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- PDB-6vy6: Crystal structure of Hendra receptor binding protein head domain ... -

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Basic information

Entry
Database: PDB / ID: 6vy6
TitleCrystal structure of Hendra receptor binding protein head domain in complex with human neutralizing antibody HENV-26
Components
  • (Anti-Hendra receptor binding protein antibody HENV-26 Fab ...) x 2
  • receptor binding protein
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


exo-alpha-sialidase activity / host cell surface / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Glycoprotein / Glycoprotein G
Similarity search - Component
Biological speciesHendra henipavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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
A: receptor binding protein
H: Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain
L: Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,67315
Polymers96,0893
Non-polymers1,58412
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-95 kcal/mol
Surface area35750 Å2
Unit cell
Length a, b, c (Å)70.807, 79.767, 177.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Anti-Hendra receptor binding protein antibody HENV-26 Fab ... , 2 types, 2 molecules HL

#2: 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)
#3: 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)

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein receptor binding protein / Glycoprotein


Mass: 48887.309 Da / Num. of mol.: 1 / Fragment: head domain (UNP residues 185-604)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra henipavirus / Production host: Homo sapiens (human) / References: UniProt: F4YH71, UniProt: O89343*PLUS
#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


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

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Non-polymers , 5 types, 199 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% MPD, 0.1 imidazole, pH 6.5, 0.2 M ammonium sulfate, 10% PEG3350

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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: Jun 26, 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: 2.6→47.46 Å / Num. obs: 31674 / % possible obs: 99.9 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 16.8
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.757 / Num. unique obs: 4550

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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 2X9M

2x9m


Resolution: 2.6→45.347 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.78
RfactorNum. reflection% reflection
Rfree0.2469 1526 4.83 %
Rwork0.1967 --
obs0.199 31626 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.07 Å2 / Biso mean: 52.0148 Å2 / Biso min: 26.39 Å2
Refinement stepCycle: final / Resolution: 2.6→45.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 91 191 6803
Biso mean--79.74 46.4 -
Num. residues----853
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6001-2.6840.33671360.27942691
2.684-2.77990.31651290.28192664
2.7799-2.89120.3261300.26392719
2.8912-3.02270.27191510.25192675
3.0227-3.18210.26231360.24422723
3.1821-3.38140.32381310.22362709
3.3814-3.64230.25931410.20042722
3.6423-4.00870.22991380.1812725
4.0087-4.58830.17591290.14812772
4.5883-5.77880.19591550.1522786
5.7788-45.3470.25981500.18982914
Refinement TLS params.Method: refined / Origin x: -11.9176 Å / Origin y: 95.7803 Å / Origin z: 40.4917 Å
111213212223313233
T0.3036 Å20.0368 Å2-0.0572 Å2-0.2925 Å20.0377 Å2--0.3344 Å2
L0.5655 °20.017 °2-0.7354 °2-0.3572 °20.1371 °2--1.3906 °2
S-0.004 Å °0.0014 Å °-0.0973 Å °-0.021 Å °-0.0904 Å °-0.0348 Å °-0.0478 Å °-0.0629 Å °0.0851 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA186 - 601
2X-RAY DIFFRACTION1allH1 - 230
3X-RAY DIFFRACTION1allL2 - 213
4X-RAY DIFFRACTION1allB1 - 5
5X-RAY DIFFRACTION1allC1 - 195
6X-RAY DIFFRACTION1allD1
7X-RAY DIFFRACTION1allF1
8X-RAY DIFFRACTION1allG1
9X-RAY DIFFRACTION1allE609 - 613

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