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- PDB-5mwe: Complex between the Leucine Zipper (LZ, residues 490-567) and Cen... -

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Basic information

Entry
Database: PDB / ID: 5mwe
TitleComplex between the Leucine Zipper (LZ, residues 490-567) and Centrosomin-motif 2 (CM2) domains of Drosophila melanogaster Centrosomin (Cnn)
Components(CentrosominCDK5RAP2) x 2
KeywordsCELL CYCLE / Centrosome / Centriole / Coiled-coil / Mitosis
Function / homology
Function and homology information


photoreceptor cell morphogenesis / regulation of Golgi organization / pole cell formation / asymmetric cell division / regulation of centriole-centriole cohesion / asymmetric neuroblast division / positive regulation of microtubule nucleation / embryonic cleavage / peripheral nervous system development / motile cilium ...photoreceptor cell morphogenesis / regulation of Golgi organization / pole cell formation / asymmetric cell division / regulation of centriole-centriole cohesion / asymmetric neuroblast division / positive regulation of microtubule nucleation / embryonic cleavage / peripheral nervous system development / motile cilium / centrosome cycle / midgut development / pericentriolar material / centriole replication / centriole / mitotic spindle organization / ciliary basal body / meiotic cell cycle / central nervous system development / spindle pole / molecular adaptor activity / centrosome / Golgi apparatus
Similarity search - Function
Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1
Similarity search - Domain/homology
3,3',3''-phosphanetriyltripropanoic acid / Centrosomin
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsFeng, Z. / Johnson, S. / Raff, J.W. / Lea, S.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust10457 United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: Cell / Year: 2017
Title: Structural Basis for Mitotic Centrosome Assembly in Flies.
Authors: Feng, Z. / Caballe, A. / Wainman, A. / Johnson, S. / Haensele, A.F.M. / Cottee, M.A. / Conduit, P.T. / Lea, S.M. / Raff, J.W.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrosomin
C: Centrosomin
D: Centrosomin
B: Centrosomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0738
Polymers34,6344
Non-polymers4404
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-103 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.990, 36.500, 43.780
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Centrosomin / CDK5RAP2 / Protein arrow


Mass: 8198.428 Da / Num. of mol.: 2 / Fragment: CM2 domain, UNP Residues 1082-1148
Source method: isolated from a genetically manipulated source
Details: Centrosomin CM2 domain residues 1082-1148 / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pLip / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P54623
#2: Protein Centrosomin / CDK5RAP2 / Protein arrow


Mass: 9118.447 Da / Num. of mol.: 2 / Fragment: LZ domain, UNP residues 490-567
Source method: isolated from a genetically manipulated source
Details: Centrosomin LZ domain residues 490-567 / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pETM44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: P54623

