[English] 日本語
Yorodumi
- PDB-5t94: Crystal structure of Kap60 bound to yeast RCC1 (Prp20) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t94
TitleCrystal structure of Kap60 bound to yeast RCC1 (Prp20)
Components
  • Guanine nucleotide exchange factor SRM1
  • Importin subunit alpha
KeywordsPROTEIN TRANSPORT / NUCLEAR PROTEIN / Nuclear Import / Importin alpha / RCC1 like Domain / RLD / NLS / PROTEIN TRANSPORT - NUCLEAR PROTEIN complex
Function / homology
Function and homology information


proteasome localization / response to pheromone / Postmitotic nuclear pore complex (NPC) reformation / import into nucleus / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / regulation of mitotic spindle assembly / nuclear import signal receptor activity / protein targeting to membrane ...proteasome localization / response to pheromone / Postmitotic nuclear pore complex (NPC) reformation / import into nucleus / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / regulation of mitotic spindle assembly / nuclear import signal receptor activity / protein targeting to membrane / poly(A)+ mRNA export from nucleus / nucleus organization / ribosomal subunit export from nucleus / regulation of mitotic cell cycle / guanyl-nucleotide exchange factor activity / protein import into nucleus / disordered domain specific binding / nuclear envelope / cell division / chromatin / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation (RCC1) repeat / : / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II ...Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation (RCC1) repeat / : / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Guanine nucleotide exchange factor SRM1 / Importin subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.631 Å
AuthorsSankhala, R.S. / Lokareddy, R.K. / Pumroy, R.A. / Cingolani, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074846 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
CitationJournal: Nat Commun / Year: 2017
Title: Three-dimensional context rather than NLS amino acid sequence determines importin alpha subtype specificity for RCC1.
Authors: Sankhala, R.S. / Lokareddy, R.K. / Begum, S. / Pumroy, R.A. / Gillilan, R.E. / Cingolani, G.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Database references
Category: citation / citation_author / pdbx_struct_assembly_auth_evidence
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 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine nucleotide exchange factor SRM1
B: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)113,5822
Polymers113,5822
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-2 kcal/mol
Surface area36180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.050, 99.200, 125.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer as determined by Gel filtration chromatography and further verified using small angle x-ray scattering method.

-
Components

#1: Protein Guanine nucleotide exchange factor SRM1 / Pheromone response pathway component SRM1 / Pre-mRNA-processing protein 20 / Regulator of ...Pheromone response pathway component SRM1 / Pre-mRNA-processing protein 20 / Regulator of chromosome condensation / Suppressor of receptor mutations 1 / mRNA transport protein 1


Mass: 53082.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ran guanyl-nucleotide exchange factor
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SRM1, MTR1, PRP20, YGL097W / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21827
#2: Protein Importin subunit alpha / Karyopherin subunit alpha / Karyopherin-60 / Serine-rich RNA polymerase I suppressor protein


Mass: 60499.043 Da / Num. of mol.: 1 / Mutation: T205A, D276E, K400R
Source method: isolated from a genetically manipulated source
Details: Yeast nuclear import adapter protein
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SRP1, KAP60, YNL189W, N1606 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q02821
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.49 Å3/Da / Density % sol: 50.52 % / Description: Large thick block
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na cacodylate, 0.1 M NaCl and 1.1 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.63→15 Å / Num. obs: 33934 / % possible obs: 96 % / Redundancy: 4.7 % / Biso Wilson estimate: 72.8 Å2 / Rsym value: 0.049 / Net I/σ(I): 49.9
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 3.4 / % possible all: 85.8

-
Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PVZ and 3OF7

4pvz

3of7


Resolution: 2.631→14.894 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.61
RfactorNum. reflection% reflection
Rfree0.2589 1540 4.89 %
Rwork0.2167 --
obs0.2188 31489 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 84.5 Å2
Refinement stepCycle: LAST / Resolution: 2.631→14.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 0 113 6921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026941
X-RAY DIFFRACTIONf_angle_d0.4969414
X-RAY DIFFRACTIONf_dihedral_angle_d14.9934210
X-RAY DIFFRACTIONf_chiral_restr0.0391063
X-RAY DIFFRACTIONf_plane_restr0.0041226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6311-2.71550.3944690.41181404X-RAY DIFFRACTION48
2.7155-2.8120.4641030.38772306X-RAY DIFFRACTION79
2.812-2.92370.39751370.36842822X-RAY DIFFRACTION96
2.9237-3.05570.40731230.32952842X-RAY DIFFRACTION97
3.0557-3.21530.36681320.29732910X-RAY DIFFRACTION99
3.2153-3.41450.30821650.25612882X-RAY DIFFRACTION99
3.4145-3.67440.26131520.21992923X-RAY DIFFRACTION99
3.6744-4.03750.23211540.18352894X-RAY DIFFRACTION99
4.0375-4.60650.18761630.15752945X-RAY DIFFRACTION100
4.6065-5.74770.21321820.17512956X-RAY DIFFRACTION99
5.7477-14.89390.22721600.17243065X-RAY DIFFRACTION99
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)
10.31390.50320.41911.03810.21860.5993-0.0554-0.7775-0.924-0.2215-0.0478-0.11970.3572-0.54160.0040.34170.04620.01870.5827-0.0120.476219.4398103.7229-0.9316
23.94640.2034-0.03372.7781-0.13582.4940.0829-0.6807-0.43520.3425-0.15060.10070.4757-0.1666-0.00460.29210.010.01650.55510.13040.229725.0257111.747114.666
35.13290.206-0.22454.01810.16192.9226-0.02310.59340.4264-0.2547-0.0517-0.2666-0.24480.2784-0.00570.1210.05980.01430.45660.06090.286437.7198124.17390.7874
42.87260.60411.672.79580.52652.33750.42250.6473-1.0869-0.14310.1098-0.15250.73830.1661-0.19390.5010.019-0.10070.4377-0.28440.61329.611995.806-13.9251
50.2184-0.1342-0.37391.5437-0.09240.72971.1589-1.1669-1.07570.0228-0.15860.09190.6256-0.94530.00831.068-0.772-0.55811.36050.42871.1945-32.397578.6453-14.2015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 331 )
3X-RAY DIFFRACTION3chain 'A' and (resid 332 through 482 )
4X-RAY DIFFRACTION4chain 'B' and (resid 88 through 284 )
5X-RAY DIFFRACTION5chain 'B' and (resid 285 through 509 )

+
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