[English] 日本語
Yorodumi
- PDB-3jrp: SEC13 with NUP145C (AA109-179) insertion blade -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jrp
TitleSEC13 with NUP145C (AA109-179) insertion blade
ComponentsFUSION PROTEIN OF PROTEIN TRANSPORT PROTEIN SEC13 AND NUCLEOPORIN NUP145
KeywordsTRANSPORT PROTEIN / STRUCTURAL PROTEIN / PROTEIN COMPLEX / CYTOPLASMIC VESICLE / ENDOPLASMIC RETICULUM / ER-GOLGI TRANSPORT / MEMBRANE / MRNA TRANSPORT / NUCLEAR PORE COMPLEX / NUCLEUS / PROTEIN TRANSPORT / TRANSLOCATION / TRANSPORT / WD REPEAT / AUTOCATALYTIC CLEAVAGE / HYDROLASE / PHOSPHOPROTEIN / RNA-BINDING
Function / homology
Function and homology information


Seh1-associated complex / regulation of nucleocytoplasmic transport / COPII-coated vesicle budding / nuclear pore localization / nuclear pore central transport channel / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / positive regulation of ER to Golgi vesicle-mediated transport / regulation of TORC1 signaling / telomere tethering at nuclear periphery ...Seh1-associated complex / regulation of nucleocytoplasmic transport / COPII-coated vesicle budding / nuclear pore localization / nuclear pore central transport channel / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / positive regulation of ER to Golgi vesicle-mediated transport / regulation of TORC1 signaling / telomere tethering at nuclear periphery / nuclear pore outer ring / protein localization to nuclear inner membrane / nuclear pore cytoplasmic filaments / COPII vesicle coat / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / positive regulation of protein exit from endoplasmic reticulum / tRNA export from nucleus / structural constituent of nuclear pore / RNA export from nucleus / NLS-bearing protein import into nucleus / vacuolar membrane / nucleocytoplasmic transport / nuclear localization sequence binding / poly(A)+ mRNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / endoplasmic reticulum exit site / nuclear pore / subtelomeric heterochromatin formation / positive regulation of TOR signaling / mRNA transport / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / nuclear envelope / double-strand break repair / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / RNA binding
Similarity search - Function
Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Sec13/Seh1 family / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. ...Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Sec13/Seh1 family / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
Nucleoporin NUP145 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBrohawn, S.G. / Gogola, M. / Schwartz, T.U.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice.
Authors: Brohawn, S.G. / Schwartz, T.U.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 13, 2012Group: Other
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Sep 6, 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: FUSION PROTEIN OF PROTEIN TRANSPORT PROTEIN SEC13 AND NUCLEOPORIN NUP145


Theoretical massNumber of molelcules
Total (without water)41,7011
Polymers41,7011
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.280, 93.878, 55.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein FUSION PROTEIN OF PROTEIN TRANSPORT PROTEIN SEC13 AND NUCLEOPORIN NUP145


Mass: 41700.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q04491, UniProt: P49687
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M Tris, 22% PEG 4000, 0.25 M LiCl, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 11394 / Num. obs: 11148 / % possible obs: 97.84 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 63.6 Å2
Reflection shellResolution: 2.6→2.66 Å / % possible all: 96.9

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PM6

2pm6


Resolution: 2.6→35.717 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.779 / SU ML: 0.99 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1101 9.88 %Random
Rwork0.217 ---
obs0.221 11148 97.84 %-
all-11394 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.406 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 198.98 Å2 / Biso mean: 70.814 Å2 / Biso min: 22.86 Å2
Baniso -1Baniso -2Baniso -3
1--11.514 Å20 Å20 Å2
2--10.902 Å2-0 Å2
3---0.612 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 0 67 2687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032685
X-RAY DIFFRACTIONf_angle_d0.6793649
X-RAY DIFFRACTIONf_chiral_restr0.047408
X-RAY DIFFRACTIONf_plane_restr0.002454
X-RAY DIFFRACTIONf_dihedral_angle_d14.282935
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 (%)
2.6-2.7180.361410.291218135997
2.718-2.8620.3721250.2921234135998
2.862-3.0410.2571270.2641249137699
3.041-3.2750.311410.2341249139098
3.275-3.6050.2381510.2121238138999
3.605-4.1260.2391240.2051271139599
4.126-5.1950.1921430.1691269141297
5.195-35.720.2491490.2131319146896
Refinement TLS params.Method: refined / Origin x: -24.6989 Å / Origin y: -18.3084 Å / Origin z: 13.9571 Å
111213212223313233
T0.0938 Å20.0291 Å20.0121 Å2-0.0279 Å2-0.0375 Å2--0.1207 Å2
L2.6994 °20.079 °20.1872 °2-1.5426 °2-0.5001 °2--3.0147 °2
S0.0976 Å °-0.0849 Å °0.2225 Å °-0.0243 Å °-0.0282 Å °0.0748 Å °-0.1508 Å °-0.043 Å °-0.0089 Å °
Refinement TLS groupSelection details: NOT WATER

+
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