[English] 日本語
Yorodumi- PDB-5uwr: Crystal Structure of CDC7 NES Peptide (extended) in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uwr | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of CDC7 NES Peptide (extended) in complex with CRM1-Ran-RanBP1 | ||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||
Keywords | PROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin | ||||||||||||||||||||||||
Function / homology | Function and homology information positive regulation of nuclear cell cycle DNA replication / Transcriptional and post-translational regulation of MITF-M expression and activity / cell cycle phase transition / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus ...positive regulation of nuclear cell cycle DNA replication / Transcriptional and post-translational regulation of MITF-M expression and activity / cell cycle phase transition / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / tRNA export from nucleus / Activation of the pre-replicative complex / protein localization to kinetochore / SUMOylation of RNA binding proteins / double-strand break repair via break-induced replication / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMOylation of chromatin organization proteins / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / Activation of ATR in response to replication stress / spindle pole body / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / intercellular bridge / positive regulation of G2/M transition of mitotic cell cycle / MAPK6/MAPK4 signaling / Transcriptional Regulation by E2F6 / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / male germ cell nucleus / ribosomal subunit export from nucleus / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / centriole / viral process / protein export from nucleus / GTPase activator activity / mitotic spindle organization / G protein activity / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G1/S transition of mitotic cell cycle / recycling endosome / mitotic spindle / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / nuclear envelope / GDP binding / melanosome / positive regulation of protein binding / kinase activity / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein domain specific binding / protein heterodimerization activity / cell division / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / GTPase activity / positive regulation of cell population proliferation / chromatin / nucleolus / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / signal transduction / protein-containing complex / RNA binding / extracellular exosome Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||||||||||||||||||||
Authors | Fung, H.Y.J. / Chook, Y.M. | ||||||||||||||||||||||||
Funding support | United States, Hong Kong, 7items
| ||||||||||||||||||||||||
Citation | Journal: Elife / Year: 2017 Title: Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals. Authors: Fung, H.Y. / Fu, S.C. / Chook, Y.M. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5uwr.cif.gz | 818.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5uwr.ent.gz | 681.5 KB | Display | PDB format |
PDBx/mmJSON format | 5uwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uwr_validation.pdf.gz | 796.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5uwr_full_validation.pdf.gz | 802 KB | Display | |
Data in XML | 5uwr_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 5uwr_validation.cif.gz | 72.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/5uwr ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uwr | HTTPS FTP |
-Related structure data
Related structure data | 5uwhC 5uwiC 5uwjC 5uwoC 5uwpC 5uwqC 5uwsC 5uwtC 5uwuC 5uwwC 4hb2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 26758.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826 |
---|---|
#2: Protein | Mass: 16521.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920 |
#3: Protein | Mass: 117458.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGex-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822 |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 3019.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC7, CDC7L1 / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00311 |
---|
-Non-polymers , 5 types, 528 molecules
#5: Chemical | ChemComp-GNP / | ||||
---|---|---|---|---|---|
#6: Chemical | ChemComp-MG / | ||||
#7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.84 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 17% PEG3350, 100 mM Bis-Tris, pH 6.4, 200 mM ammonium nitrate, 10 mM spermine-HCl |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 84118 / % possible obs: 99.4 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.24→2.28 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4085 / Num. unique obs: 4085 / CC1/2: 0.384 / Rpim(I) all: 0.503 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4HB2 Resolution: 2.24→47.443 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→47.443 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|