+Open data
-Basic information
Entry | Database: PDB / ID: 2ve7 | ||||||
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Title | Crystal structure of a bonsai version of the human Ndc80 complex | ||||||
Components |
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Keywords | CELL CYCLE / MITOSIS / CENTROMERE / MICROTUBULE / KINETOCHORE / CELL DIVISION / CALPONIN HOMOLOGY | ||||||
Function / homology | Function and homology information G2/MI transition of meiotic cell cycle / kinetochore adaptor activity / skeletal muscle satellite cell proliferation / Ndc80 complex / kinetochore organization / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / meiotic chromosome segregation / attachment of spindle microtubules to kinetochore / centrosome duplication ...G2/MI transition of meiotic cell cycle / kinetochore adaptor activity / skeletal muscle satellite cell proliferation / Ndc80 complex / kinetochore organization / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / meiotic chromosome segregation / attachment of spindle microtubules to kinetochore / centrosome duplication / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / spindle assembly involved in female meiosis I / mitotic spindle assembly checkpoint signaling / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / chromosome, centromeric region / cyclin binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / regulation of protein stability / kinetochore / Separation of Sister Chromatids / mitotic cell cycle / microtubule binding / cell division / centrosome / protein-containing complex binding / nucleolus / nucleoplasm / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å | ||||||
Authors | Ciferri, C. / Pasqualato, S. / Dos Reis, G. / Screpanti, E. / Maiolica, A. / Polka, J. / De Luca, J.G. / De Wulf, P. / Salek, M. / Rappsilber, J. ...Ciferri, C. / Pasqualato, S. / Dos Reis, G. / Screpanti, E. / Maiolica, A. / Polka, J. / De Luca, J.G. / De Wulf, P. / Salek, M. / Rappsilber, J. / Moores, C.A. / Salmon, E.D. / Musacchio, A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 Title: Implications for Kinetochore-Microtubule Attachment from the Structure of an Engineered Ndc80 Complex Authors: Ciferri, C. / Pasqualato, S. / Screpanti, E. / Varetti, G. / Santaguida, S. / Dos Reis, G. / Maiolica, A. / Polka, J. / De Luca, J.G. / De Wulf, P. / Salek, M. / Rappsilber, J. / Moores, C.A. ...Authors: Ciferri, C. / Pasqualato, S. / Screpanti, E. / Varetti, G. / Santaguida, S. / Dos Reis, G. / Maiolica, A. / Polka, J. / De Luca, J.G. / De Wulf, P. / Salek, M. / Rappsilber, J. / Moores, C.A. / Salmon, E.D. / Musacchio, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ve7.cif.gz | 219.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ve7.ent.gz | 176.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ve7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ve7_validation.pdf.gz | 485.3 KB | Display | wwPDB validaton report |
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Full document | 2ve7_full_validation.pdf.gz | 516 KB | Display | |
Data in XML | 2ve7_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 2ve7_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2ve7 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2ve7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 36351.297 Da / Num. of mol.: 2 Fragment: CHIMERA OF NDC80 RESIDUES 80-286 WITH SPC25 RESIDUES 118-224 Source method: isolated from a genetically manipulated source Details: PEPTIDE LINK BETWEEN RESI 286 AND RESI 1118 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14777, UniProt: Q9HBM1 #2: Protein | Mass: 28993.418 Da / Num. of mol.: 2 Fragment: CHIMERA OF NUF2 RESIDUES 1-169 WITH SPC24 RESIDUES 122-197 Mutation: YES Source method: isolated from a genetically manipulated source Details: PEPTIDE LINK BETWEEN RESI 169 AND RESI 1122 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BZD4, UniProt: Q8NBT2 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 4.62 Å3/Da / Density % sol: 75 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 4.5-6.5 PEG 6000, 1.5-2 MPD, 0.1 M NAHEPES PH 7.5, 16 MM TCEP, 15 MM PHENOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→50 Å / Num. obs: 52754 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.88→3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.88→50 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.88 / SU B: 24.976 / SU ML: 0.225 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.479 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS CHAIN A AND B ARE CHIMERAS OF NDC80 (RESIDUES 80-286) AND SPC25 (RESIDUES 118-224). FOR CLARITY SPC25 RESIDUES ARE NUMBERED 1118-1224. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS CHAIN A AND B ARE CHIMERAS OF NDC80 (RESIDUES 80-286) AND SPC25 (RESIDUES 118-224). FOR CLARITY SPC25 RESIDUES ARE NUMBERED 1118-1224. RESIDUE 286 IS FUSED TO RESIDUE 1118 CHAIN C AND D ARE CHIMERAS OF NUF2 (RESIDUES 1- 169) AND SPC24 (RESIDUES 122-197). FOR CLARITY SPC24 RESIDUES ARE NUMBERED 1122-1197. RESIDUE 169 IS FUSED TO RESIDUE 1122 RESIDUES MET 79A, LYS 1122A, ILE 1161A, TRP 211B, ARG 1202B HAVE BEEN BUILT AS ALANINES BECAUSE THERE WAS NO ELECTRON DENSITY FOR THEIR SIDE CHAINS (SEE REMARK 470)
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.88→50 Å
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Refine LS restraints |
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