[English] 日本語
Yorodumi
- PDB-3bg0: Architecture of a Coat for the Nuclear Pore Membrane -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bg0
TitleArchitecture of a Coat for the Nuclear Pore Membrane
Components
  • Nucleoporin NUP145
  • Protein SEC13 homolog
KeywordsPROTEIN TRANSPORT / HYDROLASE / NPC / Transport / WD repeat / Autocatalytic cleavage / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / RNA-binding / Translocation
Function / homology
Function and homology information


GATOR2 complex / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore central transport channel / nuclear pore localization / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / COPII-coated vesicle cargo loading / nuclear pore outer ring ...GATOR2 complex / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore central transport channel / nuclear pore localization / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / COPII-coated vesicle cargo loading / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / COPII vesicle coat / 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) / Amino acids regulate mTORC1 / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / COPII-mediated vesicle transport / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / nuclear localization sequence binding / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / subtelomeric heterochromatin formation / cellular response to nutrient levels / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of TORC1 signaling / Resolution of Sister Chromatid Cohesion / positive regulation of TORC1 signaling / MHC class II antigen presentation / SUMOylation of chromatin organization proteins / HCMV Late Events / RHO GTPases Activate Formins / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / intracellular protein transport / ER to Golgi transport vesicle membrane / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / double-strand break repair / nuclear envelope / snRNP Assembly / nuclear membrane / chromosome, telomeric region / hydrolase activity / lysosomal membrane / intracellular membrane-bounded organelle / structural molecule activity / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #690 / N-terminal domain of TfIIb - #170 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Sec13/Seh1 family / N-terminal domain of TfIIb / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #690 / N-terminal domain of TfIIb - #170 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Sec13/Seh1 family / N-terminal domain of TfIIb / 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 / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / Other non-globular / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP145 / Protein SEC13 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsHoelz, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Architecture of a coat for the nuclear pore membrane.
Authors: Hsia, K.C. / Stavropoulos, P. / Blobel, G. / Hoelz, A.
History
DepositionNov 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Protein SEC13 homolog
B: Nucleoporin NUP145
C: Nucleoporin NUP145
D: Protein SEC13 homolog
E: Protein SEC13 homolog
F: Nucleoporin NUP145
G: Nucleoporin NUP145
H: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)343,3468
Polymers343,3468
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein SEC13 homolog
B: Nucleoporin NUP145
C: Nucleoporin NUP145
D: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)171,6734
Polymers171,6734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
MethodPISA
3
E: Protein SEC13 homolog
F: Nucleoporin NUP145
G: Nucleoporin NUP145
H: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)171,6734
Polymers171,6734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13780 Å2
MethodPISA
4
A: Protein SEC13 homolog
B: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)85,8372
Polymers85,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
MethodPISA
5
C: Nucleoporin NUP145
D: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)85,8372
Polymers85,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
MethodPISA
6
E: Protein SEC13 homolog
F: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)85,8372
Polymers85,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
MethodPISA
7
G: Nucleoporin NUP145
H: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)85,8372
Polymers85,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.818, 216.575, 100.959
Angle α, β, γ (deg.)90.00, 108.11, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Protein SEC13 homolog / SEC13-related protein / SEC13-like protein 1


Mass: 34893.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC13, D3S1231E, SEC13L1, SEC13R / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: P55735
#2: Protein
Nucleoporin NUP145 / Nuclear pore protein NUP145


Mass: 50942.820 Da / Num. of mol.: 4 / Fragment: Nucleoporin NUP145C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP145, RAT10 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 294 K / pH: 7.7
Details: 16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→20 Å / Num. all: 63724 / Num. obs: 55955 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 %
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.746 / % possible all: 77.7

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 3.15→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.294 2837 4.5 %
Rwork0.252 --
obs0.252 55955 95.7 %
all-63724 -
Solvent computationBsol: 87.62 Å2
Displacement parametersBiso mean: 153.3 Å2
Baniso -1Baniso -2Baniso -3
1--36.438 Å20 Å2-1.652 Å2
2---43.02 Å20 Å2
3---79.458 Å2
Refinement stepCycle: LAST / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22566 0 0 0 22566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:PROTEIN_REP.PARAM

+
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