[English] 日本語
Yorodumi
- EMDB-52445: Cryo-EM structure of human separase-SCC1 (1-631) fusion protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52445
TitleCryo-EM structure of human separase-SCC1 (1-631) fusion protein
Map dataPostprocessed map of human separase-SCC1 (1-631) fusion protein
Sample
  • Complex: Separase-SCC1 fusion protein
    • Protein or peptide: Double-strand-break repair protein rad21 homolog,Separin
  • Ligand: ZINC ION
KeywordsSeparase / cell cycle / SCC1 / RAD21 / protease / chromosome segregation / Auto-cleavage
Function / homology
Function and homology information


negative regulation of sister chromatid cohesion / separase / meiotic chromosome separation / negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex ...negative regulation of sister chromatid cohesion / separase / meiotic chromosome separation / negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / positive regulation of sister chromatid cohesion / mitotic sister chromatid separation / homologous chromosome segregation / negative regulation of glial cell apoptotic process / establishment of mitotic spindle localization / negative regulation of G2/M transition of mitotic cell cycle / meiotic spindle organization / replication-born double-strand break repair via sister chromatid exchange / positive regulation of mitotic metaphase/anaphase transition / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / negative regulation of interleukin-1 beta production / lncRNA binding / mitotic cytokinesis / mitotic sister chromatid segregation / catalytic activity / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / SUMOylation of DNA damage response and repair proteins / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / cysteine-type peptidase activity / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / chromosome segregation / nuclear matrix / spindle pole / mitotic spindle / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA recombination / Estrogen-dependent gene expression / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / response to hypoxia / cell division / cysteine-type endopeptidase activity / apoptotic process / chromatin binding / centrosome / regulation of transcription by RNA polymerase II / chromatin / proteolysis / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein ...Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Separin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYu J / Schmidt S / Botto M / Boland A
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_185235 Switzerland
Swiss National Science FoundationTMSGI3_211581 Switzerland
CitationJournal: To Be Published
Title: Structural insights into cohesin cleavage by human separase
Authors: Yu J / Schmidt S / Botto M / Ghent CM / Morgan DO / Boland A
History
DepositionJan 2, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52445.png

Downloads & links

-
Map

FileDownload / File: emd_52445.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of human separase-SCC1 (1-631) fusion protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 360 pix.
= 351.324 Å		0.98 Å/pix.
x 360 pix.
= 351.324 Å		0.98 Å/pix.
x 360 pix.
= 351.324 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9759 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.7
Minimum - Maximum-0.09247244 - 14.583449
Average (Standard dev.)-0.017093003 (±0.3191155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 351.324 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Focused refined map of human separase-SCC1 (1-631) fusion protein

Fileemd_52445_additional_1.map
AnnotationFocused refined map of human separase-SCC1 (1-631) fusion protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map of human separase-SCC1 (1-631) fusion protein

Fileemd_52445_additional_2.map
AnnotationUnsharpened map of human separase-SCC1 (1-631) fusion protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B of human separase-SCC1 (1-631) fusion protein

Fileemd_52445_half_map_1.map
AnnotationHalf map B of human separase-SCC1 (1-631) fusion protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A of human separase-SCC1 (1-631) fusion protein

Fileemd_52445_half_map_2.map
AnnotationHalf map A of human separase-SCC1 (1-631) fusion protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Separase-SCC1 fusion protein

EntireName: Separase-SCC1 fusion protein
Components
  • Complex: Separase-SCC1 fusion protein
    • Protein or peptide: Double-strand-break repair protein rad21 homolog,Separin
  • Ligand: ZINC ION

-
Supramolecule #1: Separase-SCC1 fusion protein

SupramoleculeName: Separase-SCC1 fusion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

