+Open data
-Basic information
Entry | Database: PDB / ID: 3zv0 | ||||||
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Title | Structure of the SHQ1P-CBF5P complex | ||||||
Components |
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Keywords | CELL CYCLE / RNP ASSEMBLY / X-LINKED DYSKERATOSIS CONGENITA / TELOMERASE | ||||||
Function / homology | Function and homology information snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / Isomerases; Intramolecular transferases; Transferring other groups / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis ...snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / Isomerases; Intramolecular transferases; Transferring other groups / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / rRNA modification / chromosome, centromeric region / 90S preribosome / rRNA processing / unfolded protein binding / microtubule / cell division / mRNA binding / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Walbott, H. / Machado-Pinilla, R. / Liger, D. / Blaud, M. / Rety, S. / Grozdanov, P.N. / Godin, K. / vanTilbeurgh, H. / Varani, G. / Meier, U.T. / Leulliot, N. | ||||||
Citation | Journal: Genes Dev. / Year: 2011 Title: The H/Aca Rnp Assembly Factor Shq1 Functions as an RNA Mimic. Authors: Walbott, H. / Machado-Pinilla, R. / Liger, D. / Blaud, M. / Rety, S. / Grozdanov, P.N. / Godin, K. / Van Tilbeurgh, H. / Varani, G. / Meier, U.T. / Leulliot, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zv0.cif.gz | 404.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zv0.ent.gz | 334.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zv0_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 3zv0_full_validation.pdf.gz | 472.9 KB | Display | |
Data in XML | 3zv0_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 3zv0_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/3zv0 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/3zv0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 43503.730 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 145-507 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: P40486 #2: Protein | Mass: 21851.266 Da / Num. of mol.: 2 / Fragment: DCAT DOMAIN, RESIDUES 1-60,258-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS References: UniProt: P33322, Isomerases; Intramolecular transferases; Transferring other groups #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.08 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: CRYSTALLIZED AT 291 KELVIN BY THE HANGING DROP VAPOR DIFFUSION METHOD FROM A 1:1 UL OF PROTEIN AND PRECIPITANT CONTAINING 4 TO 8 % PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 36623 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 66.7 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.21 Å / Cor.coef. Fo:Fc: 0.9284 / Cor.coef. Fo:Fc free: 0.9095 / Cross valid method: THROUGHOUT / σ(F): 0 Details: CHAINS A, B, RESIDUES 145-164 DISORDERED. CHAINS C, D, RESIDUES 6XHISTAG, 1-18, 43-46, 378-386 ARE DISORDERED. IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 59.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.345 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→39.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.88 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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