[English] 日本語
Yorodumi
- EMDB-3583: Cryo-EM structure of a Separase-Securin complex from Caenorhabdit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3583
TitleCryo-EM structure of a Separase-Securin complex from Caenorhabditis elegans at 3.8 A resolution
Map dataMap of the C. elegans Separase-Securin complex. Manual B-factor sharpening of 140 applied.
Sample
  • Complex: Caenorhabditis elegans Separase-Securin complex
    • Protein or peptide: SEParase
    • Protein or peptide: Interactor of FizzY protein
Function / homology
Function and homology information


Separation of Sister Chromatids / separase-securin complex / eggshell formation / metaphase plate / regulation of nematode larval development / separase / cortical granule exocytosis / maintenance of meiotic sister chromatid cohesion / meiotic chromosome separation / maintenance of mitotic sister chromatid cohesion ...Separation of Sister Chromatids / separase-securin complex / eggshell formation / metaphase plate / regulation of nematode larval development / separase / cortical granule exocytosis / maintenance of meiotic sister chromatid cohesion / meiotic chromosome separation / maintenance of mitotic sister chromatid cohesion / polarity specification of anterior/posterior axis / polar body extrusion after meiotic divisions / cortical granule / regulation of centriole-centriole cohesion / mitotic sister chromatid separation / regulation of exocytosis / multicellular organismal reproductive process / meiotic spindle / regulation of locomotion / centrosome localization / cleavage furrow / centrosome duplication / mitotic cytokinesis / condensed chromosome / condensed nuclear chromosome / spindle microtubule / protein localization / mitotic spindle / spindle / protein processing / nuclear envelope / chromosome / cell cortex / midbody / protease binding / protein stabilization / cysteine-type endopeptidase activity / centrosome / ubiquitin protein ligase binding / nucleus / cytoplasm
Similarity search - Function
Peptidase family C50 / Peptidase C50, separase / SEPARIN core domain / SEPARIN core domain profile.
Similarity search - Domain/homology
Separin homolog sep-1 / Securin-like protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBoland A / Martin TG / Zhang Z / Yang J / Bai XC / Chang L / Scheres SHW / Barford D
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Cryo-EM structure of a metazoan separase-securin complex at near-atomic resolution.
Authors: Andreas Boland / Thomas G Martin / Ziguo Zhang / Jing Yang / Xiao-Chen Bai / Leifu Chang / Sjors H W Scheres / David Barford /
Abstract: Separase is a caspase-family protease that initiates chromatid segregation by cleaving the kleisin subunits (Scc1 and Rec8) of cohesin, and regulates centrosome duplication and mitotic spindle ...Separase is a caspase-family protease that initiates chromatid segregation by cleaving the kleisin subunits (Scc1 and Rec8) of cohesin, and regulates centrosome duplication and mitotic spindle function through cleavage of kendrin and Slk19. To understand the mechanisms of securin regulation of separase, we used single-particle cryo-electron microscopy (cryo-EM) to determine a near-atomic-resolution structure of the Caenorhabditis elegans separase-securin complex. Separase adopts a triangular-shaped bilobal architecture comprising an N-terminal tetratricopeptide repeat (TPR)-like α-solenoid domain docked onto the conserved C-terminal protease domain. Securin engages separase in an extended antiparallel conformation, interacting with both lobes. It inhibits separase by interacting with the catalytic site through a pseudosubstrate mechanism, thus revealing that in the inhibited separase-securin complex, the catalytic site adopts a conformation compatible with substrate binding. Securin is protected from cleavage because an aliphatic side chain at the P1 position represses protease activity by disrupting the organization of catalytic site residues.
History
DepositionJan 31, 2017-
Header (metadata) releaseFeb 15, 2017-
Map releaseMar 8, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5mz6
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3583.png

Downloads & links

-
Map

FileDownload / File: emd_3583.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the C. elegans Separase-Securin complex. Manual B-factor sharpening of 140 applied.
Voxel sizeX=Y=Z: 1.43 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.29977334 - 0.39163244
Average (Standard dev.)0.00042302595 (±0.009249026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 257.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z257.400257.400257.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.3000.3920.000

-
Supplemental data

-
Sample components

-
Entire : Caenorhabditis elegans Separase-Securin complex

EntireName: Caenorhabditis elegans Separase-Securin complex
Components
  • Complex: Caenorhabditis elegans Separase-Securin complex
    • Protein or peptide: SEParase
    • Protein or peptide: Interactor of FizzY protein

-
Supramolecule #1: Caenorhabditis elegans Separase-Securin complex

SupramoleculeName: Caenorhabditis elegans Separase-Securin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: C. elegans Separase-Securin complex at 3.8 Angstrom resolution refined with Relion.
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 170 KDa

