[English] 日本語
Yorodumi
- PDB-7eyq: Cryo-EM (SPA) structure of human Nup155 Longer N-terminus (19-106... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eyq
TitleCryo-EM (SPA) structure of human Nup155 Longer N-terminus (19-1069) at 5.4 Angstrom resolution
ComponentsG protein/GFP fusion protein,Nuclear pore complex protein Nup155
KeywordsNUCLEAR PROTEIN / Human Nucleoporin
Function / homology
Function and homology information


nuclear pore inner ring / protein localization to nuclear inner membrane / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / atrial cardiac muscle cell action potential / 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) / miRNA processing ...nuclear pore inner ring / protein localization to nuclear inner membrane / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / atrial cardiac muscle cell action potential / 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) / miRNA processing / 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 / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / SUMOylation of chromatin organization proteins / bioluminescence / HCMV Late Events / generation of precursor metabolites and energy / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / nuclear envelope / snRNP Assembly / nuclear membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / membrane / cytosol
Similarity search - Function
Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Green fluorescent protein, GFP / Green fluorescent protein-related ...Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
G protein/GFP fusion protein / Nuclear pore complex protein Nup155
Similarity search - Component
Biological speciesRecombinant vesicular stomatitis Indiana virus rVSV-G/GFP
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsNiranjan, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)(DBT/PR/26398) India
CitationJournal: To Be Published
Title: Cryo-EM (SPA) structure of human Nup155 Longer N-terminus (19-1069) at 5.4 Angstrom resolution
Authors: Niranjan, S.
History
DepositionMay 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: G protein/GFP fusion protein,Nuclear pore complex protein Nup155


Theoretical massNumber of molelcules
Total (without water)183,5331
Polymers183,5331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area43330 Å2

-
Components

#1: Protein G protein/GFP fusion protein,Nuclear pore complex protein Nup155 / 155 kDa nucleoporin / Nucleoporin Nup155


Mass: 183532.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human cell line
Source: (gene. exp.) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP, (gene. exp.) Homo sapiens (human)
Tissue: Kidney / Cell: Epithelial / Cell line: HEK293 / Gene: G, GFP, NUP155, KIAA0791 / Plasmid: pEGFP-C1 / Details (production host): Mammalian expression vector / Cell (production host): Epithelial / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / Tissue (production host): Kidney / References: UniProt: B7UCZ6, UniProt: O75694

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Purified human Nup155 protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 182 kDa/nm / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDOrganTissue
21Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP582817
31Homo sapiens (human)9606Kidneyembryonic cells
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Homo sapiens (human)9606
31Homo sapiens (human)9606Human embryonic kidney cell linepEGFP-C1
Buffer solutionpH: 7.5 / Details: Buffer was freshly made.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris-Cl1
2150 mMSodium ChlorideNaClSodium chloride1
30.05 mMn-Dodecyl-B-D-MaltosideDDM1
41 mMEthylenediamine tetraacetic acidEDTAEthylenediaminetetraacetic acid1
51 %GlycerolGlycerol1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: Blot for 3 seconds before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 1.15 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 50 / Used frames/image: 3-46

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
4RELION3.1-betaCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCv3.2.0initial Euler assignment
11cryoSPARCv3.2.0final Euler assignment
12cryoSPARCv3.2.0classification
13cryoSPARCv3.2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 500000
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37100 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 253.03 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01746703
ELECTRON MICROSCOPYf_angle_d1.25189072
ELECTRON MICROSCOPYf_chiral_restr0.1751033
ELECTRON MICROSCOPYf_plane_restr0.00721168
ELECTRON MICROSCOPYf_dihedral_angle_d27.43162503

+
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