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- PDB-2y3w: N-terminal head domain and beginning of coiled coil domain of Dan... -

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Basic information

Entry
Database: PDB / ID: 2y3w
TitleN-terminal head domain and beginning of coiled coil domain of Danio rerio SAS-6
ComponentsSPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON / BASAL BODY / CENTRIOLE / CARTWHEEL / CARTWHEEL HUB
Function / homology
Function and homology information


positive regulation of mitotic spindle organization / deuterosome / procentriole replication complex / positive regulation of centriole replication / nuclear division / positive regulation of spindle assembly / embryonic cleavage / centriole replication / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle ...positive regulation of mitotic spindle organization / deuterosome / procentriole replication complex / positive regulation of centriole replication / nuclear division / positive regulation of spindle assembly / embryonic cleavage / centriole replication / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle / centriole / mitotic spindle organization / spermatogenesis / centrosome / cytoplasm
Similarity search - Function
SAS-6 coiled-coil domain / Sas6/XLF/XRCC4 coiled-coil domain / Spindle assembly abnormal protein 6, N-terminal domain / Dna Repair Protein Xrcc4; Chain: A, domain 1 / Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Spindle assembly abnormal protein 6 homolog
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
Authorsvan Breugel, M.
CitationJournal: Science / Year: 2011
Title: Structures of SAS-6 suggest its organization in centrioles.
Authors: van Breugel, M. / Hirono, M. / Andreeva, A. / Yanagisawa, H.A. / Yamaguchi, S. / Nakazawa, Y. / Morgner, N. / Petrovich, M. / Ebong, I.O. / Robinson, C.V. / Johnson, C.M. / Veprintsev, D. / Zuber, B.
History
DepositionDec 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
B: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
C: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)62,9643
Polymers62,9643
Non-polymers00
Water2,630146
1
A: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG
B: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)41,9762
Polymers41,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-18.4 kcal/mol
Surface area20190 Å2
MethodPISA
2
C: SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)20,9881
Polymers20,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.360, 79.360, 79.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9826, -0.1455, 0.1153), (0.1272, -0.9801, -0.1525), (0.1352, -0.1352, 0.9816)
Vector: -41.47, -13.51, 0.8596)

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Components

#1: Protein SPINDLE ASSEMBLY ABNORMAL PROTEIN 6 HOMOLOG / SAS6


Mass: 20987.885 Da / Num. of mol.: 3
Fragment: HEAD DOMAIN AND START OF COILED-COIL DOMAIN, RESIDUES 1-179
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Description: CDNA FROM ZEBRAFISH / Plasmid: PET28 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q7ZVT3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 131 TO ASP ENGINEERED RESIDUE IN CHAIN B, PHE 131 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, PHE 131 TO ASP ENGINEERED RESIDUE IN CHAIN B, PHE 131 TO ASP ENGINEERED RESIDUE IN CHAIN C, PHE 131 TO ASP
Sequence detailsTHE N-TERMINAL THREE AMINO ACIDS (GPH) STEM FROM THE EXPRESSION VECTOR. THE F131D MUTATION WAS ...THE N-TERMINAL THREE AMINO ACIDS (GPH) STEM FROM THE EXPRESSION VECTOR. THE F131D MUTATION WAS ENGINEERED INTO THE CONSTRUCT TO PREVENT THE HEAD-HEAD INTERACTION OF THE N-TERMINAL DOMAINS OF SAS-6. THE S102N MUTATION PROBABLY STEMS FROM STRAIN VARIATION. IT WAS FOUND IN ALL INDEPENDENT PCR REACTION MADE WITH THE CDNA. S102 IS NON- CONSERVED EVOLUTIONARY AND STRUCTURALLY IS SITUATED IN A LOOP REGION.

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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: 48.54 % / Description: NONE
Crystal growpH: 9.2 / Details: 0.1 M CHES PH 9.2, 36% PEG 600, 1MM DTT.

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.98→35.49 Å / Num. obs: 38948 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.5
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3V

2y3v


Resolution: 1.98→35.492 Å / SU ML: 0.32 / σ(F): 2.05 / Phase error: 26.47 / Stereochemistry target values: ML
Details: RESIDUES A-2, A36 TO A41, AND A177 TO A179, RESIDUES B-2 TO B0, B16 TO B20, B112 TO B117, B178 TO B179, RESIDUES C-2 TO C1, C15 TO C21, C34 TO C43, C63 TO C64, C73 TO C78, C112 TO C118, C129 ...Details: RESIDUES A-2, A36 TO A41, AND A177 TO A179, RESIDUES B-2 TO B0, B16 TO B20, B112 TO B117, B178 TO B179, RESIDUES C-2 TO C1, C15 TO C21, C34 TO C43, C63 TO C64, C73 TO C78, C112 TO C118, C129 TO C136, AND C145 TO C179 ARE DISORDERED. CHAIN C SHOWED GOOD DENSITY MAINLY IN THE REGIONS CONTACTING CHAIN A AND B.
RfactorNum. reflection% reflection
Rfree0.244 1953 5 %
Rwork0.2205 --
obs0.2218 38923 99.93 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 58.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.8344 Å20 Å20 Å2
2--3.8344 Å20 Å2
3---4.1692 Å2
Refinement stepCycle: LAST / Resolution: 1.98→35.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 0 146 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043658
X-RAY DIFFRACTIONf_angle_d0.7594924
X-RAY DIFFRACTIONf_dihedral_angle_d12.2461423
X-RAY DIFFRACTIONf_chiral_restr0.049591
X-RAY DIFFRACTIONf_plane_restr0.002623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9801-2.02960.35651310.31832689X-RAY DIFFRACTION100
2.0296-2.08450.27621250.2972669X-RAY DIFFRACTION100
2.0845-2.14580.30921500.26582629X-RAY DIFFRACTION100
2.1458-2.2150.28421430.24852640X-RAY DIFFRACTION100
2.215-2.29420.28711370.24392601X-RAY DIFFRACTION100
2.2942-2.3860.28781440.25012684X-RAY DIFFRACTION100
2.386-2.49460.29351380.24792609X-RAY DIFFRACTION100
2.4946-2.62610.3081280.24332659X-RAY DIFFRACTION100
2.6261-2.79060.28061590.24022631X-RAY DIFFRACTION100
2.7906-3.00590.30051340.23792646X-RAY DIFFRACTION100
3.0059-3.30820.24671410.22832646X-RAY DIFFRACTION100
3.3082-3.78650.23911310.21112623X-RAY DIFFRACTION100
3.7865-4.76870.18631360.17642665X-RAY DIFFRACTION100
4.7687-35.49750.2241560.22182579X-RAY DIFFRACTION99

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