+Open data
-Basic information
Entry | Database: PDB / ID: 1ukl | ||||||
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Title | Crystal structure of Importin-beta and SREBP-2 complex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/DNA BINDING PROTEIN / Transcription factor / Nuclear transport factor / HEAT repeat / Helix-Loop-Helix Leucine zipper / PROTEIN TRANSPORT-DNA BINDING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information Regulation of cholesterol biosynthesis by SREBP (SREBF) / SREBP-SCAP-Insig complex / Assembly of the ORC complex at the origin of replication / Apoptosis induced DNA fragmentation / Initiation of Nuclear Envelope (NE) Reformation / Ran protein signal transduction / positive regulation of cholesterol storage / regulation of cholesterol biosynthetic process / RNA import into nucleus / SREBP signaling pathway ...Regulation of cholesterol biosynthesis by SREBP (SREBF) / SREBP-SCAP-Insig complex / Assembly of the ORC complex at the origin of replication / Apoptosis induced DNA fragmentation / Initiation of Nuclear Envelope (NE) Reformation / Ran protein signal transduction / positive regulation of cholesterol storage / regulation of cholesterol biosynthetic process / RNA import into nucleus / SREBP signaling pathway / Interferon alpha/beta signaling / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / negative regulation of cholesterol efflux / : / regulation of Notch signaling pathway / establishment of mitotic spindle localization / astral microtubule organization / regulation of autophagy of mitochondrion / chromatin => GO:0000785 / positive regulation of cholesterol biosynthetic process / EGR2 and SOX10-mediated initiation of Schwann cell myelination / cellular response to laminar fluid shear stress / Regulation of cholesterol biosynthesis by SREBP (SREBF) / ribosomal protein import into nucleus / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / positive regulation of protein targeting to mitochondrion / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / response to lipid / E-box binding / kinesin binding / cellular response to low-density lipoprotein particle stimulus / mitotic spindle assembly / nuclear pore / cholesterol metabolic process / cellular response to starvation / Neutrophil degranulation / cholesterol homeostasis / Activation of gene expression by SREBF (SREBP) / Hsp90 protein binding / establishment of protein localization / ER to Golgi transport vesicle membrane / lipid metabolic process / PPARA activates gene expression / small GTPase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / cytoplasmic stress granule / protein import into nucleus / sequence-specific double-stranded DNA binding / nuclear envelope / nuclear membrane / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / Golgi membrane / intracellular membrane-bounded organelle / protein-containing complex binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Lee, S.J. / Sekimoto, T. / Yamashita, E. / Nagoshi, E. / Nakagawa, A. / Imamoto, N. / Yoshimura, M. / Sakai, H. / Tsukihara, T. / Yoneda, Y. | ||||||
Citation | Journal: Science / Year: 2003 Title: The Structure of Importin-beta Bound to SREBP-2: Nuclear Import of a Transcription Factor Authors: Lee, S.J. / Sekimoto, T. / Yamashita, E. / Nagoshi, E. / Nakagawa, A. / Imamoto, N. / Yoshimura, M. / Sakai, H. / Chong, K.T. / Tsukihara, T. / Yoneda, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ukl.cif.gz | 389.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ukl.ent.gz | 317.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ukl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1ukl ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1ukl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 97271.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P70168 #2: Protein | Mass: 7277.164 Da / Num. of mol.: 4 / Fragment: residues 343-403 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12772 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: PEG 8000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3→80 Å / Num. obs: 105485 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 93.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.7 | |||||||||||||||
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / % possible all: 97.5 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 80 Å / Num. obs: 55607 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 97.5 % / Num. unique obs: 5720 / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 1QGK, 1AM9 Resolution: 3→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2985930.88 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.0847 Å2 / ksol: 0.258279 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 105.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | |||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.237 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.389 / Rfactor Rwork: 0.352 |