[English] 日本語
Yorodumi
- PDB-6bw9: Hendra virus W protein C-terminus in complex with Importin alpha ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bw9
TitleHendra virus W protein C-terminus in complex with Importin alpha 3 crystal form 1
Components
  • Importin subunit alpha-3
  • Protein W
KeywordsTRANSPORT PROTEIN / Complex / Hendra virus / Importin / Karyopherin / phosphoprotein / W
Function / homology
Function and homology information


response to leptomycin B / dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / nuclear pore / male germ cell nucleus / response to hydrogen peroxide ...response to leptomycin B / dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / nuclear pore / male germ cell nucleus / response to hydrogen peroxide / ISG15 antiviral mechanism / protein import into nucleus / nuclear membrane / gene expression / amyloid fibril formation / host cell nucleus / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-3 / Protein W
Similarity search - Component
Biological speciesHomo sapiens (human)
Hendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsTsimbalyuk, S. / Smith, K.M. / Edwards, M.R. / Aragao, D. / Cross, E.M. / Basler, C.F. / Forwood, J.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for importin alpha 3 specificity of W proteins in Hendra and Nipah viruses.
Authors: Smith, K.M. / Tsimbalyuk, S. / Edwards, M.R. / Cross, E.M. / Batra, J. / Soares da Costa, T.P. / Aragao, D. / Basler, C.F. / Forwood, J.K.
History
DepositionDec 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 29, 2023Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Importin subunit alpha-3
B: Protein W


Theoretical massNumber of molelcules
Total (without water)55,0422
Polymers55,0422
Non-polymers00
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-11 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.430, 65.740, 74.190
Angle α, β, γ (deg.)90.00, 99.76, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Importin subunit alpha-3 / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


Mass: 50325.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00629
#2: Protein/peptide Protein W


Mass: 4715.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus / Gene: P/V/C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0C1C6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium citrate pH 5.0, 20% w/v PEG 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→19.84 Å / Num. obs: 58984 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.989 / Rpim(I) all: 0.061 / Net I/σ(I): 7.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2917 / CC1/2: 0.899 / Rpim(I) all: 0.174 / % possible all: 99.6

-
Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.6→19.578 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.19
RfactorNum. reflection% reflection
Rfree0.1963 2894 4.91 %
Rwork0.1713 --
obs0.1725 58886 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 338 3738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153464
X-RAY DIFFRACTIONf_angle_d1.2164729
X-RAY DIFFRACTIONf_dihedral_angle_d19.8571272
X-RAY DIFFRACTIONf_chiral_restr0.069568
X-RAY DIFFRACTIONf_plane_restr0.009615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62620.23911340.20562666X-RAY DIFFRACTION99
1.6262-1.65420.24591280.1922645X-RAY DIFFRACTION99
1.6542-1.68430.25391440.19112660X-RAY DIFFRACTION99
1.6843-1.71670.21351620.17732604X-RAY DIFFRACTION99
1.7167-1.75170.19481330.17792652X-RAY DIFFRACTION99
1.7517-1.78980.2241210.17112650X-RAY DIFFRACTION100
1.7898-1.83140.20251440.17252716X-RAY DIFFRACTION99
1.8314-1.87710.17321510.17622604X-RAY DIFFRACTION100
1.8771-1.92790.21441280.17012706X-RAY DIFFRACTION100
1.9279-1.98450.20321390.16452675X-RAY DIFFRACTION100
1.9845-2.04850.20261290.16772669X-RAY DIFFRACTION100
2.0485-2.12160.16681220.16662683X-RAY DIFFRACTION100
2.1216-2.20650.20741530.16312678X-RAY DIFFRACTION100
2.2065-2.30680.19471450.16452672X-RAY DIFFRACTION100
2.3068-2.42820.19291490.16672648X-RAY DIFFRACTION100
2.4282-2.580.21441290.16752671X-RAY DIFFRACTION100
2.58-2.77870.20491430.1782703X-RAY DIFFRACTION100
2.7787-3.05740.20341260.17722667X-RAY DIFFRACTION99
3.0574-3.49760.16311390.17382712X-RAY DIFFRACTION100
3.4976-4.39830.18491220.15562709X-RAY DIFFRACTION99
4.3983-19.5790.18651530.17852602X-RAY DIFFRACTION95

+
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