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- PDB-7b7n: Human herpesvirus-8 gH/gL in complex with EphA2 -

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Basic information

Entry
Database: PDB / ID: 7b7n
TitleHuman herpesvirus-8 gH/gL in complex with EphA2
Components
  • (Envelope glycoprotein ...) x 2
  • Ephrin type-A receptor 2
KeywordsVIRAL PROTEIN / Complex / Receptor
Function / homology
Function and homology information


notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / virion component => GO:0044423 / positive regulation of bicellular tight junction assembly ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / virion component => GO:0044423 / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / negative regulation of chemokine production / ephrin receptor activity / leading edge membrane / bone remodeling / post-anal tail morphogenesis / response to growth factor / activation of GTPase activity / regulation of lamellipodium assembly / tight junction / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell chemotaxis / negative regulation of angiogenesis / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / host cell endosome membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / skeletal system development / molecular function activator activity / cell motility / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / virus receptor activity / lamellipodium / host cell Golgi apparatus / receptor complex / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / cadherin binding / inflammatory response / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / phosphorylation / focal adhesion / viral envelope / host cell plasma membrane / virion membrane / cell surface / ATP binding / membrane / plasma membrane
Similarity search - Function
Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Ephrin type-A receptor 2, ligand binding domain ...Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Envelope glycoprotein L / Ephrin type-A receptor 2 / Envelope glycoprotein L / Envelope glycoprotein H
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsPederzoli, R. / Guardado-Calvo, P. / Rey, F.A. / Backovic, M.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur InstituteRecurrent funding France
CitationJournal: Plos Biol. / Year: 2021
Title: Human herpesvirus 8 molecular mimicry of ephrin ligands facilitates cell entry and triggers EphA2 signaling.
Authors: Light, T.P. / Brun, D. / Guardado-Calvo, P. / Pederzoli, R. / Haouz, A. / Neipel, F. / Rey, F.A. / Hristova, K. / Backovic, M.
History
DepositionDec 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Ephrin type-A receptor 2
H: Envelope glycoprotein H
L: Envelope glycoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,37721
Polymers119,7143
Non-polymers1,66318
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-164 kcal/mol
Surface area39030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.940, 129.000, 267.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 24043.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Cell line (production host): Schneider's Drosophila Line 2 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: P29317, receptor protein-tyrosine kinase

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Envelope glycoprotein ... , 2 types, 2 molecules HL

#2: Protein Envelope glycoprotein H / gH


Mass: 76018.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF22, gH, HHV8GK18_gp26 / Plasmid: pT350 / Cell line (production host): Schneider's Drosophila Line 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q98142
#3: Protein Envelope glycoprotein L / gL


Mass: 19651.018 Da / Num. of mol.: 1 / Mutation: C58S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF47, gL, ORF46, HHV8GK18_gp49 / Plasmid: pT350 / Cell line (production host): Schneider's Drosophila Line 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q76RG7, UniProt: F5HDB7*PLUS

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Sugars , 2 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 68 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Na-malonate pH 5, 14.2% PEG 3350 , 14 mM adenosine-5'-triphosphate disodium salt hydrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.9786
SYNCHROTRONSOLEIL PROXIMA 120.9876
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELFeb 7, 2020
DECTRIS EIGER X 16M2PIXELFeb 7, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.98761
ReflectionResolution: 2.69→46.44 Å / Num. obs: 35358 / % possible obs: 99.6 % / Redundancy: 13.6 % / Biso Wilson estimate: 76.73 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.9
Reflection shellResolution: 2.69→2.83 Å / Num. unique obs: 4540 / CC1/2: 0.596

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXphasing
PHENIX1.17.1_3660refinement
BUSTERrefinement
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HEI, 3PHF

3hei

3phf


Resolution: 2.69→46.44 Å / SU ML: 0.519 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.237
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2649 1762 4.99 %
Rwork0.2226 33520 -
obs0.2247 35282 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.67 Å2
Refinement stepCycle: LAST / Resolution: 2.69→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7082 0 98 54 7234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00257320
X-RAY DIFFRACTIONf_angle_d0.53439947
X-RAY DIFFRACTIONf_chiral_restr0.04191169
X-RAY DIFFRACTIONf_plane_restr0.00411251
X-RAY DIFFRACTIONf_dihedral_angle_d13.8122608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.770.40811260.40762423X-RAY DIFFRACTION95.18
2.77-2.850.48991350.40362564X-RAY DIFFRACTION99.93
2.85-2.940.39591340.36832548X-RAY DIFFRACTION99.89
2.94-3.040.3711330.31112549X-RAY DIFFRACTION99.85
3.04-3.170.35621340.27442552X-RAY DIFFRACTION99.93
3.17-3.310.33051350.25732576X-RAY DIFFRACTION99.93
3.31-3.490.31181360.24972564X-RAY DIFFRACTION99.96
3.49-3.70.28521360.21862588X-RAY DIFFRACTION99.96
3.7-3.990.2811350.20452562X-RAY DIFFRACTION100
3.99-4.390.21951370.17782611X-RAY DIFFRACTION100
4.39-5.020.19051370.15972597X-RAY DIFFRACTION99.96
5.03-6.330.21691380.19652636X-RAY DIFFRACTION100
6.33-46.440.23741460.22282750X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: 28.3565823752 Å / Origin y: 104.071508037 Å / Origin z: 105.423907521 Å
111213212223313233
T0.468993436144 Å20.0274576292273 Å20.0238726132902 Å2-0.455424385562 Å2-0.007334226925 Å2--0.536922315385 Å2
L0.240637335337 °2-0.461010289335 °20.682855454642 °2-1.47953042117 °2-1.85813675649 °2--2.46807060419 °2
S0.0599180112284 Å °0.0228084118588 Å °-0.00790164980653 Å °-0.00601794273914 Å °-0.0494914945663 Å °0.0142608729598 Å °0.136530580943 Å °0.0834078743433 Å °-0.0128232465096 Å °
Refinement TLS groupSelection details: all

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