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- PDB-2ggm: Human centrin 2 xeroderma pigmentosum group C protein complex -

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Basic information

Entry
Database: PDB / ID: 2ggm
TitleHuman centrin 2 xeroderma pigmentosum group C protein complex
Components
  • Centrin-2
  • DNA-repair protein complementing XP-C cells
KeywordsCELL CYCLE / EF-Hand Superfamily / DNA repair complex
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 / 9+2 motile cilium / nucleotide-excision repair complex / photoreceptor connecting cilium / DNA damage sensor activity / heterotrimeric G-protein binding / transcription export complex 2 ...heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / 9+2 motile cilium / nucleotide-excision repair complex / photoreceptor connecting cilium / DNA damage sensor activity / heterotrimeric G-protein binding / transcription export complex 2 / 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 / glial cell projection / mRNA transport / mismatch repair / SUMOylation of DNA damage response and repair proteins / centriole / 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 / AURKA Activation by TPX2 / regulation of cytokinesis / nucleotide-excision repair / DNA Damage Recognition in GG-NER / G-protein beta/gamma-subunit complex binding / microtubule cytoskeleton organization / Formation of Incision Complex in GG-NER / apical part of cell / Regulation of PLK1 Activity at G2/M Transition / protein transport / mitotic cell cycle / single-stranded DNA binding / microtubule binding / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / ciliary basal body / response to xenobiotic stimulus / cell division / DNA repair / intracellular membrane-bounded organelle / centrosome / calcium ion binding / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / nucleolus / 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 / Papain-like cysteine peptidase superfamily / EF-hand domain pair / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsThompson, J.R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The structure of the human centrin 2-xeroderma pigmentosum group C protein complex.
Authors: Thompson, J.R. / Ryan, Z.C. / Salisbury, J.L. / Kumar, R.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrin-2
B: Centrin-2
C: DNA-repair protein complementing XP-C cells
D: DNA-repair protein complementing XP-C cells
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5838
Polymers44,4234
Non-polymers1604
Water3,909217
1
A: Centrin-2
C: DNA-repair protein complementing XP-C cells
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2924
Polymers22,2112
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-38 kcal/mol
Surface area10630 Å2
MethodPISA
2
B: Centrin-2
D: DNA-repair protein complementing XP-C cells
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2924
Polymers22,2112
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-39 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.150, 59.000, 104.240
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number5
Space group name H-MC121
DetailsTwo biological assemblies contained within one asymmetric unit are unrelated by symmetry.

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Components

#1: Protein Centrin-2 / Caltractin isoform 1


Mass: 20097.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CETN2, CALT, CEN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P41208
#2: Protein/peptide DNA-repair protein complementing XP-C cells / Xeroderma pigmentosum group C complementing protein / p125


Mass: 2113.639 Da / Num. of mol.: 2 / Fragment: Centrin Binding Region (residues 846-862) / Source method: obtained synthetically / Details: Naturally occurring sequence in humans. / References: UniProt: Q01831
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5-3.2 M (NH4)2SO4, 0.1-0.4 M Na2HPO4, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2005
RadiationMonochromator: channel-cut Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. all: 15268 / Num. obs: 15095 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 18
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.74 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 16.482 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.264 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24535 603 4 %RANDOM
Rwork0.19222 ---
all0.19439 14921 --
obs0.19439 14318 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.142 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-0.12 Å2
2---1.17 Å20 Å2
3---0.43 Å2
Refine analyzeLuzzati coordinate error obs: 0.474 Å
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 4 217 2898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222702
X-RAY DIFFRACTIONr_angle_refined_deg2.1392.0013589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3035329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43925.956136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.90715604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8421517
X-RAY DIFFRACTIONr_chiral_restr0.150.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021971
X-RAY DIFFRACTIONr_nbd_refined0.2660.21384
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2820.2201
X-RAY DIFFRACTIONr_metal_ion_refined0.2030.215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.40.226
X-RAY DIFFRACTIONr_mcbond_it1.2961.51704
X-RAY DIFFRACTIONr_mcangle_it2.04922608
X-RAY DIFFRACTIONr_scbond_it3.2931127
X-RAY DIFFRACTIONr_scangle_it4.974.5981
LS refinement shellResolution: 2.35→2.404 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 44 -
Rwork0.238 927 -
obs-927 88.3 %

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