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- PDB-8fwp: Crystal Structure of CDC10 - CDC3 heterocomplex from Saccharomyce... -

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Basic information

Entry
Database: PDB / ID: 8fwp
TitleCrystal Structure of CDC10 - CDC3 heterocomplex from Saccharomyces cerevisiae
Components(Cell division control protein ...) x 2
KeywordsCELL CYCLE / Septin
Function / homology
Function and homology information


ascospore-type prospore / septin ring disassembly / septin filament array / cellular bud neck septin ring organization / Gin4 complex / ascospore wall / mating projection base / cellular bud neck septin ring / sporulation / septin complex ...ascospore-type prospore / septin ring disassembly / septin filament array / cellular bud neck septin ring organization / Gin4 complex / ascospore wall / mating projection base / cellular bud neck septin ring / sporulation / septin complex / septin ring assembly / prospore membrane / 1-phosphatidylinositol binding / cytoskeleton-dependent cytokinesis / phosphatidylinositol-5-phosphate binding / septum digestion after cytokinesis / septin ring / cellular bud neck / mating projection tip / phosphatidylinositol-4-phosphate binding / meiotic spindle / exit from mitosis / cell division site / mitotic cytokinesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton / molecular adaptor activity / GTPase activity / GTP binding
Similarity search - Function
Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Cell division control protein 10 / Cell division control protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsSilva, R.M. / Leonardo, D.A. / Pereira, H.M. / Garratt, R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2020/02897-1 Brazil
CitationJournal: J.Struct.Biol. / Year: 2023
Title: A key piece of the puzzle: The central tetramer of the Saccharomyces cerevisiae septin protofilament and its implications for self-assembly.
Authors: Marques da Silva, R. / Christe Dos Reis Saladino, G. / Antonio Leonardo, D. / D'Muniz Pereira, H. / Andrea Sculaccio, S. / Paula Ulian Araujo, A. / Charles Garratt, R.
History
DepositionJan 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 10
B: Cell division control protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7735
Polymers67,7822
Non-polymers9913
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-28 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.547, 83.547, 220.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Cell division control protein ... , 2 types, 2 molecules AB

#1: Protein Cell division control protein 10


Mass: 32256.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CDC10, YCR002C, YCR022, YCR2C / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P25342
#2: Protein Cell division control protein 3


Mass: 35525.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CDC3, YLR314C, L8543.7 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P32457

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Non-polymers , 4 types, 186 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium formate 0.1 M Bis-Tris propane 6.5 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.22→46.03 Å / Num. obs: 39667 / % possible obs: 99.9 % / Redundancy: 26 % / CC1/2: 0.996 / Rmerge(I) obs: 0.297 / Rpim(I) all: 6.8 / Rrim(I) all: 0.303 / Net I/σ(I): 11.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.22-2.353.571.262480.44880.23.637
2.35-2.512.36959380.7162.414
2.51-2.711.62755230.851.658
2.71-2.970.96351070.950.983
2.97-3.320.50446470.9880.514
3.32-3.830.24641390.9950.251
3.83-4.680.13835460.9980.141
4.68-6.590.11328170.9980.116
6.59-43.030.06717020.9960.069

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→46.03 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1982 5 %Random selection
Rwork0.1901 ---
obs0.192 39645 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 61 185 4452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084342
X-RAY DIFFRACTIONf_angle_d0.9515881
X-RAY DIFFRACTIONf_dihedral_angle_d16.6961634
X-RAY DIFFRACTIONf_chiral_restr0.057666
X-RAY DIFFRACTIONf_plane_restr0.009746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.270.37721380.30562634X-RAY DIFFRACTION99
2.27-2.330.34021380.26832628X-RAY DIFFRACTION100
2.33-2.40.28031390.26412637X-RAY DIFFRACTION100
2.4-2.480.34831380.26692622X-RAY DIFFRACTION100
2.48-2.570.34081400.26232662X-RAY DIFFRACTION100
2.57-2.670.29371390.23552648X-RAY DIFFRACTION100
2.67-2.790.26241400.21172663X-RAY DIFFRACTION100
2.79-2.940.21851410.20752663X-RAY DIFFRACTION100
2.94-3.130.2651400.21972671X-RAY DIFFRACTION100
3.13-3.370.29411420.20582698X-RAY DIFFRACTION100
3.37-3.710.21081420.18072698X-RAY DIFFRACTION100
3.71-4.240.17681440.15832734X-RAY DIFFRACTION100
4.24-5.340.16251460.13942763X-RAY DIFFRACTION100
5.34-46.030.1961550.17432942X-RAY DIFFRACTION100
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)
18.0462-0.8763-1.21935.4284-0.43786.1203-0.0964-0.30530.01690.24230.05-0.183-0.114-0.05950.04360.26740.00670.01040.2988-0.00620.306219.933-41.786722.1369
21.2084-0.8866-0.18016.65590.73511.4054-0.13-0.06170.0833-0.09890.2212-0.51130.13070.0656-0.08450.3316-0.01830.00790.3044-0.01360.312231.7678-48.801519.4231
33.2886-0.92080.26014.16560.69263.1368-0.03120.3398-0.2332-0.8677-0.05830.43210.1264-0.28240.13740.5236-0.0781-0.09930.3437-0.0540.34216.0034-40.32446.6215
45.3573-4.9638-1.40687.31151.93331.42440.13280.2812-0.524-0.6456-0.26210.89890.1453-0.22640.16730.4774-0.0595-0.06230.30270.00510.346317.2365-48.849511.223
51.601-0.2050.50614.6706-0.21391.4549-0.05910.28040.3918-1.03660.08520.2088-0.2867-0.1265-0.02660.77610.0492-0.10480.3821-0.00040.415718.9208-9.98514.1093
65.2811-2.19881.58065.905-2.98476.1484-0.15860.062-0.0398-1.05480.34990.405-0.5371-0.7417-0.19150.8097-0.0176-0.06720.4509-0.02880.454723.0346-8.50974.1291
73.32984.6974-1.10897.7051-0.46581.0136-0.16090.22540.016-1.59170.2624-0.5811-0.0680.0651-0.04950.77770.00950.09580.3668-0.04710.391833.80751.72156.7814
83.01311.30980.34863.69660.19511.2813-0.0951-0.04040.3254-0.1745-0.05940.5328-0.2877-0.24650.17330.41020.0548-0.06820.2911-0.07030.368416.598-16.084719.0073
99.13267.5366-0.44129.11790.01770.79630.2976-0.09410.8205-0.1784-0.20371.0265-0.3483-0.1404-0.10650.60940.065-0.030.3548-0.06460.47319.7057-0.961716.8809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 144 )
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 252 )
4X-RAY DIFFRACTION4chain 'A' and (resid 253 through 302 )
5X-RAY DIFFRACTION5chain 'B' and (resid 118 through 182 )
6X-RAY DIFFRACTION6chain 'B' and (resid 183 through 215 )
7X-RAY DIFFRACTION7chain 'B' and (resid 216 through 251 )
8X-RAY DIFFRACTION8chain 'B' and (resid 252 through 368 )
9X-RAY DIFFRACTION9chain 'B' and (resid 369 through 409 )

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