[English] 日本語
Yorodumi
- PDB-6v3v: Assembly of VIQKI I456(beta-L-homoisoleucine)with human parainflu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v3v
TitleAssembly of VIQKI I456(beta-L-homoisoleucine)with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain
Components(Fusion glycoprotein F1) x 2
KeywordsVIRAL PROTEIN / Fusion glycoprotein / six-helix bundle / foldamer
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman parainfluenza 3 virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsOutlaw, V.K. / Gellman, S.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM122263 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI114736 United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Effects of Single alpha-to-beta Residue Replacements on Recognition of an Extended Segment in a Viral Fusion Protein.
Authors: Outlaw, V.K. / Kreitler, D.F. / Stelitano, D. / Porotto, M. / Moscona, A. / Gellman, S.H.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 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 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fusion glycoprotein F1
B: Fusion glycoprotein F1
C: Fusion glycoprotein F1
D: Fusion glycoprotein F1
E: Fusion glycoprotein F1
F: Fusion glycoprotein F1


Theoretical massNumber of molelcules
Total (without water)29,5966
Polymers29,5966
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Circular dichroism spectroscopy was used to identify the formation of this assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-120 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.340, 52.200, 56.660
Angle α, β, γ (deg.)90.000, 98.420, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Fusion glycoprotein F1


Mass: 5656.473 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Human parainfluenza 3 virus (strain Wash/47885/57)
References: UniProt: P06828
#2: Protein/peptide Fusion glycoprotein F1


Mass: 4208.922 Da / Num. of mol.: 3
Mutation: I456(beta-L-homoisoleucine), E459V, A463I, D466Q, Q479K, K480I
Source method: obtained synthetically
Source: (synth.) Human parainfluenza 3 virus (strain Wash/47885/57)
References: UniProt: P06828
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM HEPES/MOPS buffer (pH 7.5), 12.5% PEG1000, 12.5% PEG3350, 12.5% 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.17→28.02 Å / Num. obs: 12097 / % possible obs: 99.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 52.31 Å2 / CC1/2: 1 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Rsym value: 0.067 / Net I/σ(I): 15.31
Reflection shellResolution: 2.17→2.248 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 1195 / CC1/2: 0.521 / Rpim(I) all: 0.7275 / Rrim(I) all: 2.008 / Rsym value: 1.87 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NRO

6nro


Resolution: 2.17→28.02 Å / SU ML: 0.355 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.1648
RfactorNum. reflection% reflection
Rfree0.2875 1209 9.99 %
Rwork0.2406 --
obs0.2453 12097 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 76.63 Å2
Refinement stepCycle: LAST / Resolution: 2.17→28.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 0 10 1906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021905
X-RAY DIFFRACTIONf_angle_d0.39452568
X-RAY DIFFRACTIONf_chiral_restr0.0449322
X-RAY DIFFRACTIONf_plane_restr0.0028323
X-RAY DIFFRACTIONf_dihedral_angle_d16.5281720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.260.38771340.34951206X-RAY DIFFRACTION99.55
2.26-2.360.3311330.30171197X-RAY DIFFRACTION99.85
2.36-2.480.3231340.26761206X-RAY DIFFRACTION99.85
2.48-2.640.36711340.26171205X-RAY DIFFRACTION99.93
2.64-2.840.34861350.28261216X-RAY DIFFRACTION99.93
2.84-3.130.30541340.26191198X-RAY DIFFRACTION99.78
3.13-3.580.30371360.25221229X-RAY DIFFRACTION99.85
3.58-4.510.21671340.20131203X-RAY DIFFRACTION99.55
4.51-28.020.29281350.22981229X-RAY DIFFRACTION97.71
Refinement TLS params.Method: refined / Origin x: -7.73623289111 Å / Origin y: -6.0967237848 Å / Origin z: -6.92619532569 Å
111213212223313233
T0.368071503468 Å2-0.025864448399 Å2-0.0990838541886 Å2-0.303765453232 Å2-0.0107077533668 Å2--0.418098589603 Å2
L8.86443072928 °2-0.279332172346 °2-6.70749756555 °2-1.8482727899 °2-0.708322811816 °2--8.89782769175 °2
S0.110089078013 Å °-0.0267378127244 Å °0.196903887307 Å °-0.0458077974406 Å °-0.0879196464857 Å °-0.082515480059 Å °-0.046538479785 Å °0.393643386935 Å °-0.0520560465141 Å °
Refinement TLS groupSelection details: all

+
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