[English] 日本語
Yorodumi
- PDB-4xmm: Structure of the yeast coat nucleoporin complex, space group C2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xmm
TitleStructure of the yeast coat nucleoporin complex, space group C2
Components
  • Antibody 57 heavy chain
  • Antibody 57 light chain
  • Nucleoporin NUP120
  • Nucleoporin NUP145
  • Nucleoporin NUP84
  • Nucleoporin NUP85
  • Nucleoporin SEH1
  • Protein transport protein SEC13
KeywordsTransport Protein/Immune System / Structural protein / Immune System / Transport Protein-Immune System complex
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / COPII-mediated vesicle transport ...mRNA export from nucleus in response to heat stress / positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / COPII-mediated vesicle transport / regulation of TORC1 signaling / telomere tethering at nuclear periphery / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / COPII vesicle coat / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / SUMOylation of SUMOylation proteins / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / RNA export from nucleus / SUMOylation of chromatin organization proteins / vacuolar membrane / silent mating-type cassette heterochromatin formation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / mRNA transport / nuclear pore / subtelomeric heterochromatin formation / mRNA export from nucleus / ERAD pathway / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein export from nucleus / cell periphery / protein import into nucleus / nuclear envelope / double-strand break repair / protein transport / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding
Similarity search - Function
: / Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nucleoporin FG repeat / Nucleoporin FG repeat region ...: / Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Sec13/Seh1 family / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nucleoporin NUP120 / Nucleoporin NUP85 / Nucleoporin NUP145 / Nucleoporin NUP84 / Nucleoporin SEH1 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.384 Å
AuthorsStuwe, T. / Correia, A.R. / Lin, D.H. / Paduch, M. / Lu, V.T. / Kossiakoff, A.A. / Hoelz, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 T32 GM07616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM094588 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM087519 United States
CitationJournal: Science / Year: 2015
Title: Nuclear pores. Architecture of the nuclear pore complex coat.
Authors: Stuwe, T. / Correia, A.R. / Lin, D.H. / Paduch, M. / Lu, V.T. / Kossiakoff, A.A. / Hoelz, A.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Structure summary
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein transport protein SEC13
B: Nucleoporin NUP145
C: Nucleoporin SEH1
D: Nucleoporin NUP85
E: Nucleoporin NUP120
F: Nucleoporin NUP84
H: Antibody 57 heavy chain
L: Antibody 57 light chain


Theoretical massNumber of molelcules
Total (without water)454,6448
Polymers454,6448
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18810 Å2
ΔGint-131 kcal/mol
Surface area164350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.645, 186.297, 199.570
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 6 types, 6 molecules ABCDEF

#1: Protein Protein transport protein SEC13


Mass: 33082.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SEC13, ANU3, YLR208W, L8167.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04491
#2: Protein Nucleoporin NUP145 / Nuclear pore protein NUP145


Mass: 74618.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP145, RAT10, YGL092W / Production host: Escherichia coli (E. coli)
References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein Nucleoporin SEH1 / Nuclear pore protein SEH1 / SEC13 homolog 1


Mass: 39170.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SEH1, YGL100W / Production host: Escherichia coli (E. coli) / References: UniProt: P53011
#4: Protein Nucleoporin NUP85 / Nuclear pore protein NUP85


Mass: 81568.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP85, RAT9, YJR042W, J1624 / Production host: Escherichia coli (E. coli) / References: UniProt: P46673
#5: Protein Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 121577.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP120, RAT2, YKL057C, YKL313, YKL314 / Production host: Escherichia coli (E. coli) / References: UniProt: P35729
#6: Protein Nucleoporin NUP84 / Nuclear pore protein NUP84


Mass: 52059.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP84, YDL116W / Production host: Escherichia coli (E. coli) / References: UniProt: P52891

-
Antibody , 2 types, 2 molecules HL

#7: Antibody Antibody 57 heavy chain


Mass: 28977.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#8: Antibody Antibody 57 light chain


Mass: 23588.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 20000, ethanol, MES / PH range: 6.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 7.384→70 Å / Num. obs: 10375 / % possible obs: 99 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.3
Reflection shellResolution: 7.384→7.8 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 1.4 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1809)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IKO, 3F3F, 3F7F, and 3PGF

3iko

3f3f

3f7f

3pgf


Resolution: 7.384→67.516 Å / SU ML: 1.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3527 1022 9.99 %Random selection
Rwork0.3299 ---
obs0.3322 10227 99.47 %-
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7.384→67.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26139 0 0 0 26139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626637
X-RAY DIFFRACTIONf_angle_d1.21736184
X-RAY DIFFRACTIONf_dihedral_angle_d15.7619280
X-RAY DIFFRACTIONf_chiral_restr0.0514198
X-RAY DIFFRACTIONf_plane_restr0.0074616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.384-7.77250.39961420.39081265X-RAY DIFFRACTION98
7.7725-8.25860.37751450.36661325X-RAY DIFFRACTION100
8.2586-8.8950.37961450.3121298X-RAY DIFFRACTION100
8.895-9.78770.36381470.29641323X-RAY DIFFRACTION100
9.7877-11.19850.27921470.27761315X-RAY DIFFRACTION100
11.1985-14.08780.33381480.31991332X-RAY DIFFRACTION100
14.0878-67.51910.3821480.35981347X-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