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- PDB-7czf: Crystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ... -

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Basic information

Entry
Database: PDB / ID: 7czf
TitleCrystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ) gHgL in complex with the ligand binding domian (LBD) of EphA2
Components
  • (Envelope glycoprotein ...) x 2
  • Ephrin type-A receptor 2
KeywordsVIRAL PROTEIN / glycoprotein / receptor / complex / virus entry
Function / homology
Function and homology information


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / tight junction / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / molecular function activator activity / negative regulation of angiogenesis / skeletal system development / protein localization to plasma membrane / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / host cell endosome / host cell Golgi apparatus / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / fusion of virus membrane with host plasma membrane / focal adhesion / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / cell surface / ATP binding / membrane / plasma membrane
Similarity search - Function
Herpesvirus glycoprotein H, C-terminal domain / Gammaherpesvirus glycoprotein L (gL) domain profile. / 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 / Gammaherpesvirus glycoprotein L (gL) domain profile. / 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 / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-A receptor 2 / Core gene UL1 family protein / Core gene UL22 family protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.4Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)233,53524
Polymers227,5726
Non-polymers5,96418
Water00
1
A: Ephrin type-A receptor 2
B: Envelope glycoprotein H
C: Envelope glycoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,53212
Polymers113,7863
Non-polymers2,7479
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-9 kcal/mol
Surface area42440 Å2
MethodPISA
2
D: Ephrin type-A receptor 2
E: Envelope glycoprotein H
F: Envelope glycoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,00312
Polymers113,7863
Non-polymers3,2179
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-2 kcal/mol
Surface area41260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.803, 153.196, 275.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AD

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


Mass: 21323.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P29317, receptor protein-tyrosine kinase

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Envelope glycoprotein ... , 2 types, 4 molecules BECF

#2: Protein Envelope glycoprotein H / gH


Mass: 75374.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF22, gH, HHV8GK18_gp26 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q98142
#3: Protein Envelope glycoprotein L / gL


Mass: 17088.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF47, gL, ORF46, HHV8GK18_gp49 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q76RG7

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Sugars , 4 types, 18 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DManpa1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-3-2/a3-b1_a4-c1_a6-f1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated 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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Details

Has ligand of interestN
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: 3.69 Å3/Da / Density % sol: 66.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.25 M Potassium phosphate dibasic, 17% 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: BL17U / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 57447 / % possible obs: 99.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 54.09 Å2 / CC1/2: 0.997 / Net I/σ(I): 18.3
Reflection shellResolution: 3.2→3.31 Å / Num. unique obs: 5657 / CC1/2: 0.527

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Processing

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

5w0k

3fl7


Resolution: 3.2→31.65 Å / SU ML: 0.3647 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2765
RfactorNum. reflection% reflection
Rfree0.2721 2199 4.87 %
Rwork0.2393 --
obs0.2409 45163 78.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.67 Å2
Refinement stepCycle: LAST / Resolution: 3.2→31.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14901 0 0 0 14901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001615227
X-RAY DIFFRACTIONf_angle_d0.476720696
X-RAY DIFFRACTIONf_chiral_restr0.04082451
X-RAY DIFFRACTIONf_plane_restr0.00272608
X-RAY DIFFRACTIONf_dihedral_angle_d17.86495559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.270.4341240.3818434X-RAY DIFFRACTION12.91
3.27-3.340.3225620.33791005X-RAY DIFFRACTION30.32
3.34-3.430.4251830.30211423X-RAY DIFFRACTION42.78
3.43-3.520.3794970.28721809X-RAY DIFFRACTION53.78
3.52-3.620.28181280.26962128X-RAY DIFFRACTION63.93
3.62-3.740.3022980.27692554X-RAY DIFFRACTION74.66
3.74-3.870.30121560.26152926X-RAY DIFFRACTION86.82
3.87-4.030.29091890.26533266X-RAY DIFFRACTION96.4
4.03-4.210.27861690.2473379X-RAY DIFFRACTION99.97
4.21-4.430.25661740.21923380X-RAY DIFFRACTION99.89
4.43-4.710.21421730.20573400X-RAY DIFFRACTION99.69
4.71-5.070.22941570.21273425X-RAY DIFFRACTION99.5
5.07-5.580.24821670.22173404X-RAY DIFFRACTION99.8
5.58-6.380.29912030.24933445X-RAY DIFFRACTION99.75
6.38-8.020.24741760.24363456X-RAY DIFFRACTION99.26
8.02-31.650.24741430.21123530X-RAY DIFFRACTION95.93
Refinement TLS params.Method: refined / Origin x: -13.9892797237 Å / Origin y: -19.6402367002 Å / Origin z: 111.46558376 Å
111213212223313233
T0.0952767475536 Å2-0.117121187213 Å20.0161178731386 Å2-0.076825748675 Å2-0.0493549110697 Å2--0.109824714091 Å2
L-0.0630591634348 °20.0172219711132 °2-0.0781835955591 °2--0.0400428732222 °20.222512600536 °2--0.172991077118 °2
S-0.205189409675 Å °-0.0284860191894 Å °0.00755999402 Å °0.00784995435979 Å °-0.145195176399 Å °0.0368277105625 Å °0.0960206020645 Å °-0.0590862344058 Å °-0.451852220105 Å °
Refinement TLS groupSelection details: all

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