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- PDB-4by2: SAS-4 (dCPAP) TCP domain in complex with a Proline Rich Motif of ... -

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Basic information

Entry
Database: PDB / ID: 4by2
TitleSAS-4 (dCPAP) TCP domain in complex with a Proline Rich Motif of Ana2 (dSTIL) of Drosophila Melanogaster
ComponentsANASTRAL SPINDLE 2, SAS 4
KeywordsSTRUCTURAL PROTEIN / CPAP / STIL / MICROCEPHALY / MCPH / CENTRIOLE / TCP DOMAIN / EXTENDED BETA SHEET
Function / homology
Function and homology information


protein localization to pericentriolar material / ciliary basal body organization / centriole elongation / syncytial blastoderm mitotic cell cycle / centriole-centriole cohesion / microtubule anchoring at centrosome / centriole assembly / asymmetric cell division / centrosome separation / asymmetric neuroblast division ...protein localization to pericentriolar material / ciliary basal body organization / centriole elongation / syncytial blastoderm mitotic cell cycle / centriole-centriole cohesion / microtubule anchoring at centrosome / centriole assembly / asymmetric cell division / centrosome separation / asymmetric neuroblast division / male meiotic nuclear division / locomotion / centrosome cycle / pericentriolar material / establishment of mitotic spindle orientation / centriole replication / microtubule polymerization / cilium assembly / centriole / tubulin binding / ciliary basal body / molecular adaptor activity / centrosome / cytoplasm
Similarity search - Function
lipopolysaccharide transport protein A fold - #20 / 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
Spindle assembly abnormal 4 / Anastral spindle 2, isoform A
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.57 Å
AuthorsCottee, 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.
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 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Jan 17, 2018Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
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_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: ANASTRAL SPINDLE 2, SAS 4
B: ANASTRAL SPINDLE 2, SAS 4
C: ANASTRAL SPINDLE 2, SAS 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8804
Polymers85,8183
Non-polymers621
Water1,17165
1
A: ANASTRAL SPINDLE 2, SAS 4


Theoretical massNumber of molelcules
Total (without water)28,6061
Polymers28,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANASTRAL SPINDLE 2, SAS 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6682
Polymers28,6061
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ANASTRAL SPINDLE 2, SAS 4


Theoretical massNumber of molelcules
Total (without water)28,6061
Polymers28,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.640, 69.910, 69.980
Angle α, β, γ (deg.)86.96, 88.64, 67.69
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.92953, 0.10599, 0.35317), (-0.3563, 0.01155, 0.9343), (0.09495, -0.9943, 0.04849)13.08102, -27.73312, 15.23109
2given(0.95548, 0.2863, -0.07136), (0.28583, -0.95813, -0.01704), (-0.07325, -0.00411, -0.99731)28.24953, -28.00523, 17.41055

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Components

#1: Protein ANASTRAL SPINDLE 2, SAS 4 / ANA2_1-47 FUSED TO SAS-4_700-901


Mass: 28606.064 Da / Num. of mol.: 3
Fragment: PROLINE-RICH-MOTIF RESIDUES 2-47 BOUND TO TCP DOMAIN, RESIDUES 700-901
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly)
Description: CODON-OPTIMISED SEQUENCE BASED ON UNIPROT ENTRIES Q9XZ31 (ANA2) AND Q9VI72 (SAS-4)
Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / Variant (production host): (DE3) / References: UniProt: Q9XZ31, UniProt: Q9VI72
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.09 Å3/Da / Density % sol: 60.25 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 100 MM MES/IMIDAZOLE MIX PH 6.5, 30 MM MGCL2, 30 MM CACL2, 20 % ETHYLENE GLYCOL, 10 % PEG LIQUOR, IN A 0.2UL SITTING DROP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.57→64.6 Å / Num. obs: 31911 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 71.41 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.6
Reflection shellResolution: 2.57→8.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.57→64.6 Å / Cor.coef. Fo:Fc: 0.8539 / Cor.coef. Fo:Fc free: 0.836 / SU R Cruickshank DPI: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.287 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 1611 5.05 %RANDOM
Rwork0.2451 ---
obs0.246 31908 97.57 %-
Displacement parametersBiso mean: 70.8 Å2
Baniso -1Baniso -2Baniso -3
1--40.2592 Å24.0959 Å28.5473 Å2
2--17.7741 Å2-2.7126 Å2
3---22.4851 Å2
Refine analyzeLuzzati coordinate error obs: 0.474 Å
Refinement stepCycle: LAST / Resolution: 2.57→64.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 4 65 3859
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073878HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.95240HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1383SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes542HARMONIC5
X-RAY DIFFRACTIONt_it3878HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.71
X-RAY DIFFRACTIONt_other_torsion19.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion500SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3768SEMIHARMONIC4
LS refinement shellResolution: 2.57→2.65 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3599 149 5.07 %
Rwork0.3212 2790 -
all0.3232 2939 -
obs--97.57 %

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