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- PDB-7eyf: Cryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at ... -

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Entry
Database: PDB / ID: 7eyf
TitleCryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at 5.3 Angstroms resolution
ComponentsNuclear pore complex protein Nup155
KeywordsNUCLEAR PROTEIN / Human Nucleoporin 155
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear pore inner ring / 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) / Transport of the SLBP independent Mature mRNA ...protein localization to nuclear inner membrane / nuclear pore inner ring / 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) / Transport of the SLBP independent Mature mRNA / miRNA processing / 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 / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / 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 / tRNA processing in the nucleus / RNA export from 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 / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / nuclear envelope / snRNP Assembly / nuclear membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / membrane / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Nuclear pore complex protein Nup155
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 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 C-terminus (864-1337) at 5.3 Angstroms 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: Nuclear pore complex protein Nup155


Theoretical massNumber of molelcules
Total (without water)60,5891
Polymers60,5891
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 area28920 Å2

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Components

#1: Protein Nuclear pore complex protein Nup155 / 155 kDa nucleoporin / Nucleoporin Nup155


Mass: 60589.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human cell line / Source: (gene. exp.) Homo sapiens (human) / Tissue: Kidney / Cell: Epithelial / Cell line: HEK293 / Gene: NUP155, KIAA0791 / Plasmid: pEGFP-C1 / Details (production host): Mammalian expression vector / Cell (production host): Epithelial / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / Tissue (production host): Kidney / References: 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 Nup155 protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 58 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: embryonic cells
Source (recombinant)Organism: Homo sapiens (human) / Cell: Human embryonic kidney cell line / Plasmid: pEGFP-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: 600000
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69538 / 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: 330.48 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00753911
ELECTRON MICROSCOPYf_angle_d1.40495290
ELECTRON MICROSCOPYf_chiral_restr0.0705593
ELECTRON MICROSCOPYf_plane_restr0.0095683
ELECTRON MICROSCOPYf_dihedral_angle_d27.76261491

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