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- PDB-9gd4: Crystal structure of septin complex Shs1-Cdc12-Cdc3-Cdc10 from Sa... -

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Basic information

Entry
Database: PDB / ID: 9gd4
TitleCrystal structure of septin complex Shs1-Cdc12-Cdc3-Cdc10 from Saccharomyces cerevisiae
Components
  • (Cell division control protein ...) x 3
  • Seventh homolog of septin 1
KeywordsSTRUCTURAL PROTEIN / septins / complex / guanine nucleotide binding protein
Function / homology
Function and homology information


cellular bud scar / ascospore-type prospore / mating projection / septin ring disassembly / septin filament array / endoplasmic reticulum polarization / protein localization to bud neck / cellular bud neck septin ring organization / Gin4 complex / mating projection base ...cellular bud scar / ascospore-type prospore / mating projection / septin ring disassembly / septin filament array / endoplasmic reticulum polarization / protein localization to bud neck / cellular bud neck septin ring organization / Gin4 complex / mating projection base / ascospore wall / cellular bud neck septin ring / mitotic actomyosin contractile ring assembly / actomyosin contractile ring assembly / sporulation / septin complex / 1-phosphatidylinositol binding / prospore membrane / septin ring assembly / Release of apoptotic factors from the mitochondria / septum digestion after cytokinesis / phosphatidylinositol-5-phosphate binding / septin ring / cytoskeleton-dependent cytokinesis / maintenance of cell polarity / cellular bud neck / mating projection tip / division septum assembly / phosphatidylinositol-4-phosphate binding / meiotic spindle / exit from mitosis / cell division site / mitotic cytokinesis / spindle microtubule / structural constituent of cytoskeleton / G1/S transition of mitotic cell cycle / intracellular protein localization / microtubule cytoskeleton / molecular adaptor activity / GTPase activity / GTP binding / cytosol / cytoplasm
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 / Cell division control protein 10 / Cell division control protein 3 / Cell division control protein 12 / Seventh homolog of septin 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.039 Å
AuthorsGrupp, B. / Seifermann, J. / Gerhardt, S. / Gronemeyer, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of septin complex Shs1-Cdc12-Cdc3-Cdc10 from Saccharomyces cerevisiae
Authors: Grupp, B. / Seifermann, J. / Gerhardt, S. / Graser, J. / Johnsson, N. / Gronemeyer, T.
History
DepositionAug 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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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
C: Cell division control protein 12
D: Seventh homolog of septin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,09110
Polymers147,1984
Non-polymers1,8936
Water10,557586
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17470 Å2
ΔGint-100 kcal/mol
Surface area47380 Å2
Unit cell
Length a, b, c (Å)98.205, 47.845, 148.885
Angle α, β, γ (deg.)90, 103.29, 90
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Cell division control protein ... , 3 types, 3 molecules ABC

#1: Protein Cell division control protein 10


Mass: 34658.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC10, YCR002C, YCR022, YCR2C / Plasmid: pACYCDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25342
#2: Protein Cell division control protein 3


Mass: 38564.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC3, YLR314C, L8543.7 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32457
#3: Protein Cell division control protein 12 / Septin


Mass: 37554.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC12, CLA10, PSL7, YHR107C / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32468

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Protein , 1 types, 1 molecules D

#4: Protein Seventh homolog of septin 1 / Septation protein 7


Mass: 36420.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SHS1, SEP7, YDL225W / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07657

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Non-polymers , 4 types, 592 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17.5 % PEG 5000, 0.2 M ammonium sulphate, 0.1 M BIS-TRIS pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873129 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873129 Å / Relative weight: 1
ReflectionResolution: 2.039→144.9 Å / Num. obs: 41902 / % possible obs: 89.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 17 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.145 / Rrim(I) all: 0.338 / Net I/σ(I): 5.2
Reflection shellResolution: 2.039→2.355 Å / Redundancy: 5 % / Rmerge(I) obs: 1.567 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2095 / CC1/2: 0.431 / Rpim(I) all: 0.774 / Rrim(I) all: 1.753 / % possible all: 61.7

