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- PDB-4bxr: Structure of the wild-type TCP10 domain of Danio rerio CPAP in co... -

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Basic information

Entry
Database: PDB / ID: 4bxr
TitleStructure of the wild-type TCP10 domain of Danio rerio CPAP in complex with a peptide of Danio rerio STIL
Components
  • CPAP
  • SCL-INTERRUPTING LOCUS PROTEIN HOMOLOG
KeywordsCELL CYCLE / CENTRIOLE DUPLICATION
Function / homology
Function and homology information


TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of mitotic spindle organization / body morphogenesis / centriole elongation / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / microtubule organizing center organization / positive regulation of spindle assembly / protein localization to centrosome ...TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of mitotic spindle organization / body morphogenesis / centriole elongation / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / microtubule organizing center organization / positive regulation of spindle assembly / protein localization to centrosome / smoothened signaling pathway / microtubule organizing center / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / spindle assembly / centriole / tubulin binding / mitotic spindle organization / neuron cellular homeostasis / cell cortex / protein domain specific binding / centrosome / cytosol / cytoplasm
Similarity search - Function
lipopolysaccharide transport protein A fold - #20 / SCL-interrupting locus protein / SCL-interrupting locus protein N-terminus / T-complex protein 10, C-terminal domain / T-complex protein 10 family / T-complex protein 10 C-terminus / lipopolysaccharide transport protein A fold / : / Sandwich / Mainly Beta
Similarity search - Domain/homology
Centromere protein J / SCL-interrupting locus protein homolog
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
Authorsvan Breugel, M.
CitationJournal: Elife / Year: 2013
Title: Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly.
Authors: Cottee, M.A. / Muschalik, N. / Wong, Y.L. / Johnson, C.M. / Johnson, S. / Andreeva, A. / Oegema, K. / Lea, S.M. / Raff, J.W. / van Breugel, M.
History
DepositionJul 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CPAP
B: CPAP
C: SCL-INTERRUPTING LOCUS PROTEIN HOMOLOG
D: SCL-INTERRUPTING LOCUS PROTEIN HOMOLOG


Theoretical massNumber of molelcules
Total (without water)49,9804
Polymers49,9804
Non-polymers00
Water97354
1
A: CPAP
C: SCL-INTERRUPTING LOCUS PROTEIN HOMOLOG


Theoretical massNumber of molelcules
Total (without water)24,9902
Polymers24,9902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-5.1 kcal/mol
Surface area12270 Å2
MethodPISA
2
B: CPAP
D: SCL-INTERRUPTING LOCUS PROTEIN HOMOLOG


Theoretical massNumber of molelcules
Total (without water)24,9902
Polymers24,9902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-6.7 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.250, 67.470, 61.650
Angle α, β, γ (deg.)90.00, 113.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRAA944 - 112212 - 190
21SERSERTHRTHRBB944 - 112212 - 190
12ASPASPHISHISCC414 - 4248 - 18
22ASPASPHISHISDD414 - 4248 - 18

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.8304, 0.5385, -0.1433), (-0.1606, 0.01509, 0.9869), (0.5336, 0.8425, 0.07394)-74.87, -36.59, 30.56
2given(-0.8045, 0.5492, -0.2264), (-0.2091, 0.09493, 0.9733), (0.556, 0.8303, 0.03844)-71.72, -37.82, 31.52

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Components

#1: Protein CPAP


Mass: 21891.539 Da / Num. of mol.: 2 / Fragment: TCP-10 DOMAIN, RESIDUES 937-1124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: E7FCY1
#2: Protein/peptide SCL-INTERRUPTING LOCUS PROTEIN HOMOLOG


Mass: 3098.250 Da / Num. of mol.: 2 / Fragment: STIL PEPTIDE, RESIDUES 408-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q8JGS1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.5
Details: 100 MM TRIS PH 8.5, 200 MM CA ACETATE, 17% PEG-2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Oct 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→56.4 Å / Num. obs: 23051 / % possible obs: 99.9 % / Observed criterion σ(I): 1.4 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BXP (DISTORTED)

4bxp


Resolution: 2.2→51.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.205 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALY
RfactorNum. reflection% reflectionSelection details
Rfree0.27668 1145 5 %RANDOM
Rwork0.23427 ---
obs0.23642 21892 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.692 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å2-0.74 Å2
2---2.75 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→51.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 0 54 3169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193195
X-RAY DIFFRACTIONr_bond_other_d0.0050.023002
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9654329
X-RAY DIFFRACTIONr_angle_other_deg1.14936954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43524.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43415553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9371524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213620
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02712
X-RAY DIFFRACTIONr_nbd_refined0.2380.2641
X-RAY DIFFRACTIONr_nbd_other0.2070.22755
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21535
X-RAY DIFFRACTIONr_nbtor_other0.0890.21943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2610.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3115.9353195
X-RAY DIFFRACTIONr_mcbond_other1.4186.0783002
X-RAY DIFFRACTIONr_mcangle_it7.8648.8124329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A92400.17
12B92400.17
21C3730.13
22D3730.13
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 78 -
Rwork0.338 1607 -
obs--99.88 %

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