd1kg0b2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1kg0c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain

CATH v4.4 (5 domains)

Domain ID domain_id1kg0A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1kg0A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1kg0B01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1kg0B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1kg0C00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A

8. Citations (1)

9. Files and Curves (10)