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Yorodumi- PDB-1zmz: Solution structure of the N-terminal domain (M1-S98) of human cen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zmz | ||||||
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Title | Solution structure of the N-terminal domain (M1-S98) of human centrin 2 | ||||||
Components | Centrin-2 | ||||||
Keywords | STRUCTURAL PROTEIN / human centrins / EF-hand domains / Ca2+ binding / solution structure / self-associations | ||||||
Function / homology | Function and homology information XPC complex / 9+2 motile cilium / photoreceptor connecting cilium / heterotrimeric G-protein binding / transcription export complex 2 / nuclear pore nuclear basket / centriole replication / mRNA transport / SUMOylation of DNA damage response and repair proteins / Loss of Nlp from mitotic centrosomes ...XPC complex / 9+2 motile cilium / photoreceptor connecting cilium / heterotrimeric G-protein binding / transcription export complex 2 / nuclear pore nuclear basket / centriole replication / mRNA transport / SUMOylation of DNA damage response and repair proteins / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / ciliary basal body / regulation of cytokinesis / nucleotide-excision repair / DNA Damage Recognition in GG-NER / G-protein beta/gamma-subunit complex binding / Formation of Incision Complex in GG-NER / Regulation of PLK1 Activity at G2/M Transition / protein transport / apical part of cell / mitotic cell cycle / spermatogenesis / microtubule binding / cell division / centrosome / calcium ion binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Yang, A. / Miron, S. / Duchambon, P. / Assairi, L. / Blouquit, Y. / Craescu, C.T. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: The N-terminal domain of human centrin 2 has a closed structure, binds calcium with a very low affinity, and plays a role in the protein self-assembly Authors: Yang, A. / Miron, S. / Duchambon, P. / Assairi, L. / Blouquit, Y. / Craescu, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zmz.cif.gz | 610.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zmz.ent.gz | 514.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zmz_validation.pdf.gz | 355.9 KB | Display | wwPDB validaton report |
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Full document | 1zmz_full_validation.pdf.gz | 474.5 KB | Display | |
Data in XML | 1zmz_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 1zmz_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/1zmz ftp://data.pdbj.org/pub/pdb/validation_reports/zm/1zmz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11129.856 Da / Num. of mol.: 1 / Fragment: N-terminal domain (M1-S98) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CETN2, CALT, CEN2 / Plasmid: pETblue / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner DE3placI / References: UniProt: P41208 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
NMR spectrometer | Type: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz |
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-Processing
NMR software | Name: Discover / Version: 2.98 / Classification: refinement |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: The structures are based on a total of 1245 restraints, 1159 are NOE-derived distance constraints, 50 dihedral angle restraints,36 distance restraints from hydrogen bonds. |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |