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- PDB-2vsm: Nipah virus attachment glycoprotein in complex with human cell su... -

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Basic information

Entry
Database: PDB / ID: 2vsm
TitleNipah 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 / membrane fusion involved in viral entry into host cell / cell migration involved in sprouting angiogenesis ...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 / membrane fusion involved in viral entry into host cell / 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 / cellular response to lipopolysaccharide / presynaptic membrane / virus receptor activity / clathrin-dependent endocytosis of virus by host cell / cell adhesion / host cell surface receptor binding / focal adhesion / positive regulation of cell population proliferation / viral envelope / dendrite / virion attachment to host cell / host cell plasma membrane / glutamatergic synapse / virion membrane / identical protein binding / 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
ISOPROPYL ALCOHOL / Ephrin-B2 / Glycoprotein G
Similarity search - Component
Biological speciesNipah virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 25, 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 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8347
Polymers62,8892
Non-polymers9455
Water12,701705
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-16.1 kcal/mol
Surface area27940 Å2
MethodPQS
Unit cell
Length a, b, c (Å)63.236, 95.834, 97.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEMAGGLUTININ-NEURAMINIDASE / NIV-G


Mass: 46839.293 Da / Num. of mol.: 1
Fragment: B-PROPELLER, EPHRIN BINDING DOMAIN, RESIDUES 188-602
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN / Source: (gene. exp.) Nipah virus / Description: SYNTHETICALLY OPTIMIZED CDNA (GENEART) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9IH62, exo-alpha-sialidase
#2: Protein EPHRIN-B2 / EFNB2 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5 / LERK-5 / HTK LIGAND / HTK-L


Mass: 16049.366 Da / Num. of mol.: 1 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 28-165
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE LINKAGE OBSERVED IN / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P52799
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 5.6
Details: 18% ISOPROPANOL, 18% PEG 3350 AND 0.1 M TRI-CITRATE BUFFER PH 5.6

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2006 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 55159 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NUK AND 1V3E

1nuk

1v3e


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.237 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2800 5.1 %RANDOM
Rwork0.152 ---
obs0.154 52300 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 60 705 5138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224700
X-RAY DIFFRACTIONr_bond_other_d0.0010.023211
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9756415
X-RAY DIFFRACTIONr_angle_other_deg0.9393.0057823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.6875582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5824.67212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26615801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4051523
X-RAY DIFFRACTIONr_chiral_restr0.1920.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02923
X-RAY DIFFRACTIONr_nbd_refined0.190.2842
X-RAY DIFFRACTIONr_nbd_other0.1930.23432
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22229
X-RAY DIFFRACTIONr_nbtor_other0.0940.22510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2544
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.253690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5884638
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.178102204
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7151773
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 188
Rwork0.197 3330

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