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- PDB-8pfh: Crystal structure of the yeast septin complex Shs1-Cdc12-Cdc3-Cdc10 -

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Basic information

Entry
Database: PDB / ID: 8pfh
TitleCrystal structure of the yeast septin complex Shs1-Cdc12-Cdc3-Cdc10
Components
  • CDC10 isoform 1
  • CDC12 isoform 1
  • Cell division control protein 3
  • SHS1 isoform 1
KeywordsSTRUCTURAL PROTEIN / Septins / complex
Function / homology
Function and homology information


septin ring disassembly / septin filament array / cellular bud neck septin ring organization / Gin4 complex / mating projection base / ascospore wall / cellular bud neck septin ring / cell cycle / septin complex / septin ring assembly ...septin ring disassembly / septin filament array / cellular bud neck septin ring organization / Gin4 complex / mating projection base / ascospore wall / cellular bud neck septin ring / cell cycle / septin complex / septin ring assembly / prospore membrane / phosphatidylinositol-5-phosphate binding / septum digestion after cytokinesis / septin ring / cytoskeleton-dependent cytokinesis / cellular bud neck / phosphatidylinositol-4-phosphate binding / cell division site / mitotic cytokinesis / structural constituent of cytoskeleton / intracellular protein localization / 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 / CDC12 isoform 1 / CDC10 isoform 1 / SHS1 isoform 1 / Cell division control protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsGrupp, B. / Denkhaus, L. / Gerhardt, S. / Gronemeyer, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2024
Title: The structure of a tetrameric septin complex reveals a hydrophobic element essential for NC-interface integrity.
Authors: Grupp, B. / Denkhaus, L. / Gerhardt, S. / Vogele, M. / Johnsson, N. / Gronemeyer, T.
History
DepositionJun 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDC10 isoform 1
B: Cell division control protein 3
C: CDC12 isoform 1
D: SHS1 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9708
Polymers147,1984
Non-polymers1,7734
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)258.178, 69.373, 92.533
Angle α, β, γ (deg.)90.000, 109.680, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein CDC10 isoform 1


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 / Plasmid: pACYC-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8H4BSX4
#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: pACYC-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32457
#3: Protein CDC12 isoform 1


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 / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6A5PZQ6
#4: Protein SHS1 isoform 1


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 / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8H8UM78
#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
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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 % PEG 5000, 0.3 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: 0.885602 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885602 Å / Relative weight: 1
ReflectionResolution: 3.24→121.55 Å / Num. obs: 15695 / % possible obs: 63.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 39.32 Å2 / CC1/2: 0.937 / Rpim(I) all: 0.334 / Net I/σ(I): 3.2
Reflection shellResolution: 3.24→3.65 Å / Num. unique obs: 786 / CC1/2: 0.579 / Rpim(I) all: 0.877 / % possible all: 10.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→121.55 Å / SU ML: 0.3423 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2897 779 4.96 %RANDOM
Rwork0.2822 14913 --
obs0.2826 15692 63.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.79 Å2
Refinement stepCycle: LAST / Resolution: 3.24→121.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8974 0 112 0 9086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319261
X-RAY DIFFRACTIONf_angle_d0.519112593
X-RAY DIFFRACTIONf_chiral_restr0.04111443
X-RAY DIFFRACTIONf_plane_restr0.00531643
X-RAY DIFFRACTIONf_dihedral_angle_d13.04363426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.450.242650.32184X-RAY DIFFRACTION4.59
3.45-3.710.2712550.3377889X-RAY DIFFRACTION23.08
3.71-4.080.35181280.3082345X-RAY DIFFRACTION60.32
4.09-4.680.27831800.27153538X-RAY DIFFRACTION90.33
4.68-5.890.26421900.2763938X-RAY DIFFRACTION99.66
5.89-121.550.29342210.27364019X-RAY DIFFRACTION99.51
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)
12.434788443150.191290764167-0.8510786160651.80128770708-0.8803244984762.083806830550.2377175606430.03371226762560.326000576077-0.269267969311-0.09199948307060.027105606654-0.145873167182-0.110384160882-0.1409091316330.4232715494820.06379938916320.1396437950260.39522862201-0.002040850012650.318535330433-77.127666557254.013318277268.9492353257
22.69952235772-1.920206519350.6559729667142.26676404592-0.8185471743631.010610996620.08792488756330.2133540985530.00631297899492-0.104101423833-0.0444063238519-0.1794783527170.001907443767050.0223782898014-0.04584903834010.3467361315710.07705019777510.1422855660350.389672028456-0.01332638294980.340052852256-45.406152299531.897941901667.1687041934
32.21939707879-1.127687851110.416280350722.70240264068-0.437605349923-0.003531372763910.0402401252440.0740271378464-0.0424679960938-0.167150900824-0.003156027383570.115198867807-0.1735664984810.039544389449-0.04330189989930.479675520292-0.01519583310590.1706810562440.367539724265-0.09778978949760.324163777387-11.6331957594.8489903414766.7855380209
42.01753851822-1.42995811001-0.0451140003132.89017507911-0.1405265183131.488433631560.09741927020370.254943076886-0.0399888259729-0.377686026311-0.0225838341235-0.2281921570940.0544921874990.202060797452-0.04765827717530.391993359682-0.05325131459980.128740793420.32193939551-0.04936694907630.28974837943716.0220991688-20.441205347866.9889009951
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 31 through 401)AA31 - 3061 - 272
22(chain 'B' and resid 98 through 501)BC98 - 4091 - 287
33(chain 'C' and resid 12 through 401)CE12 - 3131 - 289
44(chain 'D' and resid 22 through 401)DG22 - 3391 - 291

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