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- PDB-4lzf: A novel domain in the microcephaly protein CPAP suggests a role i... -

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Basic information

Entry
Database: PDB / ID: 4lzf
TitleA novel domain in the microcephaly protein CPAP suggests a role in centriole architecture
Components
  • Centrosomal P4.1-associated protein
  • SCL-interrupting locus protein homolog
Keywordsstructural protein / protein binding / G-box / beta-sheet / Centriole organisation
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 / positive regulation of spindle assembly / protein localization to centrosome / smoothened signaling pathway ...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 / positive regulation of spindle assembly / protein localization to centrosome / smoothened signaling pathway / centrosome duplication / cilium assembly / spindle assembly / positive regulation of G1/S transition of mitotic cell cycle / 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
TRIETHYLENE GLYCOL / Centromere protein J / SCL-interrupting locus protein homolog
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsHatzopoulos, G.N. / Erat, M.C. / Cutts, E. / Rogala, K. / Slatter, L. / Stansfeld, P.J. / Vakonakis, I.
CitationJournal: Structure / Year: 2013
Title: Structural analysis of the G-box domain of the microcephaly protein CPAP suggests a role in centriole architecture.
Authors: Hatzopoulos, G.N. / Erat, M.C. / Cutts, E. / Rogala, K.B. / Slater, L.M. / Stansfeld, P.J. / Vakonakis, I.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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: Centrosomal P4.1-associated protein
B: SCL-interrupting locus protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0716
Polymers22,4902
Non-polymers5814
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.580, 38.390, 70.050
Angle α, β, γ (deg.)90.000, 126.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Centrosomal P4.1-associated protein


Mass: 20860.330 Da / Num. of mol.: 1 / Fragment: unp residues 942-1121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cenpj / Plasmid: pGEX6p2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7FCY1
#2: Protein/peptide SCL-interrupting locus protein homolog


Mass: 1629.771 Da / Num. of mol.: 1 / Fragment: unp residues 414-428 / Source method: obtained synthetically / Source: (synth.) Danio rerio (zebrafish) / References: UniProt: Q8JGS1

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Non-polymers , 4 types, 103 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.34 Å3/Da / Density % sol: 47.42 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.72→48.42 Å / Num. all: 64649 / Num. obs: 20094 / % possible obs: 74.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.3 % / Biso Wilson estimate: 30.03 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 19.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.72-1.760.60.4032.1164987531.8
7.69-48.421.40.03236.569525578.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LD1

4ld1


Resolution: 1.72→48.42 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.7961 / SU ML: 0.18 / σ(F): 1.36 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1022 5.09 %RANDOM
Rwork0.1898 ---
obs0.1917 20091 89.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.65 Å2 / Biso mean: 42.1292 Å2 / Biso min: 15.85 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 33 99 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061434
X-RAY DIFFRACTIONf_angle_d1.1141947
X-RAY DIFFRACTIONf_chiral_restr0.071205
X-RAY DIFFRACTIONf_plane_restr0.006261
X-RAY DIFFRACTIONf_dihedral_angle_d18.501551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.81070.2817830.25941742182557
1.8107-1.92410.24711500.22762397254780
1.9241-2.07270.25271540.18842932308697
2.0727-2.28130.23591610.19182996315799
2.2813-2.61140.26211510.21193002315399
2.6114-3.290.22811600.21483000316099
3.29-48.44050.21611630.16753000316396
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5721.1616-1.64621.0519-1.3245.60420.14920.46040.15760.1859-0.13760.0329-0.1662-0.6491-0.11460.22580.04030.02640.16870.03310.156-7.433914.0531-6.9944
24.62381.5739-0.29933.2682-0.47694.1021-0.04540.1469-0.5117-0.05890.0369-0.2541-0.28140.15420.01320.2086-0.0691-0.01180.34150.02830.2082-30.1489-5.376419.7523
34.543-0.6147-0.56125.3743-1.95554.13920.13640.4948-0.0695-0.2910.0659-0.42950.83610.14150.34350.45-0.0335-0.13470.4360.04250.31886.234410.2853-6.5098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 953 through 1046 )A953 - 1046
2X-RAY DIFFRACTION2chain A and (resid 1047 through 1107)A1047 - 1107
3X-RAY DIFFRACTION3chain B and (resid 414 through 425)B414 - 425

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