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- PDB-1kg0: Structure of the Epstein-Barr Virus gp42 Protein Bound to the MHC... -

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Basic information

Entry
Database: PDB / ID: 1kg0
TitleStructure of the Epstein-Barr Virus gp42 Protein Bound to the MHC class II Receptor HLA-DR1
Components
  • (MHC class II Receptor HLA-DR1) x 2
  • Hemagglutinin HA Peptide
  • gp42 Protein
KeywordsViral protein/Immune system / virus / c-type lectin domain / membrane fusion / MHC / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / CD4 receptor binding / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / host cell membrane / Co-inhibition by PD-1 / epidermis development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / positive regulation of protein phosphorylation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / carbohydrate binding / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / host cell surface receptor binding / immune response / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Mannose-Binding Protein A; Chain A ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / C-type lectin fold / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Glycoprotein 42 / Hemagglutinin / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMullen, M.M. / Haan, K.M. / Longnecker, R. / Jardetzky, T.S.
CitationJournal: Mol.Cell / Year: 2002
Title: Structure of the Epstein-Barr virus gp42 protein bound to the MHC class II receptor HLA-DR1.
Authors: Mullen, M.M. / Haan, K.M. / Longnecker, R. / Jardetzky, T.S.
History
DepositionNov 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 23, 2016Group: Structure summary
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class II Receptor HLA-DR1
B: MHC class II Receptor HLA-DR1
D: Hemagglutinin HA Peptide
C: gp42 Protein


Theoretical massNumber of molelcules
Total (without water)59,9614
Polymers59,9614
Non-polymers00
Water11,097616
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.400, 170.400, 101.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein MHC class II Receptor HLA-DR1


Mass: 20913.568 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN, EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01903
#2: Protein MHC class II Receptor HLA-DR1


Mass: 21908.523 Da / Num. of mol.: 1 / Fragment: BETA CHAIN, EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide Hemagglutinin HA Peptide


Mass: 1506.807 Da / Num. of mol.: 1 / Fragment: Antigenic Peptide / Source method: obtained synthetically
Details: Synthetic peptide derived from influenza hemagglutinin sequence
Source: (synth.) synthetic construct (others) / References: UniProt: P03437*PLUS
#4: Protein gp42 Protein


Mass: 15631.763 Da / Num. of mol.: 1 / Fragment: Extracellular Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Genus: Lymphocryptovirus / Strain: GD1 / Plasmid: pBAC-gus3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03205
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, Ammonium Acetate, Sodium Chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Temperature: 27 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
29 %PEG40001reservoir
30.1 Mammonium acetate1reservoirpH4.6
475 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 25595 / Num. obs: 25186 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 67 Å2
Reflection shellResolution: 2.65→2.82 Å / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 181993 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 1216 Random
Rwork0.221 --
all-25595 -
obs-25186 -
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 0 616 4844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0079
X-RAY DIFFRACTIONo_angle_deg1.58
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

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