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- PDB-6vy5: Crystal structure of Nipah receptor binding protein head domain i... -

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Basic information

Entry
Database: PDB / ID: 6vy5
TitleCrystal structure of Nipah receptor binding protein head domain in complex with human neutralizing antibody HENV-26
Components
  • Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain
  • Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain
  • receptor binding proteinReceptor (biochemistry)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / henipavirus / Hendra virus / receptor binding protein / antibody / antibody-antigen complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Nipah henipavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsDong, J. / Crowe, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142764 United States
CitationJournal: Cell / Year: 2020
Title: Potent Henipavirus Neutralization by Antibodies Recognizing Diverse Sites on Hendra and Nipah Virus Receptor Binding Protein.
Authors: Dong, J. / Cross, R.W. / Doyle, M.P. / Kose, N. / Mousa, J.J. / Annand, E.J. / Borisevich, V. / Agans, K.N. / Sutton, R. / Nargi, R. / Majedi, M. / Fenton, K.A. / Reichard, W. / Bombardi, R. ...Authors: Dong, J. / Cross, R.W. / Doyle, M.P. / Kose, N. / Mousa, J.J. / Annand, E.J. / Borisevich, V. / Agans, K.N. / Sutton, R. / Nargi, R. / Majedi, M. / Fenton, K.A. / Reichard, W. / Bombardi, R.G. / Geisbert, T.W. / Crowe Jr., J.E.
History
DepositionFeb 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain
L: Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain
A: receptor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1858
Polymers96,0793
Non-polymers1,1065
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-11 kcal/mol
Surface area35110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.701, 186.701, 81.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain


Mass: 24446.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain


Mass: 22755.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein receptor binding protein / Receptor (biochemistry)


Mass: 48877.441 Da / Num. of mol.: 1 / Fragment: head domain (UNP residues 183-602)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah henipavirus / Production host: Homo sapiens (human) / References: UniProt: Q9IH62
#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.: 5
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
Has ligand of interestN

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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: 4.26 Å3/Da / Density % sol: 71.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.0 M sodium malonate, pH 7.0, 0.1 M Bis-Tris propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 20, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.4→48.85 Å / Num. obs: 22696 / % possible obs: 100 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 7.2
Reflection shellResolution: 3.4→3.58 Å / Rmerge(I) obs: 0.514 / Num. unique obs: 3283

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VWD

2vwd


Resolution: 3.4→44.924 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.46
RfactorNum. reflection% reflection
Rfree0.2498 1157 5.11 %
Rwork0.2084 --
obs0.2105 22663 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.24 Å2 / Biso mean: 86.0533 Å2 / Biso min: 35.82 Å2
Refinement stepCycle: final / Resolution: 3.4→44.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6182 0 70 0 6252
Biso mean--93.14 --
Num. residues----835
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.4-3.55470.33341390.26562656
3.5547-3.7420.29331440.23022656
3.742-3.97640.28181220.21622683
3.9764-4.28320.25081710.19442643
4.2832-4.71380.1961310.16972694
4.7138-5.39490.2141440.17652696
5.3949-6.79320.27841390.22672723
6.7932-44.9240.23931670.22252755
Refinement TLS params.Method: refined / Origin x: 61.9822 Å / Origin y: -55.4921 Å / Origin z: -18.8434 Å
111213212223313233
T0.6428 Å2-0.0931 Å2-0.0829 Å2-0.3982 Å2-0.0044 Å2--0.4894 Å2
L2.273 °2-0.6408 °2-0.0707 °2-1.6907 °20.0921 °2--0.5683 °2
S-0.1731 Å °0.1614 Å °0.2559 Å °-0.1428 Å °0.0139 Å °0.3838 Å °-0.1459 Å °-0.0511 Å °0.1542 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 228
2X-RAY DIFFRACTION1allL2 - 211
3X-RAY DIFFRACTION1allA186 - 602
4X-RAY DIFFRACTION1allA603 - 607

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