-
Macromolecule #1: Double-strand-break repair protein rad21 homolog,Separin

MacromoleculeName: Double-strand-break repair protein rad21 homolog,Separin
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: separase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 311.176906 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MFYAHFVLSK RGPLAKIWLA AHWDKKLTKA HVFECNLESS VESIISPKVK MALRTSGHLL LGVVRIYHRK AKYLLADCNE AFIKIKMAF RPGVVDLPEE NREAAYNAIT LPEEFHDFDQ PLPDLDDIDV AQQFSLNQSR VEEITMREEV GNISILQEND F GDFGMDDR ...String:
MFYAHFVLSK RGPLAKIWLA AHWDKKLTKA HVFECNLESS VESIISPKVK MALRTSGHLL LGVVRIYHRK AKYLLADCNE AFIKIKMAF RPGVVDLPEE NREAAYNAIT LPEEFHDFDQ PLPDLDDIDV AQQFSLNQSR VEEITMREEV GNISILQEND F GDFGMDDR EIMREGSAFE DDDMLVSTTT SNLLLESEQS TSNLNEKINH LEYEDQYKDD NFGEGNDGGI LDDKLISNND GG IFDDPPA LSEAGVMLPE QPAHDDMDED DNVSMGGPDS PDSVDPVEPM PTMTDQTTLV PNEEEAFALE PIDITVKETK AKR KRKLIV DSVKELDSKT IRAQLSDYSD IVTTLDLAPP TKKLMMWKET GGVEKLFSLP AQPLWNNRLL KLFTRCLTPL VPED LRKRR KGGEADNLDE FLKEFENPEV PREDQQQQHQ QRDVIDEPII EEPSRLQESV MEASRTNIDE SAMPPPPPQG VKRKA GQID PEPVMPPQQV EQMEIPPVEL PPEEPPNICQ LIPELELLPE KEKEKEKEKE DDEEEEDEDA SGGDQDQEER RWNKRT QQM LHGLQRALAK TGAESISLLE LCRNTNRKQA AAKFYSFLVL KKQQAIELTQ EEPYSDIIAT PGPRFHIIGG SGGGGSG GG GSGGSGGSGG GSGGGSGMRS FKRVNFGTLL SSQKEAEELL PDLKEFLSNP PAGFPSSRSD AERRQACDAI LRACNQQL T AKLACPRHLG SLLELAELAC DGYLVSTPQR PPLYLERILF VLLRNAAAQG SPEVTLRLAQ PLHACLVQCS REAAPQDYE AVARGSFSLL WKGAEALLER RAAFAARLKA LSFLVLLEDE STPCEVPHFA SPTACRAVAA HQLFDASGHG LNEADADFLD DLLSRHVIR ALVGERGSSS GLLSPQRALC LLELTLEHCR RFCWSRHHDK AISAVEKAHS YLRNTNLAPS LQLCQLGVKL L QVGEEGPQ AVAKLLIKAS AVLSKSMEAP SPPLRALYES CQFFLSGLER GTKRRYRLDA ILSLFAFLGG YCSLLQQLRD DG VYGGSSK QQQSFLQMYF QGLHLYTVVV YDFAQGCQIV DLADLTQLVD SCKSTVVWML EALEGLSGQE LTDHMGMTAS YTS NLAYSF YSHKLYAEAC AISEPLCQHL GLVKPGTYPE VPPEKLHRCF RLQVESLKKL GKQAQGCKMV ILWLAALQPC SPEH MAEPV TFWVRVKMDA ARAGDKELQL KTLRDSLSGW DPETLALLLR EELQAYKAVR ADTGQERFNI ICDLLELSPE ETPAG AWAR ATHLVELAQV LCYHDFTQQT NCSALDAIRE ALQLLDSVRP EAQARDQLLD DKAQALLWLY ICTLEAKMQE GIERDR RAQ APGNLEEFEV NDLNYEDKLQ EDRFLYSNIA FNLAADAAQS KCLDQALALW KELLTKGQAP AVRCLQQTAA SLQILAA LY QLVAKPMQAL EVLLLLRIVS ERLKDHSKAA GSSCHITQLL LTLGCPSYAQ LHLEEAASSL KHLDQTTDTY LLLSLTCD L LRSQLYWTHQ KVTKGVSLLL SVLRDPALQK SSKAWYLLRV QVLQLVAAYL SLPSNNLSHS LWEQLCAQGW QTPEIALID SHKLLRSIIL LLMGSDILST QKAAVETSFL DYGENLVQKW QVLSEVLSCS EKLVCHLGRL GSVSEAKAFC LEALKLTTKL QIPRQCALF LVLKGELELA RNDIDLCQSD LQQVLFLLES CTEFGGVTQH LDSVKKVHLQ KGKQQAQVPC PPQLPEEELF L RGPALELV ATVAKEPGPI APSTNSSPVL KTKPQPIPNF LSHSPTCDCS LCASPVLTAV CLRWVLVTAG VRLAMGHQAQ GL DLLQVVL KGCPEAAERL TQALQASLNH KTPPSLVPSL LDEILAQAYT LLALEGLNQP SNESLQKVLQ SGLKFVAARI PHL EPWRAS LLLIWALTKL GGLSCCTTQL FASSWGWQPP LIKSVPGSEP SKTQGQKRSG RGRQKLASAP LSLNNTSQKG LEGR GLPCT PKPPDRIRQA GPHVPFTVFE EVCPTESKPE VPQAPRVQQR VQTRLKVNFS DDSDLEDPVS AEAWLAEEPK RRGTA SRGR GRARKGLSLK TDAVVAPGSA PGNPGLNGRS RRAKKVASRH CEERRPQRAS DQARPGPEIM RTIPEEELTD NWRKMS FEI LRGSDGEDSA SGGKTPAPGP EAASGEWELL RLDSSKKKLP SPCPDKESDK DLGPRLQLPS APVATGLSTL DSICDSL SV AFRGISHCPP SGLYAHLCRF LALCLGHRDP YATAFLVTES VSITCRHQLL THLHRQLSKA QKHRGSLEIA DQLQGLSL Q EMPGDVPLAR IQRLFSFRAL ESGHFPQPEK ESFQERLALI PSGVTVCVLA LATLQPGTVG NTLLLTRLEK DSPPVSVQI PTGQNKLHLR SVLNEFDAIQ KAQKENSSCT DKREWWTGRL ALDHRMEVLI ASLEKSVLGC WKGLLLPSSE EPGPAQEASR LQELLQDCG WKYPDRTLLK IMLSGAGALT PQDIQALAYG LCPTQPERAQ ELLNEAVGRL QGLTVPSNSH LVLVLDKDLQ K LPWESMPS LQALPVTRLP SFRFLLSYSI IKEYGASPVL SQGVDPRSTF YVLNPHNNLS STEEQFRANF SSEAGWRGVV GE VPRPEQV QEALTKHDLY IYAGHGAGAR FLDGQAVLRL SCRAVALLFG SSSAALAVHG NLEGAGIVLK YIMAGCPLFL GNL WDVTDR DIDRYTEALL QGWLGAGPGA PLLYYVNQAR QAPRLKYLIG AAPIAYGLPV SLRSSLAEEN LYFQSWSHPQ FEKG GGSGG GSGGGSWSHP QFEK

UniProtKB: Double-strand-break repair protein rad21 homolog, Separin

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHepes2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
100.0 mMKClPotassium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 5876 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3358298 / Details: The particles were automatically selected
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131299
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4

-
Atomic model buiding 1

Initial modelPDB ID:

7nj1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9hvy:
Cryo-EM structure of human separase-SCC1 (1-631) fusion protein

+
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