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- PDB-7eye: Cryo-EM (SPA) structure of Nup155 N-terminus (19-863) at 5.1 Angs... -

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Basic information

Entry
Database: PDB / ID: 7eye
TitleCryo-EM (SPA) structure of Nup155 N-terminus (19-863) at 5.1 Angstrom resolution
ComponentsG protein/GFP fusion protein,Nuclear pore complex protein Nup155
KeywordsNUCLEAR PROTEIN / Human Nucleoporin 155
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 / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / nuclear pore / SUMOylation of DNA damage response and repair proteins / 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, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like ...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, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / 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: 5.1 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 Nup155 N-terminus (19-863) at 5.2 Angstrom resolution
Authors: Niranjan, S.
History
DepositionMay 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,9621
Polymers122,9621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35840 Å2

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Components

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


Mass: 122962.055 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 exprssion 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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Purified human Nup155 protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 122 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 ChlorideNaCl1
30.05 mMn-Dodecyl-B-D-MaltosideDDM1
41 mMEthylenediamine tetraacetic acidEDTA1
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

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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 FIELD / 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

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION3.1-betaCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 500000
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88595 / 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: 231.17 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00915535
ELECTRON MICROSCOPYf_angle_d1.48167507
ELECTRON MICROSCOPYf_chiral_restr0.0771864
ELECTRON MICROSCOPYf_plane_restr0.0093965
ELECTRON MICROSCOPYf_dihedral_angle_d28.31582040

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