[English] 日本語
Yorodumi
- PDB-6vy4: Crystal structure of Hendra receptor binding protein head domain ... -

+
Open data


ID or keywords:

Loading...

-
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 / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more