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- PDB-2a4j: Solution structure of the C-terminal domain (T94-Y172) of the hum... -

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Basic information

Entry
Database: PDB / ID: 2a4j
TitleSolution structure of the C-terminal domain (T94-Y172) of the human centrin 2 in complex with a 17 residues peptide (P1-XPC) from xeroderma pigmentosum group C protein
Components
  • 17-mer peptide P1-XPC from DNA-repair protein complementing XP-C cells
  • Centrin 2
KeywordsSTRUCTURAL PROTEIN / EF-hand
Function / homology
Function and homology information


heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / nucleotide-excision repair complex / 9+2 motile cilium / photoreceptor connecting cilium / DNA damage sensor activity / transcription export complex 2 / heterotrimeric G-protein binding ...heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / nucleotide-excision repair complex / 9+2 motile cilium / photoreceptor connecting cilium / DNA damage sensor activity / transcription export complex 2 / heterotrimeric G-protein binding / response to auditory stimulus / nuclear pore nuclear basket / bubble DNA binding / UV-damage excision repair / response to UV-B / mitotic intra-S DNA damage checkpoint signaling / regulation of mitotic cell cycle phase transition / centriole replication / site of DNA damage / mRNA transport / mismatch repair / 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 / single-stranded DNA binding / spermatogenesis / microtubule binding / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / response to xenobiotic stimulus / cell division / intracellular membrane-bounded organelle / DNA repair / centrosome / calcium ion binding / protein-containing complex binding / chromatin / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rad4 beta-hairpin domain 2 / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 ...Rad4 beta-hairpin domain 2 / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / Transglutaminase-like superfamily / ATP-dependent RNA helicase DEAD-box, conserved site / : / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Papain-like cysteine peptidase superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centrin-2 / DNA repair protein complementing XP-C cells / DNA repair protein complementing XP-C cells
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, A. / Miron, S. / Mouawad, L. / Duchambon, P. / Blouquit, Y. / Craescu, C.T.
CitationJournal: Biochemistry / Year: 2006
Title: Flexibility and plasticity of human centrin 2 binding to the xeroderma pigmentosum group C protein (XPC) from nuclear excision repair.
Authors: Yang, A. / Miron, S. / Mouawad, L. / Duchambon, P. / Blouquit, Y. / Craescu, C.T.
History
DepositionJun 29, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJul 12, 2005ID: 1T2G
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrin 2
B: 17-mer peptide P1-XPC from DNA-repair protein complementing XP-C cells


Theoretical massNumber of molelcules
Total (without water)11,3482
Polymers11,3482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Centrin 2 / Caltractin isoform 1


Mass: 9234.317 Da / Num. of mol.: 1 / Fragment: c-terminal domain (residues 94-172)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: cen2 / Plasmid: PET24A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41208
#2: Protein/peptide 17-mer peptide P1-XPC from DNA-repair protein complementing XP-C cells / Xeroderma pigmentosum group C complementing protein p125


Mass: 2113.639 Da / Num. of mol.: 1 / Fragment: residues 847-863 / Source method: obtained synthetically / Details: this sequens occurs in Homo sapiens / References: UniProt: Q96AX0, UniProt: Q01831*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1423D 15N separated TOCSY
1523D 15N-separated NOESY
1622D 15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 MM UNLABELED SC_HSCEN2(T94-Y172);DEUTERATED TRIS/HCL 20 MM BUFFER; 100 MM NACL;5MM CACL2;PH 6.5; 1.4 MM UNLABELED P1-XPC;90% H2O/10% D2O
21.2 MM UNLABELED SC_HSCEN2(T94-Y172)U-15N;DEUTERATED TRIS/HCL 20 MM BUFFER; 100 MM NACL;5MM CACL2;PH 6.5; 1.4 MM UNLABELED P1-XPC;90% H2O/10% D2O
31.2 MM UNLABELED SC_HSCEN2(T94-Y172)U-15N, 13C; DEUTERATED TRIS/HCL 20 MM BUFFER; 100 MM NACL;5MM CACL2;PH 6.5; 1.4 MM UNLABELED P1-XPC;90% H2O/10% D2O
Sample conditionsIonic strength: 100Mm NaCl / pH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000.1ACCELRYSdata analysis
Discover2.98ACCELRYSprocessing
Insight II2000ACCELRYSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on 1298 NOE distance restraints, 121 dihedral angle restraints, and 84 hydrogen bond restraints.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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