-
Macromolecule #1: SEParase

MacromoleculeName: SEParase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 144.315984 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKITNKSVDK QHIEKLDELR KNVSCTVIGF AEQTAELQQE ISELFIAEFG VNGPIDMNSL SKLARITSYY ASSEYFQGLA KYQRTACKM FITWQTLRKE AMECRSKDRE IFASIPAKLC FFYFYNGELC RAVVCLLDYI DLSDDTLAKE AALRWLMFLG E TELIEKKL ...String:
MKITNKSVDK QHIEKLDELR KNVSCTVIGF AEQTAELQQE ISELFIAEFG VNGPIDMNSL SKLARITSYY ASSEYFQGLA KYQRTACKM FITWQTLRKE AMECRSKDRE IFASIPAKLC FFYFYNGELC RAVVCLLDYI DLSDDTLAKE AALRWLMFLG E TELIEKKL KTWKMDKSSK DMFSATEFAM NYLKKSEYRV EMLEKLMKLR DKVKSDPTRS FSRYELASYV SWLCSTLSNV PV GSALREC EFPDRVSHIQ EAALKSDSLV RNRIPGLASS QFDNSVNASI WPFLDGHQED SNYYVHIGST IAWHFEMRRE CAL VNVTTA QTRDSMSAMI LNLRVALKSA SFFRVLQTTN TLAYYSSIIE EAGSEKNAKL MRVSCVNLLS SNPIIVRCST PKET GATSR AHTPMAGSSV SEKQNTMRPD LADLLGDLEL LDEQSFHPIT RSCVCNVCTI YPLHSSFAAE YMMSYAIHSD FSQLS IKHF NDEFARIRER GMSSQVLMHR DSSVRPRPNI IQNEIFGMCV IRWLTKKLDS KESADEDTME IFNNALKIVR YLQQRT TDM ILAVTQLGRQ LEFPMECNYS WMRPTIRKPR VKATIDCAVD ILRAVSPFGR RPKVEKLEKN LQPFDKERFE KVRLAMR NE MNHYGHILYR EWRCRLFAYV GRTSRDPWEA AYAWAESTQI GARNAVQSRL EKCKRGLVTM SGHDRFKTCV QSMPDEMT L VQIAMADDKT IYLVKLHADR DPIIMPLAHY SQAVELMDKF TFLLDEDEMI AKYPGDITPE EFWKRRKIVD GRMMTFVDE VQKHFLGVAA SLLMPSGQLG PKAAELAIKI HKLSKGGLLL GEAKEMVYQS KLMDAKSWEA LILRFCEMRT TDEKFKSFLP LMHRNSVEV MNQDDSIVTE KKYTYLVICP HLSQFCWERL PIFDEYPYVG RQVSIHSTFS QLEAMKSQEK QIPLQIDVQN A YYILDPDN NLGETQKRMV EYINKFNWEG TVGSAPKSNE ISAALSQRDA FFFIGHGSGS SVMPRSVLKQ STCNAISLLM GC GSVRTIP QALGFDGKTA ILDYAMAKCP LIVGCLWTVT DGEIDRFLIR MIDDCFEDSK SLTGIDKLRQ LSEAMHEARS KAR LKYLTG AAVVMYGLPV VAKQTTPFVE KDQRNLPQTP KTSARTSMRM ETVPKTPKQE FVTSKSVPMT PIFSNNENKS PSRA RMPSR VLKTPRQVKT FQEEDDEAPK RSTTRQLKPL VAPPIPATPT TRTTRSSART PSRSRNL

-
Macromolecule #2: Interactor of FizzY protein

MacromoleculeName: Interactor of FizzY protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 27.027646 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEDLNFEERG STQIPASLQQ HFSAKLGRQN ELEKTPSRGG LGLVVNSSKT PGGKSLQSLA SACKVPPSTK KNTIPIAFEC YEDETDDQI ADVATIKKTE KHPCSPIDTA NRCETFDSLA ADIEDDMLNL EDQDVVLSED RPYGDVIDPA ESEAEALAEL G VEEWDSYP ...String:
MEDLNFEERG STQIPASLQQ HFSAKLGRQN ELEKTPSRGG LGLVVNSSKT PGGKSLQSLA SACKVPPSTK KNTIPIAFEC YEDETDDQI ADVATIKKTE KHPCSPIDTA NRCETFDSLA ADIEDDMLNL EDQDVVLSED RPYGDVIDPA ESEAEALAEL G VEEWDSYP PIDPASRIGD DFNYVLRTED FAEEGDVKLE ETRHRTVIAD IDEVKMSKAE RNELFSMLAD DLDSYDLLAE EA NLPL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Details: Glow discharging was performed before applying graphene oxide solution onto the grid. Grid was washed three times, dried and sample was applied. For detailed information see: https: ...Details: Glow discharging was performed before applying graphene oxide solution onto the grid. Grid was washed three times, dried and sample was applied. For detailed information see: https://figshare.com/articles/Graphene_Oxide_Grid_Preparation/3178669
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Details: Custom Manual Plunger.
DetailsMonodisperse sample

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: -20 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Average exposure time: 0.8 sec. / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: NONE / Details: Initial model was created using SIMPLE PRIME
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 103696

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5mz6:
Cryo-EM structure of a Separase-Securin complex from Caenorhabditis elegans at 3.8 A resolution

+
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