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- PDB-6hxv: Crystal structure of the head and coiled-coil domains of zebrafis... -

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Basic information

Entry
Database: PDB / ID: 6hxv
TitleCrystal structure of the head and coiled-coil domains of zebrafish CCDC61 (F129E/D130A)
ComponentsCoiled-coil domain-containing protein 61
KeywordsSTRUCTURAL PROTEIN / Centrosome / cilia / scaffold protein / proto-filament
Function / homology
Function and homology information


centriolar subdistal appendage / centriole assembly / cell projection organization / microtubule organizing center / centriolar satellite / mitotic spindle assembly / ciliary basal body / centrosome / identical protein binding / cytoplasm
Similarity search - Function
Centrosomal protein CCDC61
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBarnabas, D. / Ochi, T. / van Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Structure / Year: 2020
Title: CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions.
Authors: Ochi, T. / Quarantotti, V. / Lin, H. / Jullien, J. / Rosa E Silva, I. / Boselli, F. / Barnabas, D.D. / Johnson, C.M. / McLaughlin, S.H. / Freund, S.M.V. / Blackford, A.N. / Kimata, Y. / ...Authors: Ochi, T. / Quarantotti, V. / Lin, H. / Jullien, J. / Rosa E Silva, I. / Boselli, F. / Barnabas, D.D. / Johnson, C.M. / McLaughlin, S.H. / Freund, S.M.V. / Blackford, A.N. / Kimata, Y. / Goldstein, R.E. / Jackson, S.P. / Blundell, T.L. / Dutcher, S.K. / Gergely, F. / van Breugel, M.
History
DepositionOct 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 10, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coiled-coil domain-containing protein 61
B: Coiled-coil domain-containing protein 61


Theoretical massNumber of molelcules
Total (without water)38,5982
Polymers38,5982
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-10 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.360, 76.310, 83.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coiled-coil domain-containing protein 61


Mass: 19299.215 Da / Num. of mol.: 2 / Mutation: F129E, D130A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ccdc61, zgc:153153 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q08CF3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 8%(w/v) PEG6,000, 100 mM Bicine, 3% Triemethylamine N-Oxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→44.81 Å / Num. obs: 25068 / % possible obs: 98.2 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Net I/σ(I): 12.6
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1702 / CC1/2: 0.756 / Rpim(I) all: 0.35 / Rrim(I) all: 0.937 / % possible all: 96.6

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HXT

6hxt


Resolution: 1.97→38.155 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.2379 1248 4.99 %
Rwork0.1732 --
obs0.1763 25023 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.75 Å2
Refinement stepCycle: LAST / Resolution: 1.97→38.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 0 299 2795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082617
X-RAY DIFFRACTIONf_angle_d1.0983563
X-RAY DIFFRACTIONf_dihedral_angle_d13.645991
X-RAY DIFFRACTIONf_chiral_restr0.042412
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.04890.31771430.23492552X-RAY DIFFRACTION96
2.0489-2.14210.26891250.20132570X-RAY DIFFRACTION96
2.1421-2.25510.2671420.19172576X-RAY DIFFRACTION97
2.2551-2.39630.2411380.17792599X-RAY DIFFRACTION97
2.3963-2.58130.28021360.17862601X-RAY DIFFRACTION98
2.5813-2.8410.25161330.18782653X-RAY DIFFRACTION98
2.841-3.25190.23891420.17652674X-RAY DIFFRACTION99
3.2519-4.09630.20511410.15412706X-RAY DIFFRACTION99
4.0963-38.16220.21921480.16052844X-RAY DIFFRACTION99
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)
10.83590.3621-0.15960.50760.09632.02830.07970.05920.01040.01970.0285-0.0131-0.1394-0.15270.0030.19960.02520.03530.17910.00320.188832.197729.601536.479
20.15370.0613-0.20180.0356-0.02140.56580.06770.0932-0.0285-0.1819-0.13140.0214-0.05190.3509-0.01080.22450.0409-0.01110.3094-0.03990.255635.356923.76748.6753
31.27190.081-0.03321.2530.85371.338-0.00550.03460.0108-0.0363-0.07540.0406-0.0488-0.0986-0.00580.13890.0217-0.01490.14260.00130.156527.568528.4412-12.1981
40.13680.1406-0.36290.4972-0.43050.98610.0696-0.0292-0.30110.04680.03390.48990.1222-0.52120.05710.245-0.0343-0.02310.2422-0.01110.200829.305622.473415.8288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq -2:144
2X-RAY DIFFRACTION2chain A and resseq 145:166
3X-RAY DIFFRACTION3chain B and resseq 2:144
4X-RAY DIFFRACTION4chain B and resseq 145:165

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