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- PDB-7cze: Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex... -

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Basic information

Entry
Database: PDB / ID: 7cze
TitleCrystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2
Components
  • Envelope glycoprotein H
  • Envelope glycoprotein L
  • Ephrin type-A receptor 2
KeywordsVIRAL PROTEIN / glycoprotein / receptor / complex / virus entry
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 / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...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 / 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 / cell motility / molecular function activator activity / 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 / Envelope glycoprotein H / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSu, C. / Wu, L.L. / Song, H. / Chai, Y. / Qi, J.X. / Yan, J.H. / Gao, G.F.
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis of EphA2 recognition by gHgL from gammaherpesviruses.
Authors: Su, C. / Wu, L. / Chai, Y. / Qi, J. / Tan, S. / Gao, G.F. / Song, H. / Yan, J.
History
DepositionSep 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.number_unique_obs
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.4Jan 13, 2021Group: Other / Category: pdbx_database_status
Item: _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf
Revision 1.5Sep 29, 2021Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Envelope glycoprotein H
D: Envelope glycoprotein L
E: Envelope glycoprotein H
F: Envelope glycoprotein L
G: Envelope glycoprotein H
H: Envelope glycoprotein L
I: Ephrin type-A receptor 2
J: Ephrin type-A receptor 2
K: Ephrin type-A receptor 2
L: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,83628
Polymers428,29712
Non-polymers3,53916
Water0
1
A: Envelope glycoprotein H
B: Envelope glycoprotein L
I: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9597
Polymers107,0743
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-34 kcal/mol
Surface area41270 Å2
MethodPISA
2
C: Envelope glycoprotein H
D: Envelope glycoprotein L
J: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9597
Polymers107,0743
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-35 kcal/mol
Surface area41240 Å2
MethodPISA
3
E: Envelope glycoprotein H
F: Envelope glycoprotein L
L: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9597
Polymers107,0743
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-36 kcal/mol
Surface area41260 Å2
MethodPISA
4
G: Envelope glycoprotein H
H: Envelope glycoprotein L
K: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9597
Polymers107,0743
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-37 kcal/mol
Surface area41280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.464, 113.806, 119.654
Angle α, β, γ (deg.)90.030, 90.167, 89.888
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Envelope glycoprotein H / gH


Mass: 73383.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: gH, BXLF2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03231
#2: Protein
Envelope glycoprotein L / gL


Mass: 12589.231 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: gL, BKRF2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03212
#3: Protein
Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 21101.857 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P29317, receptor protein-tyrosine kinase
#4: 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.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY

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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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 98531 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.994 / Net I/σ(I): 12.95
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 9508 / CC1/2: 0.757

