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- PDB-2vsk: Hendra virus attachment glycoprotein in complex with human cell s... -

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Basic information

Entry
Database: PDB / ID: 2vsk
TitleHendra virus attachment glycoprotein in complex with human cell surface receptor ephrinB2
Components
  • EPHRIN-B2
  • HEMAGGLUTININ-NEURAMINIDASE
KeywordsHYDROLASE / DEVELOPMENTAL PROTEIN / HENIPAVIRUS / NEUROGENESIS / GLYCOPROTEIN / PARAMYXOVIRUS / ENVELOPE PROTEIN / CELL SURFACE RECEPTOR / HENDRA / VIRION / EPHRIN / COMPLEX / MEMBRANE / B2 / EFN / NIV / EPH / HEV / HEV-G / NIPAH / VIRUS / NIV-G / PHOSPHOPROTEIN / DIFFERENTIATION / VIRAL ATTACHMENT / SIGNAL-ANCHOR / HEMAGGLUTININ / TRANSMEMBRANE
Function / homology
Function and homology information


venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / presynapse assembly / lymph vessel development / regulation of chemotaxis / adherens junction organization / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling ...venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / presynapse assembly / lymph vessel development / regulation of chemotaxis / adherens junction organization / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / blood vessel morphogenesis / Ephrin signaling / regulation of postsynaptic neurotransmitter receptor internalization / exo-alpha-sialidase activity / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / regulation of postsynaptic membrane neurotransmitter receptor levels / ephrin receptor binding / T cell costimulation / EPHB-mediated forward signaling / axon guidance / animal organ morphogenesis / adherens junction / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cell-cell signaling / negative regulation of neuron projection development / virus receptor activity / presynaptic membrane / cellular response to lipopolysaccharide / host cell surface / cell adhesion / host cell surface receptor binding / focal adhesion / positive regulation of cell population proliferation / dendrite / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / glutamatergic synapse / virion membrane / membrane / plasma membrane
Similarity search - Function
Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase ...Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glycoprotein G / Ephrin-B2
Similarity search - Component
Biological speciesHendra virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBowden, T.A. / Aricescu, A.R. / Gilbert, R.J. / Grimes, J.M. / Jones, E.Y. / Stuart, D.I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural Basis of Nipah and Hendra Virus Attachment to Their Cell-Surface Receptor Ephrin-B2
Authors: Bowden, T.A. / Aricescu, A.R. / Gilbert, R.J. / Grimes, J.M. / Jones, E.Y. / Stuart, D.I.
History
DepositionApr 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMAGGLUTININ-NEURAMINIDASE
B: EPHRIN-B2
C: HEMAGGLUTININ-NEURAMINIDASE
D: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)125,1064
Polymers125,1064
Non-polymers00
Water00
1
A: HEMAGGLUTININ-NEURAMINIDASE
B: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)62,5532
Polymers62,5532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-15.1 kcal/mol
Surface area27860 Å2
MethodPQS
2
C: HEMAGGLUTININ-NEURAMINIDASE
D: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)62,5532
Polymers62,5532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-14.7 kcal/mol
Surface area27320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)56.250, 106.170, 196.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99988, 0.00526, -0.01489), (0.0126, -0.83429, 0.55118), (-0.00952, -0.55129, -0.83426)-20.24224, -12.55933, -118.37399
2given(0.99937, 0.03533, -0.0033), (0.03003, -0.7926, 0.609), (0.01891, -0.60872, -0.79316)-19.78947, -10.97393, -118.19832

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Components

#1: Protein HEMAGGLUTININ-NEURAMINIDASE / HEV-G


Mass: 46780.117 Da / Num. of mol.: 2
Fragment: B-PROPELLER, EPHRIN BINDING DOMAIN, RESIDUES 188-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus / Description: SYNTHETICALLY OPTIMIZED CDNA (GENEART) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O89343, exo-alpha-sialidase
#2: Protein EPHRIN-B2 / EFNB2 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5 / LERK-5 / HTK LIGAND / HTK-L


Mass: 15773.072 Da / Num. of mol.: 2 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 28-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P52799
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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5.5 / Details: 25% PEG 3350 0.1 M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: May 13, 2006 / Details: MIRRORS
RadiationMonochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 17229 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 29.75 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 6.1
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 82.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VSM, NIV-G-EFNB2

2vsm


Resolution: 3.3→20 Å / SU ML: 0.7181 / Phase error: 34.349 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.35 870 5.1 %
Rwork0.3 --
obs0.3 17118 82.7 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 5.99 Å2 / ksol: 0.27 e/Å3
Displacement parametersBiso mean: 34.32 Å2
Baniso -1Baniso -2Baniso -3
1--11.51 Å2-0 Å2-0 Å2
2---25.959 Å20 Å2
3---0.467 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8443 0 0 0 8443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174857
X-RAY DIFFRACTIONf_angle_d2.51818789
X-RAY DIFFRACTIONf_dihedral_angle_d22.7019350
X-RAY DIFFRACTIONf_chiral_restr0.093282
X-RAY DIFFRACTIONf_plane_restr0.0195642

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