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Non-polymers , 4 types, 30 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.6 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 3350, 0.2M potassium/sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.02→36.1 Å / Num. obs: 19929 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.02 / Net I/σ(I): 18.2
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1450 / CC1/2: 0.677 / Rpim(I) all: 0.398 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→36.099 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.39
RfactorNum. reflection% reflection
Rfree0.2689 941 4.72 %
Rwork0.2277 --
obs0.2296 19926 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→36.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 25 26 1470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051481
X-RAY DIFFRACTIONf_angle_d0.5681968
X-RAY DIFFRACTIONf_dihedral_angle_d14.511954
X-RAY DIFFRACTIONf_chiral_restr0.034230
X-RAY DIFFRACTIONf_plane_restr0.003251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.12650.45781320.3562696X-RAY DIFFRACTION99
2.1265-2.25970.32631510.28072651X-RAY DIFFRACTION99
2.2597-2.43410.26891330.24652716X-RAY DIFFRACTION99
2.4341-2.6790.25131190.24132707X-RAY DIFFRACTION99
2.679-3.06650.29891470.23312688X-RAY DIFFRACTION99
3.0665-3.86280.28951380.22122734X-RAY DIFFRACTION99
3.8628-36.10510.22881210.2092793X-RAY DIFFRACTION97
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)
19.76886.5583-1.3965.3183-1.38285.7151-0.02870.6991-0.6017-0.2750.2290.04590.5476-0.3258-0.12250.4049-0.0134-0.00441.3075-0.09650.6594-27.5461-0.05259.1218
24.03814.13021.04654.8236-0.80713.14010.42780.7421.72590.18180.0329-0.18380.1951-0.4312-0.44780.43810.064-0.12851.2921-0.18171.0281-0.39655.382911.0638
35.649-2.99895.03329.4160.87256.19090.41531.50311.4399-0.3549-0.7096-0.1308-0.2016-0.04090.20760.45270.04770.00650.59490.15170.5130.61314.757510.1863
47.54361.3142.4923.3384-4.23797.88210.1581-0.99911.38360.36990.32030.1995-0.4489-0.7634-0.22420.50780.0884-0.08191.3506-0.08740.5898-26.24680.79411.2602
59.2338-5.53893.41064.9951-4.33663.8350.7403-0.6406-0.5064-0.0031-0.0673-0.43930.7451-0.9556-0.55180.446-0.0198-0.15851.2233-0.15830.8918-0.503-4.746411.1064
64.35931.6056-1.66226.75554.41936.43940.6635-1.9949-1.15330.7207-0.42340.14360.7013-0.9677-0.23380.5309-0.1129-0.03250.6220.15820.543427.164-4.23525.5469
74.22213.1743-3.73434.5486-5.67088.11740.78710.31840.3936-0.8658-0.1725-0.85270.49921.6636-0.2350.77140.02250.01550.54010.04850.931550.17795.972817.9212
86.1801-3.044-4.56111.8313.0125.12320.1323-0.96840.01490.4454-0.2991-0.91160.16530.0393-0.07240.5558-0.0061-0.12980.32070.02850.819642.22374.378721.2304
96.53044.7789-3.91714.9465-1.05524.78030.3717-0.85592.09380.33180.5790.0757-0.6231-0.2138-0.44460.45960.0289-0.04480.3154-0.09370.666932.81885.213320.3969
104.6994.5622-2.85814.7554-3.14932.4110.6147-1.1621.18420.78860.23310.4618-1.0506-1.3923-0.61230.41390.00520.06160.7123-0.04260.61121.93464.34521.8524
113.55353.4414-3.3115.0434-4.79125.62230.1509-1.46890.35611.0241-0.4209-0.3709-1.33961.29770.49150.7628-0.0105-0.09740.59820.12970.87648.3171-5.17427.6396
127.06162.53374.03847.03246.15236.1397-0.12890.66510.7418-0.19620.0327-2.1046-0.24590.9276-0.19810.5279-0.0249-0.08570.35590.01090.954444.0222-3.762822.0411
136.3734-5.06063.70084.8617-3.39172.65550.7389-0.2594-1.55260.0710.12960.16571.27610.5545-0.45120.50120.0245-0.08340.3784-0.07030.670435.7206-5.278517.4243
143.3857-1.56190.84836.4151-4.9934.03030.3531.2308-0.7551-0.5090.258-0.07951.1884-0.6139-0.60130.4816-0.0113-0.08920.5845-0.04660.48825.0039-3.724611.8492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1082:1099)
2X-RAY DIFFRACTION2(chain A and resid 1100:1120)
3X-RAY DIFFRACTION3(chain A and resid 1121:1140)
4X-RAY DIFFRACTION4(chain B and resid 1081:1099)
5X-RAY DIFFRACTION5(chain B and resid 1100:1120)
6X-RAY DIFFRACTION6(chain B and resid 1121:1140)
7X-RAY DIFFRACTION7(chain C and resid 518:523)
8X-RAY DIFFRACTION8(chain C and resid 524:530)
9X-RAY DIFFRACTION9(chain C and resid 531:535)
10X-RAY DIFFRACTION10(chain C and resid 536:544)
11X-RAY DIFFRACTION11(chain D and resid 518:522)
12X-RAY DIFFRACTION12(chain D and resid 523:528)
13X-RAY DIFFRACTION13(chain D and resid 529:534)
14X-RAY DIFFRACTION14(chain D and resid 535:544)

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