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Processing

Software
NameVersionClassification
autoPROC1.0.5 (20230614)data processing
XDSJun 30, 2023 (BUILT 20230630)data reduction
STARANISO2.3.94 (20230525)data scaling
PHASER2.8.3phasing
BUSTER2.10.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.039→23.49 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.46 / SU Rfree Blow DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.2535 2096 -RANDOM
Rwork0.2161 ---
obs0.218 41834 48.2 %-
Displacement parametersBiso mean: 26.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.128 Å20 Å2-1.9562 Å2
2--2.1296 Å20 Å2
3----2.0016 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.039→23.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9026 0 118 586 9730
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00618249HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8132955HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5494SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2926HARMONIC5
X-RAY DIFFRACTIONt_it9387HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1271SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact17040SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion17.5
LS refinement shellResolution: 2.04→2.24 Å
RfactorNum. reflection% reflection
Rfree0.3888 41 -
Rwork0.2691 --
obs0.2747 837 3.99 %
Refinement TLS params.

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)
16.251-2.19410.06793.86910.63092.4788-0.10710.3626-0.10980.3626-0.05160.1771-0.10980.17710.1587-0.1945-0.1128-0.07810.02970.0909-0.137845.7431-22.8929.3605
22.4436-1.3411.04770.8461-0.63951.0274-0.04430.05180.10430.05180.1063-0.02210.1043-0.0221-0.062-0.0745-0.0823-0.0490.04180.0614-0.159439.4006-34.029731.8087
31.366-0.70111.23350.6324-0.88873.02830.2083-0.13450.2485-0.1345-0.0882-0.11270.2485-0.1127-0.1202-0.0833-0.0705-0.1024-0.03250.0362-0.166219.5706-23.2977-5.688
40.8229-0.12350.51880.5101-0.19473.8658-0.0116-0.0367-0.227-0.0367-0.04610.2182-0.2270.21820.0577-0.129-0.0603-0.0710.03480.0872-0.13625.4723-17.22261.0289
50.9653-0.38650.71730.4851-0.5762.2787-0.01920.05-0.27920.05-0.03080.1737-0.27920.17370.0499-0.0578-0.051-0.0437-0.06860.016-0.069114.3948-6.5859-35.0651
61.0422-0.31390.73760.71070.01521.4554-0.01240.10610.06840.10610.0029-0.1010.0684-0.1010.0095-0.0354-0.0109-0.0169-0.01060.0163-0.08881.3344-9.1303-39.9383
70.75080.04670.03830.6049-0.30672.43290.0055-0.15990.0893-0.15990.0183-0.19460.0893-0.1946-0.0238-0.01140.0401-0.0768-0.10990.0104-0.0548-6.3893-3.5655-71.9332
8-0.10670.17480.96412.8476-1.03113.2056-0.282-0.2204-0.4944-0.22040.2729-0.7201-0.4944-0.72010.0091-0.04940.0695-0.0916-0.1696-0.0293-0.1051-9.87610.8887-64.1199
92.8645-0.5472-2.4672.15680.17247.1382-0.0011-0.0196-0.7853-0.01960.0960.0991-0.78530.0991-0.0949-0.03020.0808-0.1496-0.18640.0312-0.1456-7.86947.9541-78.8702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|31 - 94}A31 - 94
2X-RAY DIFFRACTION2{A|95 - 303}A95 - 303
3X-RAY DIFFRACTION3{B|91 - 225}B91 - 225
4X-RAY DIFFRACTION4{B|226 - 410}B226 - 410
5X-RAY DIFFRACTION5{C|10 - 134}C10 - 134
6X-RAY DIFFRACTION6{C|135 - 313}C135 - 313
7X-RAY DIFFRACTION7{D|21 - 239}D21 - 239
8X-RAY DIFFRACTION8{D|240 - 296}D240 - 296
9X-RAY DIFFRACTION9{D|297 - 338}D297 - 338

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