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Yorodumi- EMDB-31384: Cryo-EM (SPA) structure of human Nup155 Longer N-terminus (19-106... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31384 | |||||||||
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Title | Cryo-EM (SPA) structure of human Nup155 Longer N-terminus (19-1069) at 5.4 Angstrom resolution | |||||||||
Map data | Cryo-EM single particle analysis of human Nup155 Longer N-terminus (19-1069) | |||||||||
Sample |
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Keywords | Human Nucleoporin / 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 / 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 | |||||||||
Biological species | Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Niranjan S | |||||||||
Funding support | India, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31384.map.gz | 42.6 MB | EMDB map data format | |
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Header (meta data) | emd-31384-v30.xml emd-31384.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_31384.png | 95.6 KB | ||
Filedesc metadata | emd-31384.cif.gz | 6.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31384 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31384 | HTTPS FTP |
-Related structure data
Related structure data | 7eyqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31384.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM single particle analysis of human Nup155 Longer N-terminus (19-1069) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.823 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Purified human Nup155 protein
Entire | Name: Purified human Nup155 protein |
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Components |
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-Supramolecule #1: Purified human Nup155 protein
Supramolecule | Name: Purified human Nup155 protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP |
Molecular weight | Theoretical: 182 kDa/nm |
-Macromolecule #1: G protein/GFP fusion protein,Nuclear pore complex protein Nup155
Macromolecule | Name: G protein/GFP fusion protein,Nuclear pore complex protein Nup155 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Tissue: Kidney / Cell: Epithelial |
Molecular weight | Theoretical: 183.532594 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 LHLQDICPLL YST DDAICS KANELLQRSR QVQNKTEKER MLRESLKEYQ KISNQVDLSN VCAQYRQVRF YEGVVELSLT AAEKKDPQGL GLHF YKHGE PEEDIVGLQA FQERLNSYKC ITDTLQELVN QSKAAPQSPS VPKKPGPPVL SSDPNMLSNE EAGHHFEQML KLSQR SKDE LFSIALYNWL IQVDLADKLL QVASPFLEPH LVRMAKVDQN RVRYMDLLWR YYEKNRSFSN AARVLSRLAD MHSTEI SLQ QRLEYIARAI LSAKSSTAIS SIAADGEFLH ELEEKMEVAR IQLQIQETLQ RQYSHHSSVQ DAVSQLDSEL MDITKLY GE FADPFKLAEC KLAIIHCAGY SDPILVQTLW QDIIEKELSD SVTLSSSDRM HALSLKIVLL GKIYAGTPRF FPLDFIVQ F LEQQVCTLNW DVGFVIQTMN EIGVPLPRLL EVYDQLFKSR DPFWNRMKKP LHLLDCIHVL LIRYVENPSQ VLNCERRRF TNLCLDAVCG YLVELQSMSS SVAVQAITGN FKSLQAKLER LH UniProtKB: G protein/GFP fusion protein, Nuclear pore complex protein Nup155 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Buffer was freshly made. | ||||||||||||||||||
Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 3 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-46 / Average electron dose: 1.15 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 500000 |
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Startup model | Type of model: OTHER / Details: Nup155 Longer N-terminus structure (19-1069aa) |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v3.2.0) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v3.2.0) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.2.0) / Number images used: 37100 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7eyq: |