[English] 日本語
Yorodumi
- PDB-3f7f: Structure of Nup120 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f7f
TitleStructure of Nup120
ComponentsNucleoporin NUP120
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / Nuclear Pore Complex / Macromolecular Assembly / Membrane Coat / Nucleocytoplasmic Transport / beta-propeller / alpha-helical solenoid domain / Coiled coil / mRNA transport / Nucleus / Protein transport / Translocation
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins ...mRNA export from nucleus in response to heat stress / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / ribosomal large subunit export from nucleus / nuclear pore / subtelomeric heterochromatin formation / mRNA export from nucleus / protein export from nucleus / protein import into nucleus / nuclear envelope / double-strand break repair / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding
Similarity search - Function
: / Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup120/160
Similarity search - Domain/homology
: / Nucleoporin NUP120
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsSeo, H.S. / Ma, Y. / Debler, E.W. / Blobel, G. / Hoelz, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex.
Authors: Seo, H.S. / Ma, Y. / Debler, E.W. / Wacker, D. / Kutik, S. / Blobel, G. / Hoelz, A.
History
DepositionNov 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoporin NUP120
B: Nucleoporin NUP120
C: Nucleoporin NUP120
D: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,93016
Polymers335,5234
Non-polymers2,40712
Water00
1
A: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4824
Polymers83,8811
Non-polymers6023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4824
Polymers83,8811
Non-polymers6023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4824
Polymers83,8811
Non-polymers6023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4824
Polymers83,8811
Non-polymers6023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Nucleoporin NUP120
B: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,9658
Polymers167,7612
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-32.6 kcal/mol
Surface area59970 Å2
MethodPISA
6
C: Nucleoporin NUP120
hetero molecules

D: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,9658
Polymers167,7612
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3050 Å2
ΔGint-32.9 kcal/mol
Surface area59900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.680, 117.478, 146.287
Angle α, β, γ (deg.)89.94, 89.77, 89.89
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 83880.680 Da / Num. of mol.: 4 / Fragment: UNP residues 1-729 / Mutation: S207C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP120, RAT2, YKL057C, YKL314, YKL313 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL / References: UniProt: P35729
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Hg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Succinic acid, PEG 3350, Sodium bromide, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0049
SYNCHROTRONAPS 23-ID-D21.0049
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 26, 2008
ADSC QUANTUM 3152CCDJul 26, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.0049 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 217205 / Num. obs: 208082 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.041
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 21664 / Rsym value: 0.417 / % possible all: 81

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.254 18489
Rwork0.232 -
all0.232 190898
obs0.232 190898
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22864 0 12 0 22876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3

+
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