[English] 日本語
Yorodumi
- PDB-8g8q: RelB NLS in complex with Importin alpha 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g8q
TitleRelB NLS in complex with Importin alpha 2
Components
  • Importin subunit alpha-1
  • bacterial peptide
  • monopartite p52 NLS
KeywordsTRANSCRIPTION / Nuclear import / transcription factors / Nf-kB
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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule ...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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 ...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
Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTsimbslyuk, S. / Stewart, M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: p52 monopartite NLS in complex with Importin alpha 2
Authors: Tsimbslyuk, S. / Stewart, M. / Forwood, J.K.
History
DepositionFeb 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Importin subunit alpha-1
B: monopartite p52 NLS
C: bacterial peptide


Theoretical massNumber of molelcules
Total (without water)58,5953
Polymers58,5953
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.850, 88.755, 98.692
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 BL21(DE3) (bacteria) / References: UniProt: P52293
#2: Protein/peptide monopartite p52 NLS


Mass: 2579.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RELB / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein/peptide bacterial peptide


Mass: 746.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.01M DTT, 0.1M sodium HEPES pH7.5, 0.8.5M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→33.84 Å / Num. obs: 22000 / % possible obs: 98.39 % / Redundancy: 5.7 % / Biso Wilson estimate: 52.28 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.6 Å / Num. unique obs: 1053 / CC1/2: 0.636

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bw0

6bw0


Resolution: 2.6→19.86 Å / SU ML: 0.3472 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2099 974 5.08 %
Rwork0.1788 18182 -
obs0.1805 19156 88.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 0 31 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053442
X-RAY DIFFRACTIONf_angle_d0.78634679
X-RAY DIFFRACTIONf_chiral_restr0.0429560
X-RAY DIFFRACTIONf_plane_restr0.0064599
X-RAY DIFFRACTIONf_dihedral_angle_d13.10391279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.32591410.24852589X-RAY DIFFRACTION90.7
2.74-2.910.26231260.2152640X-RAY DIFFRACTION90.78
2.91-3.130.25561200.22632628X-RAY DIFFRACTION90.34
3.13-3.450.26531470.21332577X-RAY DIFFRACTION89.25
3.45-3.940.20071250.1792594X-RAY DIFFRACTION87.97
3.94-4.950.18121620.14822562X-RAY DIFFRACTION87.76
4.95-19.860.17511530.15282592X-RAY DIFFRACTION84.96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0104912977980.00674094117744-0.003232745636190.00810097540522-0.004491940842080.00326930745461-0.360386165829-0.181685218465-0.09942198013690.0867650813123-0.185734549493-0.254329408170.1920441062630.3651011173450.5015224778341.161545490140.0127858417616-0.0286860740931.412652650390.01034336174781.371211962952.9348577215932.12928904288.02970353543
21.45167714134-0.5624698028230.08189352138452.472781255231.044699606080.7368246578950.08777565151680.00645179535453-0.07971285070960.0970873395297-0.01085668582570.114942608030.09090987093410.00230966667486-0.06127706536170.462756331558-0.0234080817404-0.009383103897970.406924690369-0.004590472808530.3786954055814.416751886985.17618535744-15.2690288029
31.80628129068-1.00038145219-1.075730941360.9601569340530.71873694021.566267778980.131409381052-0.103783140670.297670362986-0.08100461547750.0998875157781-0.256920238772-0.1344136060880.1110568942-0.1401186244780.480508677528-0.01012809695660.02363811727990.471841871038-0.0474337138610.669029644625-7.2693952114233.08373081661.29165153619
41.673947485580.357101014952-0.5572154293023.486720381660.8453137474352.541155396160.0206808058802-0.936425344625-0.003783998393720.9449388263050.211813632652-0.6028001254080.2146460861460.603644608969-0.2407802702550.673603204410.0372337570417-0.1354334611960.921465218818-0.1351071454730.628416500556-6.585125799639.204080607125.7754792724
53.391210836810.785424254980.1814822976564.855460704382.116400951533.03732629416-0.06020788648790.1420984927920.4733036652070.437101548965-0.508594710978-0.1162878578410.266484818776-0.4785064914810.506703946640.645638529299-0.004115913542650.05687704297740.5594302697640.09380851949340.668896397838-0.7291038960446.2717165211-6.4945230991
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 337 through 341 )CD337 - 3411 - 5
22chain 'A' and (resid 72 through 279 )AA72 - 2791 - 208
33chain 'A' and (resid 280 through 390 )AA280 - 390209 - 319
44chain 'A' and (resid 391 through 497 )AA391 - 497320 - 426
55chain 'B' and (resid 335 through 342 )BB335 - 3421 - 8

+
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