[English] 日本語
Yorodumi
- PDB-4ga0: Structure of the N-terminal domain of Nup358 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ga0
TitleStructure of the N-terminal domain of Nup358
ComponentsE3 SUMO-protein ligase RanBP2
KeywordsTRANSPORT PROTEIN / TPR motif / Nuclear pore complex component Nucleocytoplasmic transport
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Transferases; Acyltransferases; Aminoacyltransferases / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / regulation of gluconeogenesis / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / protein sumoylation / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / GTPase activator activity / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Signaling by ALK fusions and activated point mutants / ISG15 antiviral mechanism / small GTPase binding / HCMV Early Events / Separation of Sister Chromatids / protein folding / nuclear envelope / snRNP Assembly / nuclear membrane / intracellular membrane-bounded organelle / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Tetratricopeptide repeat domain ...Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Tetratricopeptide repeat domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
E3 SUMO-protein ligase RanBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsKassube, S.A. / Lin, D.H. / Stuwe, T. / Hoelz, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal structure of the N-terminal domain of Nup358/RanBP2.
Authors: Kassube, S.A. / Stuwe, T. / Lin, D.H. / Antonuk, C.D. / Napetschnig, J. / Blobel, G. / Hoelz, A.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 SUMO-protein ligase RanBP2


Theoretical massNumber of molelcules
Total (without water)17,3551
Polymers17,3551
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.219, 82.768, 29.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein E3 SUMO-protein ligase RanBP2 / 358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding ...358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding protein 2 / RanBP2 / p270 / Putative peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 17354.885 Da / Num. of mol.: 1 / Fragment: unp residues 1-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P49792
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 18 % (w/v) PEG 3350 200 mM lithium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.15→48.2 Å / Num. obs: 50246 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.32 Å2 / Rsym value: 0.045 / Net I/σ(I): 25.4
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.787 / % possible all: 76.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GA2

4ga2


Resolution: 1.15→48.161 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.13 / σ(F): 1.33 / Phase error: 42.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 2565 5.11 %
Rwork0.2144 --
obs0.2157 50201 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1817 Å2
Refinement stepCycle: LAST / Resolution: 1.15→48.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 0 85 1256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061418
X-RAY DIFFRACTIONf_angle_d1.1231918
X-RAY DIFFRACTIONf_dihedral_angle_d15.238557
X-RAY DIFFRACTIONf_chiral_restr0.057201
X-RAY DIFFRACTIONf_plane_restr0.005250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.17210.4247780.4131983X-RAY DIFFRACTION72
1.1721-1.19610.34761250.31842237X-RAY DIFFRACTION82
1.1961-1.22210.32041250.30922457X-RAY DIFFRACTION90
1.2221-1.25050.40121530.36772594X-RAY DIFFRACTION96
1.2505-1.28180.41181440.40462431X-RAY DIFFRACTION90
1.2818-1.31640.32731450.32932633X-RAY DIFFRACTION97
1.3164-1.35520.30021510.24082758X-RAY DIFFRACTION100
1.3552-1.39890.31861380.29072647X-RAY DIFFRACTION97
1.3989-1.44890.3171600.24342726X-RAY DIFFRACTION100
1.4489-1.50690.29481350.24852731X-RAY DIFFRACTION99
1.5069-1.57550.23191530.21052748X-RAY DIFFRACTION99
1.5755-1.65860.20871470.17742765X-RAY DIFFRACTION100
1.6586-1.76250.22931610.192740X-RAY DIFFRACTION100
1.7625-1.89860.24031390.19472785X-RAY DIFFRACTION100
1.8986-2.08970.23811480.20242782X-RAY DIFFRACTION99
2.0897-2.3920.21711370.18482805X-RAY DIFFRACTION100
2.392-3.01370.20681510.20482860X-RAY DIFFRACTION100
3.0137-48.20350.23561750.21332954X-RAY DIFFRACTION99

+
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