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- EMDB-31382: Cryo-EM (SPA) structure of Nup155 N-terminus (19-863) at 5.1 Angs... -

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Basic information

Entry
Database: EMDB / ID: EMD-31382
TitleCryo-EM (SPA) structure of Nup155 N-terminus (19-863) at 5.1 Angstrom resolution
Map dataSingle particle Cryo-EM structure of N-terminus
Sample
  • Organelle or cellular component: Purified human Nup155 protein
    • Protein or peptide: G protein/GFP fusion protein,Nuclear pore complex protein Nup155
KeywordsHuman Nucleoporin 155 / NUCLEAR PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 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 Nup155 N-terminus (19-863) at 5.2 Angstrom 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_31382.png

Downloads & links

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Map

FileDownload / File: emd_31382.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle particle Cryo-EM structure of N-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: 0.37
Minimum - Maximum-2.91403 - 6.639228
Average (Standard dev.)0.001083501 (±0.14380386)
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 human Nup155 protein

EntireName: Purified human Nup155 protein
Components
  • Organelle or cellular component: Purified human Nup155 protein
    • Protein or peptide: G protein/GFP fusion protein,Nuclear pore complex protein Nup155

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Supramolecule #1: Purified human Nup155 protein

SupramoleculeName: Purified human Nup155 protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP
Molecular weightTheoretical: 122 kDa/nm

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Macromolecule #1: G protein/GFP fusion protein,Nuclear pore complex protein Nup155

MacromoleculeName: G protein/GFP fusion protein,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: 122.962055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSKGEELFT GVVPILVELD GDVNGHKFSV SGEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAM PEGYVQERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK N GIKVNFKI ...String:
MVSKGEELFT GVVPILVELD GDVNGHKFSV SGEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAM PEGYVQERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK N GIKVNFKI RHNIEDGSVQ LADHYQQNTP IGDGPVLLPD NHYLSTQSAL SKDPNEKRDH MVLLEFVTAA GITLGMDELY KS GLRSRAQ ASNSMPSSLL GAAMPASTSA AALQEALENA GRLIDRQLQE DRMYPDLSEL LMVSAPNNPT VSGMSDMDYP LQG PGLLSV PNLPEISSIR RVPLPPELVE QFGHMQCNCM MGVFPPISRA WLTIDSDIFM WNYEDGGDLA YFDGLSETIL AVGL VKPKA GIFQPHVRHL LVLATPVDIV ILGLSYANLQ TGSGVLNDSL SGGMQLLPDP LYSLPTDNTY LLTITSTDNG RIFLA GKDG CLYEVAYQAE AGWFSQRCRK INHSKSSLSF LVPSLLQFTF SEDDPILQIA IDNSRNILYT RSEKGVIQVY DLGQDG QGM SRVASVSQNA IVSAAGNIAR TIDRSVFKPI VQIAVIENSE SLDCQLLAVT HAGVRLYFST CPFRQPLARP NTLTLVH VR LPPGFSASST VEKPSKVHRA LYSKGILLMA ASENEDNDIL WCVNHDTFPF QKPMMETQMT AGVDGHSWAL SAIDELKV D KIITPLNKDH IPITDSPVVV QQHMLPPKKF VLLSAQGSLM FHKLRPVDQL RHLLVSNVGG DGEEIERFFK LHQEDQACA TCLILACSTA ACDREVSAWA TRAFFRYGGE AQMRFPTTLP PPSNVGPILG SPVYSSSPVP SGSPYPNPSF LGTPSHGIQP PAMSTPVCA LGNPATQATN MSCVTGPEIV YSGKHNGICI YFSRIMGNIW DASLVVERIF KSGNREITAI ESSVPCQLLE S VLQELKGL QEFLDRNSQF AGGPLGNPNT TAKVQQRLIG FMRPENGNPQ QMQQELQRKF HEAQLSEKIS LQAIQQLVRK SY QALALWK LLCEHQFTII VAELQKELQE QLKITTFKDL VIRDKELTGA LIASLINCYI RDNAAVDGIS LHLQDIC

UniProtKB: G protein/GFP fusion protein, 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: 500000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5hax


Details: Ct Nup170 Structure used to create homologous model for human Nup155
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 88595
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-7eye:
Cryo-EM (SPA) structure of Nup155 N-terminus (19-863) at 5.1 Angstrom resolution

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