[English] 日本語
Yorodumi- EMDB-31383: Cryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31383 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at 5.3 Angstroms resolution | |||||||||
Map data | Cryo-EM SPA of Nup155 C-terminus | |||||||||
Sample |
| |||||||||
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 / miRNA processing / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) ...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 / miRNA processing / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / 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 / RNA export from nucleus / 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 / 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 / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.3 Å | |||||||||
Authors | Niranjan S | |||||||||
Funding support | India, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Cryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at 5.3 Angstroms resolution Authors: Niranjan S | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_31383.map.gz | 26.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-31383-v30.xml emd-31383.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_31383.png | 93.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31383 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31383 | HTTPS FTP |
-Related structure data
Related structure data | 7eyfMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_31383.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM SPA of Nup155 C-terminus | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.823 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : Purified Nup155 protein
Entire | Name: Purified Nup155 protein |
---|---|
Components |
|
-Supramolecule #1: Purified Nup155 protein
Supramolecule | Name: 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 weight | Experimental: 58 kDa/nm |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: Human embryonic kidney cell line / Recombinant plasmid: pEGFP-C1 |
-Macromolecule #1: Nuclear pore complex protein Nup155
Macromolecule | Name: 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 weight | Theoretical: 60.58927 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
---|---|
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: 600000 |
---|---|
CTF correction | Software - Name: RELION (ver. 3.1-beta) |
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: Ct Nup170 Structure used to create homologous model of human Nup155 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 69538 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|---|
Output model | PDB-7eyf: |