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Yorodumi- PDB-5yca: Crystal structure of inner membrane protein Bqt4 in complex with LEM2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yca | ||||||
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Title | Crystal structure of inner membrane protein Bqt4 in complex with LEM2 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Chromosome organization / Membrane organization / Bouquet formation / Lap-Emerin-Man domain protein | ||||||
Function / homology | Function and homology information heterochromatin-nuclear membrane anchor activity / centromere-nuclear envelope anchor activity / : / pericentric heterochromatin organization / subnuclear spatial organization of silent mating-type cassette heterochromatin / rDNA heterochromatin => GO:0033553 / CENP-A containing chromatin => GO:0061638 / chromosome, subtelomeric region => GO:0099115 / : / centromere clustering at the mitotic interphase nuclear envelope ...heterochromatin-nuclear membrane anchor activity / centromere-nuclear envelope anchor activity / : / pericentric heterochromatin organization / subnuclear spatial organization of silent mating-type cassette heterochromatin / rDNA heterochromatin => GO:0033553 / CENP-A containing chromatin => GO:0061638 / chromosome, subtelomeric region => GO:0099115 / : / centromere clustering at the mitotic interphase nuclear envelope / meiotic telomere tethering at nuclear periphery / telomere-nuclear envelope anchor activity / nuclear membrane complex Bqt3-Bqt4 / chromosome, centromeric core domain / CENP-A containing chromatin / : / pericentric heterochromatin => GO:0005721 / protein localization to heterochromatin / mitotic telomere tethering at nuclear periphery / meiotic attachment of telomere to nuclear envelope / nuclear inner membrane organization / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / mitotic spindle pole body / SUMO is proteolytically processed / SUMOylation of transcription factors / meiotic telomere clustering / heterochromatin organization / Postmitotic nuclear pore complex (NPC) reformation / nuclear envelope organization / SUMOylation of transcription cofactors / telomere tethering at nuclear periphery / septin ring / perinuclear endoplasmic reticulum / SUMOylation of DNA damage response and repair proteins / centromeric DNA binding / SUMOylation of RNA binding proteins / perinuclear endoplasmic reticulum membrane / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / nuclear inner membrane / ubiquitin-like protein ligase binding / protein sumoylation / telomere organization / telomere maintenance / meiotic cell cycle / condensed nuclear chromosome / protein tag activity / nuclear envelope / double-stranded DNA binding / nuclear membrane / cell division / chromatin binding / DNA binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Chen, Y. / Hu, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural insights into chromosome attachment to the nuclear envelope by an inner nuclear membrane protein Bqt4 in fission yeast. Authors: Hu, C. / Inoue, H. / Sun, W. / Takeshita, Y. / Huang, Y. / Xu, Y. / Kanoh, J. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yca.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yca.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/5yca ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5yca | HTTPS FTP |
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-Related structure data
Related structure data | 5yc2SC 6a6wC 5ybxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23570.859 Da / Num. of mol.: 1 / Mutation: Q61E Source method: isolated from a genetically manipulated source Details: SUMO (residue 20 to 92) tagged Bqt4 (residue 8 to 140) Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: ATCC 204508 / S288c, 972 / ATCC 24843 / Gene: SMT3, YDR510W, D9719.15, bqt4, SPBC19C7.10 / Plasmid: pET28b-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12306, UniProt: O60158 |
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#2: Protein/peptide | Mass: 2372.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Bqt4 binding motif of LEM2 protein Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: lem2, heh1, SPAC18G6.10 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q10109 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.96 % / Description: beautiful diamond |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1600 mM Sodium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→27.392 Å / Num. obs: 36534 / % possible obs: 99.9 % / Redundancy: 3 % / Biso Wilson estimate: 17.71 Å2 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.264 / CC1/2: 0.978 / Rpim(I) all: 0.079 / Rrim(I) all: 0.276 / Χ2: 0.712 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YBX, 5YC2 Resolution: 1.57→27.392 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.96 Å2 / Biso mean: 23.33 Å2 / Biso min: 10.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.57→27.392 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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