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- PDB-8sgd: Crystal Structure of CDC3(G) - CDC10(Delta 1-10) heterocomplex fr... -

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Basic information

Entry
Database: PDB / ID: 8sgd
TitleCrystal Structure of CDC3(G) - CDC10(Delta 1-10) heterocomplex from Saccharomyces cerevisiae
Components
  • CDC10 isoform 1
  • CDC3 isoform 1
KeywordsCELL CYCLE / Septin
Function / homology
Function and homology information


septin complex / cellular bud neck / cell cycle / 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 / CDC10 isoform 1 / CDC3 isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsSaladino, G.C.R. / 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
DepositionApr 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 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: CDC10 isoform 1
B: CDC3 isoform 1
C: CDC10 isoform 1
D: CDC3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,02323
Polymers143,7434
Non-polymers2,28019
Water2,846158
1
A: CDC10 isoform 1
B: CDC3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,00011
Polymers71,8722
Non-polymers1,1299
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-106 kcal/mol
Surface area25020 Å2
MethodPISA
2
C: CDC10 isoform 1
D: CDC3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,02312
Polymers71,8722
Non-polymers1,15210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-94 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.277, 154.271, 156.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein CDC10 isoform 1


Mass: 36175.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC10 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4BSX4
#2: Protein CDC3 isoform 1


Mass: 35695.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC3 / Plasmid: pET-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A8H4BZN9

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Non-polymers , 5 types, 177 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27% polyethylene glycol 3,350, 100 mM BIS-TRIS pH 6,5 and 270 mM sodium iodide

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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: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 40940 / % possible obs: 99.2 % / Redundancy: 10.03 % / CC1/2: 0.995 / Rmerge(I) obs: 0.421 / Rrim(I) all: 0.438 / Net I/σ(I): 8.23
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.66-2.822.90164350.4713.018198.5
2.82-3.021.98261320.6782.0671
3.02-3.261.29957230.8411.3531
3.26-3.570.81852680.9590.8491
3.57-3.990.5448200.9820.5611
3.99-4.60.33843020.9910.3521
4.6-5.620.2336150.990.2421
5.62-7.90.17529030.9930.1821
7.9-500.06817420.9980.0711

