[English] 日本語
Yorodumi
- PDB-4ycz: Y-COMPLEX HUB (NUP85-NUP120-NUP145C-SEC13 COMPLEX) FROM M. THERMO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ycz
TitleY-COMPLEX HUB (NUP85-NUP120-NUP145C-SEC13 COMPLEX) FROM M. THERMOPHILA (A.K.A. T. HETEROTHALLICA)
Components
  • Fusion Protein of Sec13 and Nup145C
  • Nup120
  • Nup85
KeywordsSTRUCTURAL PROTEIN / Structural Protein Complex / Nuclear Pore Complex / Macromolecular Assemblies
Function / homology
Function and homology information


macromolecule localization / structural constituent of nuclear pore / nucleocytoplasmic transport / mRNA transport / nuclear pore / protein transport / nuclear membrane / structural molecule activity
Similarity search - Function
Nucleoporin Nup120/160 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Quinoprotein alcohol dehydrogenase-like superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Nucleoporin Nup120/160 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Quinoprotein alcohol dehydrogenase-like superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Nuclear pore complex protein Nup85 / Protein transport protein SEC13 / Nuclear pore complex protein NUP96 C-terminal domain-containing protein
Similarity search - Component
Biological speciesThielavia heterothallica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.1 Å
AuthorsKelley, K. / Knockenhauer, K.E. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077537 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Atomic structure of the Y complex of the nuclear pore.
Authors: Kelley, K. / Knockenhauer, K.E. / Kabachinski, G. / Schwartz, T.U.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 27, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fusion Protein of Sec13 and Nup145C
B: Nup85
C: Nup120


Theoretical massNumber of molelcules
Total (without water)234,4833
Polymers234,4833
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-42 kcal/mol
Surface area77250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.984, 212.022, 170.643
Angle α, β, γ (deg.)90.00, 107.21, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Fusion Protein of Sec13 and Nup145C


Mass: 96425.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia heterothallica (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2306744, MYCTH_2306912 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-LOBSTR / References: UniProt: G2QES5, UniProt: G2QEZ2
#2: Protein Nup85


Mass: 103380.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia heterothallica (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2059413 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-LOBSTR / References: UniProt: G2Q7J4
#3: Protein Nup120


Mass: 34677.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia heterothallica (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2296711 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-LOBSTR / References: UniProt: G2Q2S2
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.23
Details: 50mM Tris-HCL pH 8.23, 0.7M Ammonium Sulfate, 20mM EDTA

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 4.1→163 Å / Num. obs: 53692 / % possible obs: 98.2 % / Redundancy: 6.1 % / Rsym value: 0.19 / Net I/σ(I): 8.9
Reflection shellResolution: 4.1→4.25 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.9 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1951)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 4.1→163 Å / SU ML: 0.81 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 42.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3583 1975 7.24 %Random selection
Rwork0.3189 ---
obs0.3218 53648 97.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10051 0 0 0 10051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210226
X-RAY DIFFRACTIONf_angle_d0.6414023
X-RAY DIFFRACTIONf_dihedral_angle_d9.0033054
X-RAY DIFFRACTIONf_chiral_restr0.0271757
X-RAY DIFFRACTIONf_plane_restr0.0041756

+
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