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- PDB-6vy4: Crystal structure of Hendra receptor binding protein head domain ... -

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Basic information

Entry
Database: PDB / ID: 6vy4
TitleCrystal structure of Hendra receptor binding protein head domain in complex with human neutralizing antibody HENV-32
Components
  • (Anti-Hendra receptor binding protein antibody HENV-32 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
ISOPROPYL ALCOHOL / Glycoprotein / Glycoprotein G
Similarity search - Component
Biological speciesHendra henipavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 1.0Dec 30, 2020Provider: 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
B: receptor binding protein
C: Anti-Hendra receptor binding protein antibody HENV-32 Fab heavy chain
D: Anti-Hendra receptor binding protein antibody HENV-32 Fab light chain
H: Anti-Hendra receptor binding protein antibody HENV-32 Fab heavy chain
L: Anti-Hendra receptor binding protein antibody HENV-32 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,52223
Polymers190,8716
Non-polymers2,65117
Water12,989721
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17070 Å2
ΔGint-65 kcal/mol
Surface area69280 Å2
Unit cell
Length a, b, c (Å)195.889, 84.490, 122.834
Angle α, β, γ (deg.)90.000, 95.930, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

SO4

21B-938-

HOH

31B-1008-

HOH

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Components

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Anti-Hendra receptor binding protein antibody HENV-32 Fab ... , 2 types, 4 molecules CHDL

#2: Protein Anti-Hendra receptor binding protein antibody HENV-32 Fab heavy chain


Mass: 23790.998 Da / Num. of mol.: 2
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-32 Fab light chain


Mass: 22757.082 Da / Num. of mol.: 2
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, 11 molecules AB

#1: Protein receptor binding protein / Glycoprotein


Mass: 48887.309 Da / Num. of mol.: 2 / 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
#5: 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.: 9
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 , 3 types, 729 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.5 M ammonium sulfate, 5% isopropanol

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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→49.51 Å / Num. obs: 134705 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.743 / Num. unique obs: 19582

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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 2VSM

2vsm


Resolution: 2→49.506 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.75
RfactorNum. reflection% reflection
Rfree0.2261 6714 4.99 %
Rwork0.1832 --
obs0.1853 134683 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.96 Å2 / Biso mean: 49.5631 Å2 / Biso min: 17.36 Å2
Refinement stepCycle: final / Resolution: 2→49.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12712 0 163 721 13596
Biso mean--60.72 48.77 -
Num. residues----1674
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.02270.31162350.25714235
2.0227-2.04650.26492420.23854239
2.0465-2.07150.26582180.23144214
2.0715-2.09770.24712120.22144276
2.0977-2.12530.25692440.21944219
2.1253-2.15440.24692300.21434248
2.1544-2.18520.26972490.2114178
2.1852-2.21780.25492340.20494280
2.2178-2.25250.23162130.19834211
2.2525-2.28940.23882160.19464293
2.2894-2.32890.26032200.19354252
2.3289-2.37120.24852270.19514261
2.3712-2.41680.23092210.2034263
2.4168-2.46620.25352420.20024181
2.4662-2.51980.24372100.20224248
2.5198-2.57840.25782050.24302
2.5784-2.64290.27212100.20224256
2.6429-2.71430.26652260.20494281
2.7143-2.79420.27452270.20564231
2.7942-2.88440.24482090.19844275
2.8844-2.98750.24152030.20394291
2.9875-3.10710.23662050.20034292
3.1071-3.24840.24982010.1914287
3.2484-3.41970.2122170.18214289
3.4197-3.63390.19622310.17324278
3.6339-3.91430.18912340.16414258
3.9143-4.3080.21242100.14744313
4.308-4.93090.17042300.13724308
4.9309-6.21050.2092300.16824323
6.2105-49.5060.23352630.19184387
Refinement TLS params.Method: refined / Origin x: 22.257 Å / Origin y: 33.9878 Å / Origin z: 42.4481 Å
111213212223313233
T0.1897 Å2-0.0058 Å20.0237 Å2-0.2313 Å2-0.0226 Å2--0.2941 Å2
L0.326 °2-0.0971 °2-0.1306 °2-0.5439 °20.0772 °2--0.6749 °2
S-0.0058 Å °0.1226 Å °-0.0315 Å °-0.1485 Å °-0.025 Å °-0.0459 Å °0.0666 Å °0.0356 Å °0.0246 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA187 - 612
2X-RAY DIFFRACTION1allB187 - 612
3X-RAY DIFFRACTION1allC1 - 216
4X-RAY DIFFRACTION1allD2 - 211
5X-RAY DIFFRACTION1allE6 - 10
6X-RAY DIFFRACTION1allH1 - 217
7X-RAY DIFFRACTION1allL2 - 211
8X-RAY DIFFRACTION1allF1 - 746
9X-RAY DIFFRACTION1allG1802 - 3903

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