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→49.35 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 2047 5 %
Rwork0.206 --
obs0.2085 40926 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8800 0 135 158 9093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029089
X-RAY DIFFRACTIONf_angle_d0.50212309
X-RAY DIFFRACTIONf_dihedral_angle_d15.923422
X-RAY DIFFRACTIONf_chiral_restr0.0421388
X-RAY DIFFRACTIONf_plane_restr0.0041564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.720.37981320.31142507X-RAY DIFFRACTION98
2.72-2.790.34751330.29432529X-RAY DIFFRACTION98
2.79-2.870.29131340.28012551X-RAY DIFFRACTION100
2.87-2.950.36181350.27982562X-RAY DIFFRACTION98
2.95-3.050.36231350.27182566X-RAY DIFFRACTION100
3.05-3.160.33751330.26962533X-RAY DIFFRACTION99
3.16-3.280.35121360.24472582X-RAY DIFFRACTION99
3.28-3.430.28971360.21622584X-RAY DIFFRACTION99
3.43-3.610.24781370.20112591X-RAY DIFFRACTION100
3.61-3.840.24931360.18622586X-RAY DIFFRACTION99
3.84-4.140.22071370.16492602X-RAY DIFFRACTION100
4.14-4.550.16491370.14672608X-RAY DIFFRACTION99
4.55-5.210.2031390.15392641X-RAY DIFFRACTION100
5.21-6.560.25321390.21222630X-RAY DIFFRACTION98
6.56-49.350.23331480.20262807X-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)
12.90280.41421.42632.98821.06792.0019-0.34770.35430.2365-0.2229-0.4507-0.1116-0.16780.79010.72360.5969-0.049-0.07640.65750.06080.45936.629621.0369-23.1838
21.94010.21151.01781.70090.847.61220.0606-0.15110.18580.14910.1078-0.24630.1207-0.55490.11970.340.0551-0.05360.31830.01160.40959.441423.16148.9129
32.1370.7086-1.09981.0564-0.96823.95960.55010.13050.30170.35740.26310.1497-0.431-0.2268-0.64660.68990.0183-0.02940.5764-0.0610.40816.605430.168618.5383
41.5190.1150.0391.3149-0.59082.37480.0058-0.0960.136-0.01-0.05540.179-0.1179-0.26510.05380.48020.045-0.05550.4504-0.04040.4798-0.769823.93148.2944
51.35740.34660.30710.6672-0.80061.8575-0.0068-0.1427-0.1441-0.27430.05090.10360.107-0.3277-0.04780.4605-0.0152-0.07920.4009-0.06020.36873.061215.245110.0314
63.72824.4742-0.57175.471-0.08922.13620.173-0.1185-0.88360.4975-0.2612-0.3870.45610.3631-0.04970.54980.1123-0.06280.4295-0.05860.537115.052.817117.0019
74.8952-1.302-1.91162.9086-1.03234.6133-0.03410.8263-0.7144-0.3421-0.3942-0.08260.0893-0.21810.39150.528-0.0718-0.02180.4758-0.09570.48089.77923.2717-0.2134
81.3201-1.56032.16458.26491.56746.29690.07350.70630.1503-0.0792-0.0395-0.9215-0.70350.0068-0.07170.3607-0.01030.01560.4984-0.02040.388227.052423.453910.4282
94.1314-0.92131.54960.8244-0.19312.2610.72850.4595-0.42760.0831-0.3125-0.07170.22590.1793-0.36170.53180.0012-0.0270.34970.02980.35669.98315.05263.3689
104.944-0.6117-0.54652.1861-0.63792.7179-0.3886-0.54150.11430.00490.0899-0.30740.14180.02740.29740.51770.012-0.1320.47620.02620.420720.04597.911341.2872
111.31150.00740.47763.019-1.2496.5796-0.0319-0.2979-0.08140.1936-0.3356-0.48690.20480.34950.25410.4631-0.0416-0.09170.46390.04840.571512.66289.991347.2235
121.0236-0.0417-1.16170.20320.57253.92740.0249-0.23310.12370.1236-0.0571-0.1372-0.27930.42740.01840.4291-0.018-0.10250.35960.00190.398321.537620.682241.0633
130.64370.1208-0.95280.3057-0.04413.22840.15460.06230.13210.05320.0572-0.0007-0.37450.0973-0.21380.43160.00840.07270.3720.01390.4189-20.2951-12.192546.5683
141.8436-0.1090.26810.83290.38024.7012-0.0796-0.0925-0.11670.1570.07620.07320.642-0.4152-0.01010.4502-0.04770.08460.43370.06480.4253-24.0334-25.199839.3931
153.5121.1408-0.32142.1888-0.23821.2470.1241-0.1147-0.21320.217-0.09010.34430.528-0.3403-0.06360.4599-0.08690.05970.4885-0.01290.4555-8.4914-28.97899.1328
164.2696-0.03891.26986.50314.33983.3302-0.0656-0.2345-0.2838-0.043-0.46150.70940.4589-0.48670.43930.4186-0.0610.04320.4792-0.06490.4852-3.9122-27.8649.0681
175.5371-0.2423-3.88861.9146-1.24188.2061-0.2951-0.6405-0.02660.0557-0.3625-0.12480.12971.19920.55060.418-0.07970.050.52510.09930.49417.5728-20.4779.373
184.28470.465-1.22541.2843-0.12942.11420.05320.4150.1407-0.20790.0735-0.07160.0505-0.2366-0.13470.42630.00330.0420.40620.03570.3458-12.3839-16.70859.6657
198.481.1149-1.93971.23750.14173.44430.01871.1281-0.0226-0.24770.08970.02430.4261-0.2207-0.10710.49570.04160.02780.47830.01550.3513-6.4385-16.5487-0.2789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 185 )
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 229 )
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 252 )
9X-RAY DIFFRACTION9chain 'A' and (resid 253 through 302 )
10X-RAY DIFFRACTION10chain 'B' and (resid 118 through 182 )
11X-RAY DIFFRACTION11chain 'B' and (resid 183 through 237 )
12X-RAY DIFFRACTION12chain 'B' and (resid 238 through 409 )
13X-RAY DIFFRACTION13chain 'C' and (resid 12 through 158 )
14X-RAY DIFFRACTION14chain 'C' and (resid 159 through 302 )
15X-RAY DIFFRACTION15chain 'D' and (resid 118 through 182 )
16X-RAY DIFFRACTION16chain 'D' and (resid 183 through 215 )
17X-RAY DIFFRACTION17chain 'D' and (resid 216 through 235 )
18X-RAY DIFFRACTION18chain 'D' and (resid 236 through 368 )
19X-RAY DIFFRACTION19chain 'D' and (resid 369 through 412 )

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