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Yorodumi- PDB-4jlq: Crystal structure of human Karyopherin-beta2 bound to the PY-NLS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jlq | |||||||||
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Title | Crystal structure of human Karyopherin-beta2 bound to the PY-NLS of Saccharomyces cerevisiae NAB2 | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / HEAT REPEATS / KARYOPHERIN / NUCLEAR IMPORT / PROTEINTRANSPORT / IMPORTIN / TRANSPORTIN / NLS / NAB2 / Structural genomics / NUCLEOCYTOPLASMIC TRANSPORT: A TARGET FOR CELLULAR CONTROL (NPCXSTALS) / New York Structural Genomics Research Consortium (NYSGRC) / PSI-Biology / NPCXstals | |||||||||
Function / homology | Function and homology information ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / 7S RNA binding / poly(A) binding / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of transcription by RNA polymerase III / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus ...ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / 7S RNA binding / poly(A) binding / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of transcription by RNA polymerase III / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / regulation of mRNA stability / cilium / small GTPase binding / protein import into nucleus / 5S rRNA binding / tRNA binding / mRNA binding / RNA binding / zinc ion binding / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | |||||||||
Authors | Sampathkumar, P. / Gizzi, A. / Rout, M.P. / Chook, Y.M. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals) | |||||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2013 Title: Crystal structure of human Karyopherin beta 2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2. Authors: Soniat, M. / Sampathkumar, P. / Collett, G. / Gizzi, A.S. / Banu, R.N. / Bhosle, R.C. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / ...Authors: Soniat, M. / Sampathkumar, P. / Collett, G. / Gizzi, A.S. / Banu, R.N. / Bhosle, R.C. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Love, J.D. / Matikainen, B. / Seidel, R.D. / Toro, R. / Rajesh Kumar, P. / Bonanno, J.B. / Chook, Y.M. / Almo, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jlq.cif.gz | 178.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jlq.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jlq_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 4jlq_full_validation.pdf.gz | 441.5 KB | Display | |
Data in XML | 4jlq_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 4jlq_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/4jlq ftp://data.pdbj.org/pub/pdb/validation_reports/jl/4jlq | HTTPS FTP |
-Related structure data
Related structure data | 2qmrS 4fddS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a 1:1 complex of HsKapBeta2 and ScNAB2-PY-NLS |
-Components
#1: Protein | Mass: 96766.773 Da / Num. of mol.: 1 / Fragment: UNP residues 9-331 and 375-898 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB2, MIP1, TNPO1, TRN / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q92973 |
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#2: Protein/peptide | Mass: 4023.457 Da / Num. of mol.: 1 / Fragment: UNP residues 205-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: NAB2, YGL122C / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: P32505 |
Sequence details | THE AUTHORS STATE THAT RESIDUES 337 TO 367 WERE REPLACED WITH GGSGGSG |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: CRYSTALLIZATION CONDITIONS: PROTEIN (20 MM HEPES, PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACETATE, 20% GLYCEROL, 2MM DTT); RESERVOIR (MCSG3 #95: 0.7 M SODIUM CITRATE TRIBASIC, 100MM ...Details: CRYSTALLIZATION CONDITIONS: PROTEIN (20 MM HEPES, PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACETATE, 20% GLYCEROL, 2MM DTT); RESERVOIR (MCSG3 #95: 0.7 M SODIUM CITRATE TRIBASIC, 100MM BIS-TRISPROPANTE pH 7.0); CRYOPROTECTION (20% GLYCEROL), temperature 298K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2011 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 30914 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rsym value: 0.123 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 3.05→3.1 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.18 / Num. unique all: 1536 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QMR and 4FDD Resolution: 3.05→47.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.868 / SU ML: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.007 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.84 Å2 / Biso mean: 104.7336 Å2 / Biso min: 61.18 Å2
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Refinement step | Cycle: LAST / Resolution: 3.05→47.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.129 Å / Total num. of bins used: 20
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