[English] 日本語
Yorodumi
- PDB-8qxw: HCMV DNA polymerase processivity factor UL44 unphosphorylated NLS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qxw
TitleHCMV DNA polymerase processivity factor UL44 unphosphorylated NLS 410-433 bound to mouse importin alpha 2
Components
  • DNA polymerase processivity factor
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / importin / karyopherin / nuclear / nls
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / bidirectional double-stranded viral DNA replication / nuclear import signal receptor activity / DNA polymerase processivity factor activity / virion component / protein import into nucleus ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / bidirectional double-stranded viral DNA replication / nuclear import signal receptor activity / DNA polymerase processivity factor activity / virion component / protein import into nucleus / cytoplasmic stress granule / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA-binding transcription factor binding / symbiont-mediated suppression of host NF-kappaB cascade / DNA replication / postsynaptic density / host cell nucleus / glutamatergic synapse / DNA binding / nucleoplasm / cytosol
Similarity search - Function
Herpesvirus polymerase accessory protein / Herpesvirus polymerase accessory protein / 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. ...Herpesvirus polymerase accessory protein / Herpesvirus polymerase accessory protein / 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 / : / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
DNA polymerase processivity factor / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human betaherpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCross, E.M. / Marin, O. / Ariawan, D. / Aragao, D. / Cozza, G. / Di Iorio, E. / Forwood, J.K. / Alvisi, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs Lett. / Year: 2024
Title: Structural determinants of phosphorylation-dependent nuclear transport of HCMV DNA polymerase processivity factor UL44.
Authors: Cross, E.M. / Marin, O. / Ariawan, D. / Aragao, D. / Cozza, G. / Di Iorio, E. / Forwood, J.K. / Alvisi, G.
History
DepositionOct 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Importin subunit alpha-1
B: DNA polymerase processivity factor


Theoretical massNumber of molelcules
Total (without water)58,0052
Polymers58,0052
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-2 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.853, 90.062, 96.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 55268.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide DNA polymerase processivity factor / Polymerase accessory protein / PAP / Protein ICP36


Mass: 2736.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human betaherpesvirus 5 / References: UniProt: P16790
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate 0.65M, HEPES pH7.5, DTT 0.01M

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2→65.75 Å / Num. obs: 47035 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 40.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3420 / CC1/2: 0.637 / % possible all: 100

-
Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→59.33 Å / SU ML: 0.2388 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 2446 5.21 %
Rwork0.1911 44484 -
obs0.1927 46930 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.22 Å2
Refinement stepCycle: LAST / Resolution: 2→59.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 0 195 3490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01243375
X-RAY DIFFRACTIONf_angle_d1.13584600
X-RAY DIFFRACTIONf_chiral_restr0.0585556
X-RAY DIFFRACTIONf_plane_restr0.0104589
X-RAY DIFFRACTIONf_dihedral_angle_d4.987454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.37061210.3772522X-RAY DIFFRACTION97.53
2.04-2.080.32891410.31542587X-RAY DIFFRACTION99.89
2.08-2.130.33411480.28132596X-RAY DIFFRACTION99.89
2.13-2.180.28471410.26642587X-RAY DIFFRACTION99.89
2.18-2.240.30991560.25562547X-RAY DIFFRACTION99.93
2.24-2.310.29371520.22762611X-RAY DIFFRACTION99.86
2.31-2.380.23361390.21952586X-RAY DIFFRACTION99.96
2.38-2.470.22971200.19622601X-RAY DIFFRACTION99.85
2.47-2.570.23611430.19292600X-RAY DIFFRACTION99.82
2.57-2.690.22471470.19672606X-RAY DIFFRACTION100
2.69-2.830.24541360.21872621X-RAY DIFFRACTION99.89
2.83-30.25891490.23342627X-RAY DIFFRACTION100
3-3.240.25411500.20552605X-RAY DIFFRACTION99.93
3.24-3.560.22341420.19682655X-RAY DIFFRACTION100
3.56-4.080.21881460.16562642X-RAY DIFFRACTION100
4.08-5.140.15791570.1432689X-RAY DIFFRACTION100
5.14-59.330.18281580.162802X-RAY DIFFRACTION99.73

+
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