[English] 日本語
Yorodumi
- PDB-8pfh: Crystal structure of the yeast septin complex Shs1-Cdc12-Cdc3-Cdc10 -

+
Open data


ID or keywords:

Loading...

-
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 / ascospore wall / mating projection base / cellular bud neck septin ring / septin complex / septin ring assembly / prospore membrane ...septin ring disassembly / septin filament array / cellular bud neck septin ring organization / Gin4 complex / ascospore wall / mating projection base / cellular bud neck septin ring / septin complex / septin ring assembly / prospore membrane / phosphatidylinositol-5-phosphate binding / cytoskeleton-dependent cytokinesis / septum digestion after cytokinesis / septin ring / cellular bud neck / phosphatidylinositol-4-phosphate binding / cell division site / mitotic cytokinesis / positive regulation of protein serine/threonine kinase activity / structural constituent of cytoskeleton / microtubule cytoskeleton / molecular adaptor activity / cell cycle / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / Guanosine 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more