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w0k, 3fl7

5w0k

3fl7


Resolution: 3→41.22 Å / SU ML: 0.4912 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 36.7047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285 5117 5.21 %
Rwork0.2573 93116 -
obs0.2587 98233 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29284 0 0 0 29284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004929948
X-RAY DIFFRACTIONf_angle_d1.010440632
X-RAY DIFFRACTIONf_chiral_restr0.05964704
X-RAY DIFFRACTIONf_plane_restr0.0065124
X-RAY DIFFRACTIONf_dihedral_angle_d13.895910952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.030.4891580.4542714X-RAY DIFFRACTION86.56
3.03-3.070.45291840.43413169X-RAY DIFFRACTION98.3
3.07-3.110.44542010.41512998X-RAY DIFFRACTION98.07
3.11-3.150.44691860.4043143X-RAY DIFFRACTION98.58
3.15-3.190.39151690.38813057X-RAY DIFFRACTION97.94
3.19-3.230.35551620.38993139X-RAY DIFFRACTION98.13
3.23-3.280.38541720.37353073X-RAY DIFFRACTION98.39
3.28-3.330.38511830.35633049X-RAY DIFFRACTION98.18
3.33-3.380.45471520.36253186X-RAY DIFFRACTION98.55
3.38-3.430.33631390.32913127X-RAY DIFFRACTION97.96
3.43-3.490.30431540.31213090X-RAY DIFFRACTION98.42
3.49-3.560.40191690.30213108X-RAY DIFFRACTION98.59
3.56-3.620.31251590.29683179X-RAY DIFFRACTION98.85
3.62-3.70.34411350.29263096X-RAY DIFFRACTION98.69
3.7-3.780.3131870.28373132X-RAY DIFFRACTION98.75
3.78-3.870.30961480.28223136X-RAY DIFFRACTION98.8
3.87-3.960.2862010.2723092X-RAY DIFFRACTION98.86
3.96-4.070.31311770.26943093X-RAY DIFFRACTION98.49
4.07-4.190.27971860.24343063X-RAY DIFFRACTION98.54
4.19-4.320.27731490.24323206X-RAY DIFFRACTION99.29
4.32-4.480.24172340.21733090X-RAY DIFFRACTION98.99
4.48-4.660.27882110.20753036X-RAY DIFFRACTION99.24
4.66-4.870.20981580.19863125X-RAY DIFFRACTION99.27
4.87-5.130.23921170.20733252X-RAY DIFFRACTION99.53
5.13-5.450.25521390.23043170X-RAY DIFFRACTION99.43
5.45-5.860.26841570.24523147X-RAY DIFFRACTION99.49
5.86-6.450.29622100.23793070X-RAY DIFFRACTION99.48
6.45-7.380.27431840.23433165X-RAY DIFFRACTION99.52
7.38-9.280.20921580.20233148X-RAY DIFFRACTION99.64
9.28-41.220.23581780.22573063X-RAY DIFFRACTION97.33
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.610871591454-0.314031188997-0.1164233360081.245144175730.6871252324483.26815593981-0.0619615115655-0.00879724793631-0.04082239863390.341321573020.01884113759240.0150139140953-0.1619733266050.01069546474172.17820488379E-110.708907921026-0.0387896993538-0.03254320974860.7276539347130.0279671978770.91244893050610.23646426837.5035805437-8.90195331475
20.864397541417-0.4799990680920.5779637767280.7148133613880.4554954682420.8740972398750.004503701004190.380311023703-0.122266954674-0.745816301209-0.07400869893740.066996201116-0.255900223134-0.177114116-1.30189067708E-50.870717223049-0.127449761310.00707349179481.12121186166-0.03816857495720.97640235242117.351885318921.3232881896-59.2663862426
30.6762766643780.4208188360240.08081793933011.145904854780.5494853292812.96997425127-0.08997948229540.0368165847033-0.000338110747365-0.2988951288140.06424287286640.0186982563050.2117512287010.02038319424931.56250590681E-120.8005520934140.03750899625290.03375481906360.710493253670.004134134265260.912532168829-36.912261589477.7081155358-24.904734146
40.4057117565340.311908505518-0.1482468137850.997996902893-0.2515444140924.50748597805-0.0138142252062-0.0872149265516-0.0895383172446-0.09052517487450.02570044438970.02831369326490.0435739592153-0.1074487455241.52172401852E-110.6661279813710.0869862741325-0.01924261276210.7948134477080.01430836957650.9177022566218.678452686194.144560959423.6921872959
50.271799489892-0.3569513009520.2848620249940.202190630441-0.499418018220.768182993428-0.150107074390.09857133638930.195495638173-0.3723935742030.01840011278650.06119129154110.174548977124-0.0654627468595-2.63449111285E-91.10416010911-0.00731579410716-0.01760070858631.125280203850.06747305371560.95404640039411.655222343378.056396589774.1432417714
60.304853462655-0.3565617944290.05200063798261.10563083978-0.6988417448734.5689685034-0.008485705201070.06335807568610.1165900428780.04002389852950.03962043531580.0171104849937-0.0681574431907-0.07293658105832.01410913239E-110.804955311208-0.1271161055520.0006067231621280.819364461274-0.01405659743460.930432981294-28.842557170820.963566521662.2038939861
70.05978188488970.282369124701-0.04688869404740.162491233692-0.5012456691940.638946952421-0.280867771177-0.150328965603-0.150325239420.5703639044830.06108614591060.273328152531-0.665725845177-0.0203450620609-1.43243552713E-81.298349157640.01477940580060.00130376002121.047388095750.04711942608251.0335530891-35.513127383137.091172488611.7223519265
81.03502483554-0.6920113710530.4856901688961.171514115530.3129484745770.8885662049860.219261198899-0.2777142304310.28669100604-0.228200381296-0.2368305241560.131623360004-0.468329339506-0.2179865368261.2210790767E-90.722893425795-0.0539174534830.04013651151990.9742924174080.01350481984190.93564517606722.593601001913.2543644521-86.4663253894
91.107574093280.801099588343-0.3236158729821.076168806330.5108117641250.9941677498430.2476921229130.317404063976-0.2849234052140.0761643937126-0.2610041225170.07648097176570.445350004637-0.274941313597-3.73795560843E-90.7567365541310.0505192869014-0.04251883505870.9777638779840.04004578921620.906024431711-24.9263842062101.90483278452.7147745198
101.41946415388-0.597020218087-0.335976342711.772700796570.1854075462470.9235832338070.168753757114-0.2852922504850.007495058054170.0338249699447-0.233085769961-0.0145047271123-0.0905202424364-0.117478573615-6.11363712773E-90.929988634908-0.0651179721193-0.05132225644980.832811812056-0.02669256521160.948239611321-41.030923260945.0808078414-15.4070961435
111.33245685810.7414615285990.2876429776481.76026091532-0.01635479564210.5632096638940.2525194620780.357385415902-0.0225633381093-0.0237780156478-0.3091886364910.01853029254370.0958602423431-0.00104621447508-1.0927091582E-80.7367567740560.08322221892410.02511210405990.865443072582-0.0187345156080.9171065377135.9330677286870.0962950772101.232498364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain E
5X-RAY DIFFRACTION5chain F
6X-RAY DIFFRACTION6chain G
7X-RAY DIFFRACTION7chain H
8X-RAY DIFFRACTION8chain I
9X-RAY DIFFRACTION9chain J
10X-RAY DIFFRACTION10chain K
11X-RAY DIFFRACTION11chain L

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