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- PDB-4uf7: Ghanaian henipavirus (Gh-M74a) attachment glycoprotein in complex... -

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Basic information

Entry
Database: PDB / ID: 4uf7
TitleGhanaian henipavirus (Gh-M74a) attachment glycoprotein in complex with human ephrinB2
Components
  • EPHRIN-B2Ephrin B2
  • GLYCOPROTEIN
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / GH-M74A / HENDRA VIRUS / NIPAH VIRUS / VIRAL ATTACHMENT / GLYCOPROTEIN / PARAMYXOVIRUS / GHV-G / NIV-G / HEV-G / HNV / HNV-G
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 / lymph vessel development / regulation of chemotaxis / cell migration involved in sprouting angiogenesis / regulation of postsynaptic neurotransmitter receptor internalization / adherens junction organization / EPH-Ephrin signaling ...venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / lymph vessel development / regulation of chemotaxis / cell migration involved in sprouting angiogenesis / regulation of postsynaptic neurotransmitter receptor internalization / adherens junction organization / EPH-Ephrin signaling / Ephrin signaling / blood vessel morphogenesis / regulation of postsynaptic membrane neurotransmitter receptor levels / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / EPHB-mediated forward signaling / T cell costimulation / ephrin receptor binding / axon guidance / animal organ morphogenesis / postsynaptic density membrane / adherens junction / Schaffer collateral - CA1 synapse / virus receptor activity / cell-cell signaling / negative regulation of neuron projection development / presynaptic membrane / membrane => GO:0016020 / cell adhesion / host cell surface receptor binding / focal adhesion / viral envelope / glutamatergic synapse / positive regulation of cell population proliferation / virion attachment to host cell / virion 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/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 ...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/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
ACETATE ION / Glycoprotein / Ephrin-B2
Similarity search - Component
Biological speciesBAT PARAMYXOVIRUS EID_HEL/GH-M74A/GHA/2009
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, B. / Pernet, O. / Ahmed, A.A. / Zeltina, A. / Beaty, S.M. / Bowden, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Molecular Recognition of Human Ephrinb2 Cell Surface Receptor by an Emergent African Henipavirus.
Authors: Lee, B. / Pernet, O. / Ahmed, A.A. / Zeltina, A. / Beaty, S.M. / Bowden, T.A.
History
DepositionMar 13, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_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
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / 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 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOPROTEIN
B: GLYCOPROTEIN
C: EPHRIN-B2
E: EPHRIN-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,84737
Polymers139,6814
Non-polymers4,16633
Water18,3751020
1
B: GLYCOPROTEIN
C: EPHRIN-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,77317
Polymers69,8412
Non-polymers1,93215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-83.2 kcal/mol
Surface area23610 Å2
MethodPISA
2
A: GLYCOPROTEIN
E: EPHRIN-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,07520
Polymers69,8412
Non-polymers2,23418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-72.8 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.220, 152.530, 163.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 4 molecules ABCE

#1: Protein GLYCOPROTEIN / / GHV-G


Mass: 52333.727 Da / Num. of mol.: 2
Fragment: RECEPTOR-BINDING B-PROPELLER DOMAIN, RESIDUES 199-632
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE. ASN207, ASN255, ASN327, AND ASN396
Source: (gene. exp.) BAT PARAMYXOVIRUS EID_HEL/GH-M74A/GHA/2009
Description: SYNTHETICALLY OPTIMIZED CDNA / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: I0E093
#2: Protein EPHRIN-B2 / Ephrin B2 / EPHRINB2 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5 / LER HTK LIGAND / HTK-L


Mass: 17506.854 Da / Num. of mol.: 2 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 27-167
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE. ASN39, ASN142
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P52799

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Sugars , 1 types, 11 molecules

#6: 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.: 11
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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Non-polymers , 4 types, 1042 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1020 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.7 % / Description: NONE
Crystal growpH: 5.5
Details: 12% PEG 4000, 0.1 M SODIUM ACETATE PH 5.5, 0.1 M LISO4, AND 0.1 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2013 / Details: MIRRORS
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 172833 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VSM

2vsm


Resolution: 1.7→111.47 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.068 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 8583 5 %RANDOM
Rwork0.1748 ---
obs0.17604 162840 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.222 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å2-0 Å2-0 Å2
2--1.75 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→111.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8929 0 249 1020 10198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.029554
X-RAY DIFFRACTIONr_bond_other_d0.0020.028653
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.98313042
X-RAY DIFFRACTIONr_angle_other_deg0.926320029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77851135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05124.202445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.763151541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3571549
X-RAY DIFFRACTIONr_chiral_restr0.0870.21428
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022198
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3742.5394468
X-RAY DIFFRACTIONr_mcbond_other1.3682.5344460
X-RAY DIFFRACTIONr_mcangle_it2.3473.7845576
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6432.8955086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 636 -
Rwork0.316 11797 -
obs--97.93 %
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)
10.46380.093-0.25980.28180.04140.6837-0.0447-0.053-0.08530.0381-0.0034-0.02720.10880.01750.04810.0340.0159-0.00060.02420.00720.024239.043142.30020.9452
20.8663-0.06210.38860.3611-0.21730.37830.1133-0.0476-0.2201-0.01270.09850.09220.0238-0.0657-0.21180.0299-0.0188-0.01890.04690.04440.1348-0.925341.107838.3141
30.88730.1454-0.05370.91440.09080.44370.14630.0750.08090.0848-0.0909-0.0652-0.01230.0224-0.05540.0338-0.00720.00370.04780.02410.023722.397960.730.3051
40.46320.2071-0.05411.1164-0.16940.64410.03570.07130.0244-0.0856-0.15080.0109-0.0347-0.0350.11510.02040.0345-0.01140.0601-0.01330.028529.430461.7073-22.4185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A201 - 617
2X-RAY DIFFRACTION2B202 - 617
3X-RAY DIFFRACTION3C30 - 171
4X-RAY DIFFRACTION4E30 - 172

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