[English] 日本語
Yorodumi
- PDB-3t97: Molecular Architecture of the Transport Channel of the Nuclear Po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t97
TitleMolecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup62/Nup54
Components
  • Nuclear pore complex protein Nup54
  • Nuclear pore glycoprotein p62
KeywordsPROTEIN TRANSPORT / nucleoporin / coiled-coil / nuclear pore complex / central transport channel / alpha helical proteins / triple helix / buried polar residues / structural proteins / nucleoporins / FG repeat / nucleocytoplasmic transport / Nup58 / Nup88 / Nup93 / karyopherin / nuclear envelope / nuclear pore membrane domain / central channel
Function / homology
Function and homology information


Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins ...Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / centriole assembly / positive regulation of centriole replication / regulation of protein import into nucleus / protein localization to nuclear inner membrane / positive regulation of mitotic cytokinetic process / Regulation of HSF1-mediated heat shock response / annulate lamellae / nuclear pore central transport channel / nuclear pore organization / positive regulation of protein localization to centrosome / negative regulation of Ras protein signal transduction / structural constituent of nuclear pore / Flemming body / mitotic centrosome separation / negative regulation of programmed cell death / RNA export from nucleus / centrosome cycle / nuclear thyroid hormone receptor binding / nucleocytoplasmic transport / PTB domain binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / negative regulation of epidermal growth factor receptor signaling pathway / kinesin binding / mRNA transport / protein targeting / nuclear pore / regulation of mitotic spindle organization / Hsp70 protein binding / positive regulation of mitotic nuclear division / SH2 domain binding / ubiquitin binding / Hsp90 protein binding / mitotic spindle / phospholipid binding / spindle pole / protein import into nucleus / cellular senescence / signaling receptor complex adaptor activity / nuclear envelope / spermatogenesis / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / ribonucleoprotein complex / negative regulation of cell population proliferation / centrosome / protein-containing complex binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Single helix bin / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 ...Single helix bin / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear pore glycoprotein p62 / Nuclear pore complex protein Nup54
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsChauhan, R. / Blobel, G. / Melcak, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Molecular architecture of the transport channel of the nuclear pore complex.
Authors: Solmaz, S.R. / Chauhan, R. / Blobel, G. / Melcak, I.
History
DepositionAug 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Feb 28, 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
B: Nuclear pore complex protein Nup54
C: Nuclear pore glycoprotein p62
A: Nuclear pore glycoprotein p62


Theoretical massNumber of molelcules
Total (without water)22,7003
Polymers22,7003
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-50 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.010, 62.350, 121.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Nuclear pore complex protein Nup54 / 54 kDa nucleoporin / Nucleoporin Nup54


Mass: 7624.819 Da / Num. of mol.: 1 / Fragment: UNP residues 346-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup54 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P70582
#2: Protein Nuclear pore glycoprotein p62 / 62 kDa nucleoporin / Nucleoporin Nup62


Mass: 7537.403 Da / Num. of mol.: 2 / Fragment: UNP residues 362-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup62 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL2(DE3)RIL / References: UniProt: P17955
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 18-22% PEG 4000,0.1M Tris-acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2008
RadiationMonochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 4819 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 70.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 41.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 329 / Rsym value: 0.244 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 888 -random
Rwork0.2353 ---
obs0.2305 4802 100 %-
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 0 29 1434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.102
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection
Rfree0.449 85
Rwork0.3291 -
obs-782

+
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