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- EMDB-31383: Cryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31383
TitleCryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at 5.3 Angstroms resolution
Map dataCryo-EM SPA of Nup155 C-terminus
Sample
  • Organelle or cellular component: Purified Nup155 protein
    • Protein or peptide: Nuclear pore complex protein Nup155
KeywordsHuman Nucleoporin 155 / NUCLEAR PROTEIN
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear envelope organization / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / atrial cardiac muscle cell action potential / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / miRNA processing ...protein localization to nuclear inner membrane / nuclear envelope organization / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / atrial cardiac muscle cell action potential / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / 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 / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / protein import into nucleus / HCMV Early Events / 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, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsNiranjan S
Funding support India, 1 items
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, 2021-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31383.png

Downloads & links

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Map

FileDownload / File: emd_31383.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM SPA of Nup155 C-terminus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 240 pix.
= 197.52 Å		0.82 Å/pix.
x 240 pix.
= 197.52 Å		0.82 Å/pix.
x 240 pix.
= 197.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.823 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-4.220368 - 5.522048
Average (Standard dev.)0.0026566545 (±0.12596233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 197.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Purified Nup155 protein

EntireName: Purified Nup155 protein
Components
  • Organelle or cellular component: Purified Nup155 protein
    • Protein or peptide: Nuclear pore complex protein Nup155

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Supramolecule #1: Purified Nup155 protein

SupramoleculeName: Purified Nup155 protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: embryonic cells
Molecular weightTheoretical: 58 kDa/nm

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Macromolecule #1: Nuclear pore complex protein Nup155

MacromoleculeName: Nuclear pore complex protein Nup155 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Kidney / Cell: Epithelial
Molecular weightTheoretical: 60.58927 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PLLYSTDDAI CSKANELLQR SRQVQNKTEK ERMLRESLKE YQKISNQVDL SNVCAQYRQV RFYEGVVELS LTAAEKKDPQ GLGLHFYKH GEPEEDIVGL QAFQERLNSY KCITDTLQEL VNQSKAAPQS PSVPKKPGPP VLSSDPNMLS NEEAGHHFEQ M LKLSQRSK ...String:
PLLYSTDDAI CSKANELLQR SRQVQNKTEK ERMLRESLKE YQKISNQVDL SNVCAQYRQV RFYEGVVELS LTAAEKKDPQ GLGLHFYKH GEPEEDIVGL QAFQERLNSY KCITDTLQEL VNQSKAAPQS PSVPKKPGPP VLSSDPNMLS NEEAGHHFEQ M LKLSQRSK DELFSIALYN WLIQVDLADK LLQVASPFLE PHLVRMAKVD QNRVRYMDLL WRYYEKNRSF SNAARVLSRL AD MHSTEIS LQQRLEYIAR AILSAKSSTA ISSIAADGEF LHELEEKMEV ARIQLQIQET LQRQYSHHSS VQDAVSQLDS ELM DITKLY GEFADPFKLA ECKLAIIHCA GYSDPILVQT LWQDIIEKEL SDSVTLSSSD RMHALSLKIV LLGKIYAGTP RFFP LDFIV QFLEQQVCTL NWDVGFVIQT MNEIGVPLPR LLEVYDQLFK SRDPFWNRMK KPLHLLDCIH VLLIRYVENP SQVLN CERR RFTNLCLDAV CGYLVELQSM SSSVAVQAIT GNFKSLQAKL ERLH

UniProtKB: Nuclear pore complex protein Nup155

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris-ClTris
150.0 mMNaClSodium Chloride
0.05 mMDDMn-Dodecyl-B-D-Maltoside
1.0 mMEDTAEthylenediamine tetraacetic acid
1.0 %GlycerolGlycerol

Details: Buffer was freshly made.
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-46 / Average electron dose: 1.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 600000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5hb1


Details: Ct Nup170 Structure used to create homologous model of human Nup155
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 69538
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7eyf:
Cryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at 5.3 Angstroms resolution

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