[English] 日本語
Yorodumi
- PDB-4xzr: Structure of yeast importin a bound to the membrane protein Nucle... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xzr
TitleStructure of yeast importin a bound to the membrane protein Nuclear Localization Signal sequence of INM protein Heh1
Components
  • Importin subunit alpha
  • Inner nuclear membrane protein SRC1Nuclear envelope
KeywordsMEMBRANE PROTEIN/NUCLEAR PROTEIN / karyopherins / nuclear import / NLS / membrane proteins / MEMBRANE PROTEIN-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


proteasome localization / maintenance of rDNA / import into nucleus / establishment of mitotic sister chromatid cohesion / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear inner membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus ...proteasome localization / maintenance of rDNA / import into nucleus / establishment of mitotic sister chromatid cohesion / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear inner membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mitotic sister chromatid segregation / nuclear periphery / protein import into nucleus / disordered domain specific binding / nuclear envelope / membrane => GO:0016020 / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
HeH/LEM domain / HeH/LEM domain / MAN1, winged-helix domain / Man1/Src1, C-terminal / Man1-Src1p-C-terminal domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat ...HeH/LEM domain / HeH/LEM domain / MAN1, winged-helix domain / Man1/Src1, C-terminal / Man1-Src1p-C-terminal domain / 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 / Inner nuclear membrane protein SRC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsLokareddy, R.K. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074846 United States
CitationJournal: Structure / Year: 2015
Title: Distinctive Properties of the Nuclear Localization Signals of Inner Nuclear Membrane Proteins Heh1 and Heh2.
Authors: Lokareddy, R.K. / Hapsari, R.A. / van Rheenen, M. / Pumroy, R.A. / Bhardwaj, A. / Steen, A. / Veenhoff, L.M. / Cingolani, G.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inner nuclear membrane protein SRC1
B: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)53,2282
Polymers53,2282
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint4 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.682, 58.306, 95.372
Angle α, β, γ (deg.)90.00, 129.32, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Inner nuclear membrane protein SRC1 / Nuclear envelope / Helix-extension-helix domain-containing protein 1


Mass: 6366.884 Da / Num. of mol.: 1 / Fragment: unp resideus 170-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SRC1, HEH1, YML034W, YML033W / Production host: Escherichia coli (E. coli) / References: UniProt: Q03707
#2: Protein Importin subunit alpha / / Karyopherin subunit alpha / Karyopherin-60 / Serine-rich RNA polymerase I suppressor protein


Mass: 46861.562 Da / Num. of mol.: 1 / Fragment: unp residues 88-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SRP1, KAP60, YNL189W, N1606 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02821
#3: Water ChemComp-HOH / water / 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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM ammonium acetate, 20% PEG 8000, 100 mM BisTris

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 25906 / % possible obs: 98.9 % / Redundancy: 3.8 % / Net I/σ(I): 31.4

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1696)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.25→29.008 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.78 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 1294 5 %
Rwork0.1963 --
obs0.1973 25900 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→29.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 0 113 3546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033502
X-RAY DIFFRACTIONf_angle_d0.7924755
X-RAY DIFFRACTIONf_dihedral_angle_d11.8741326
X-RAY DIFFRACTIONf_chiral_restr0.026562
X-RAY DIFFRACTIONf_plane_restr0.004616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.241-2.33070.27791190.25552285X-RAY DIFFRACTION82
2.3307-2.43670.26441410.24232778X-RAY DIFFRACTION99
2.4367-2.56510.28061420.23952763X-RAY DIFFRACTION99
2.5651-2.72570.23631520.23412811X-RAY DIFFRACTION100
2.7257-2.9360.29191470.23452790X-RAY DIFFRACTION100
2.936-3.23110.2471440.23132790X-RAY DIFFRACTION99
3.2311-3.69780.23831500.20472784X-RAY DIFFRACTION99
3.6978-4.65580.1761480.16322770X-RAY DIFFRACTION98
4.6558-29.01050.17781510.16712835X-RAY DIFFRACTION98
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)
14.30082.3309-6.30471.922-3.77949.4418-0.45980.48170.1093-0.3436-0.378-0.14550.1598-0.56360.89440.83150.24470.19220.8409-0.09371.172946.942-19.47814.57
25.7626-5.9959-2.28656.25642.17893.162-0.0937-0.91450.52291.10570.38860.0555-0.4677-0.0625-0.14470.68970.10330.15610.9044-0.0350.690737.64-3.33921.445
32.14944.32162.22668.95723.22868.1175-0.18120.4311.49780.29850.04050.0871-0.52710.14040.28060.72470.109-0.1650.70810.01730.870727.40419.51323.358
44.525-0.6378-0.91233.50560.34613.3837-0.1647-0.64370.29890.42120.19720.1908-0.2873-0.3416-0.03780.37120.1043-0.01810.4343-0.02450.313317.98617.918.049
54.1776-1.37991.2241.5309-0.40192.0089-0.1043-0.7191-0.50660.19620.1534-0.01730.36160.0617-0.00190.39470.06540.02220.43650.08680.378151.016-12.00518.368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 173:176 )A173 - 176
2X-RAY DIFFRACTION2( CHAIN A AND RESID 177:191 )A177 - 191
3X-RAY DIFFRACTION3( CHAIN A AND RESID 192:197 )A192 - 197
4X-RAY DIFFRACTION4( CHAIN B AND RESID 87:251 )B87 - 251
5X-RAY DIFFRACTION5( CHAIN B AND RESID 252:509 )B252 - 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