[English] 日本語
Yorodumi
- PDB-4jo9: Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex 1:... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jo9
TitleCrystal structure of the human Nup49CCS2+3* Nup57CCS3* complex 1:2 stoichiometry
Components
  • Nucleoporin p54
  • Nucleoporin p58/p45
KeywordsTRANSPORT PROTEIN / nucleocytoplasmic transport
Function / homology
Function and homology information


regulation of protein import into nucleus / protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / 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 ...regulation of protein import into nucleus / protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / 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 / NLS-bearing protein import into nucleus / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / protein targeting / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / nuclear envelope / protein transport / snRNP Assembly / nuclear membrane / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / identical protein binding
Similarity search - Function
Helix Hairpins - #1350 / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin p58/p45 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Nucleoporin p54 / Nucleoporin p58/p45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsStuwe, T. / Bley, C.J. / Mayo, D.J. / Hoelz, A.
CitationJournal: Science / Year: 2015
Title: Architecture of the fungal nuclear pore inner ring complex.
Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / ...Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / Koide, A. / Lu, V. / Fischer, J. / Hurt, E. / Koide, S. / Kossiakoff, A.A. / Hoelz, A.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Structure summary
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Nucleoporin p54
B: Nucleoporin p58/p45
C: Nucleoporin p54


Theoretical massNumber of molelcules
Total (without water)19,6543
Polymers19,6543
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-37 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.483, 55.483, 191.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein/peptide Nucleoporin p54 / Nup54 / 54 kDa nucleoporin


Mass: 4729.410 Da / Num. of mol.: 2 / Fragment: UNP residues 453-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP54 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3B4
#2: Protein Nucleoporin p58/p45 / Nup58 / Nucleoporin-like protein 1


Mass: 10195.580 Da / Num. of mol.: 1 / Fragment: UNP residues 341-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUPL1, KIAA0410 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BVL2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 3.8
Details: 0.1 M sodium citrate, pH 3.8, 0.07 M calcium chloride, VAPOR DIFFUSION, temperature 294.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 7, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. all: 11003 / Num. obs: 11003 / % possible obs: 98.8 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Biso Wilson estimate: 46.29 Å2
Reflection shellHighest resolution: 2.499 Å

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.499→47.79 Å / Occupancy max: 1 / Occupancy min: 0.51 / FOM work R set: 0.678 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 35.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 1092 10.03 %
Rwork0.2465 --
obs0.2513 10891 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.2 Å2 / Biso mean: 86.2208 Å2 / Biso min: 39.04 Å2
Refinement stepCycle: LAST / Resolution: 2.499→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 17 1355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021356
X-RAY DIFFRACTIONf_angle_d0.4371822
X-RAY DIFFRACTIONf_chiral_restr0.028206
X-RAY DIFFRACTIONf_plane_restr0.001234
X-RAY DIFFRACTIONf_dihedral_angle_d14.845524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.499-2.61280.46631210.34811088120990
2.6128-2.75050.39121330.30921186131999
2.7505-2.92280.35321360.28751205134199
2.9228-3.14840.33981340.27151203133799
3.1484-3.46520.30061360.267212301366100
3.4652-3.96640.26531390.222812501389100
3.9664-4.99640.21051400.195912621402100
4.9964-47.79870.30831530.25313751528100

+
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