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- EMDB-52297: Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2 -

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Basic information

Entry
Database: EMDB / ID: EMD-52297
TitleCryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2
Map dataComposite map (postprocessed) of human separase bound to SCC1 (310-550 aa) and SA2
Sample
  • Complex: Human separase bound to SCC1 (310-550 aa) and SA2
    • Protein or peptide: Cohesin subunit SA-2
    • Protein or peptide: Double-strand-break repair protein rad21 homolog
    • Protein or peptide: Separin
  • Ligand: ZINC ION
KeywordsSeparase / cell cycle / SCC1 / RAD21 / protease / chromosome segregation / Auto-cleavage / SA1/2 / cohesin
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 / mitotic spindle pole / lncRNA binding / mitotic cytokinesis / mitotic sister chromatid segregation / positive regulation of interleukin-10 production / catalytic activity / chromosome, centromeric region / negative regulation of tumor necrosis factor production / mitotic spindle assembly / 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 / meiotic cell cycle / chromosome segregation / nuclear matrix / fibrillar center / Separation of Sister Chromatids / spindle pole / mitotic spindle / double-strand break repair / chromosome / midbody / DNA recombination / DNA-binding transcription factor binding / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / cell division / cysteine-type endopeptidase activity / apoptotic process / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / proteolysis / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Peptidase C50, separase / SEPARIN core domain / Peptidase family C50 / SEPARIN core domain profile. / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain ...Peptidase C50, separase / SEPARIN core domain / Peptidase family C50 / SEPARIN core domain profile. / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) 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 / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Separin / Cohesin subunit SA-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionDec 9, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52297.png

Downloads & links

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Map

FileDownload / File: emd_52297.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map (postprocessed) of human separase bound to SCC1 (310-550 aa) and SA2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 512 pix.
= 462.029 Å		0.9 Å/pix.
x 512 pix.
= 462.029 Å		0.9 Å/pix.
x 512 pix.
= 462.029 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9024 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.4
Minimum - Maximum-0.1111056 - 22.198345
Average (Standard dev.)-0.021971641 (±0.2905245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 462.0288 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Composite map (unsharpened) of human separase bound to...

Fileemd_52297_additional_1.map
AnnotationComposite map (unsharpened) of human separase bound to SCC1 (310-550 aa) and SA2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human separase bound to SCC1 (310-550 aa) and SA2

EntireName: Human separase bound to SCC1 (310-550 aa) and SA2
Components
  • Complex: Human separase bound to SCC1 (310-550 aa) and SA2
    • Protein or peptide: Cohesin subunit SA-2
    • Protein or peptide: Double-strand-break repair protein rad21 homolog
    • Protein or peptide: Separin
  • Ligand: ZINC ION

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Supramolecule #1: Human separase bound to SCC1 (310-550 aa) and SA2

SupramoleculeName: Human separase bound to SCC1 (310-550 aa) and SA2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Cohesin subunit SA-2

MacromoleculeName: Cohesin subunit SA-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 145.730422 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MIAAPEIPTD FNLLQESETH FSSDTDFEDI EGKNQKQGKG KTCKKGKKGP AEKGKGGNGG GKPPSGPNRM NGHHQQNGVE NMMLFEVVK MGKSAMQSVV DDWIESYKHD RDIALLDLIN FFIQCSGCKG VVTAEMFRHM QNSEIIRKMT EEFDEDSGDY P LTMAGPQW ...String:
MIAAPEIPTD FNLLQESETH FSSDTDFEDI EGKNQKQGKG KTCKKGKKGP AEKGKGGNGG GKPPSGPNRM NGHHQQNGVE NMMLFEVVK MGKSAMQSVV DDWIESYKHD RDIALLDLIN FFIQCSGCKG VVTAEMFRHM QNSEIIRKMT EEFDEDSGDY P LTMAGPQW KKFKSSFCEF IGVLVRQCQY SIIYDEYMMD TVISLLTGLS DSQVRAFRHT STLAAMKLMT ALVNVALNLS IN MDNTQRQ YEAERNKMIG KRANERLELL LQKRKELQEN QDEIENMMNA IFKGVFVHRY RDAIAEIRAI CIEEIGIWMK MYS DAFLND SYLKYVGWTM HDKQGEVRLK CLTALQGLYY NKELNSKLEL FTSRFKDRIV SMTLDKEYDV AVQAIKLLTL VLQS SEEVL TAEDCENVYH LVYSAHRPVA VAAGEFLYKK LFSRRDPEED GMMKRRGRQG PNANLVKTLV FFFLESELHE HAAYL VDSM WDCATELLKD WECMNSLLLE EPLSGEEALT DRQESALIEI MLCTIRQAAE CHPPVGRGTG KRVLTAKEKK TQLDDR TKI TELFAVALPQ LLAKYSVDAE KVTNLLQLPQ YFDLEIYTTG RLEKHLDALL RQIRNIVEKH TDTDVLEACS KTYHALC NE EFTIFNRVDI SRSQLIDELA DKFNRLLEDF LQEGEEPDED DAYQVLSTLK RITAFHNAHD LSKWDLFACN YKLLKTGI E NGDMPEQIVI HALQCTHYVI LWQLAKITES SSTKEDLLRL KKQMRVFCQI CQHYLTNVNT TVKEQAFTIL CDILMIFSH QIMSGGRDML EPLVYTPDSS LQSELLSFIL DHVFIEQDDD NNSADGQQED EASKIEALHK RRNLLAAFCK LIVYTVVEMN TAADIFKQY MKYYNDYGDI IKETMSKTRQ IDKIQCAKTL ILSLQQLFNE MIQENGYNFD RSSSTFSGIK ELARRFALTF G LDQLKTRE AIAMLHKDGI EFAFKEPNPQ GESHPPLNLA FLDILSEFSS KLLRQDKRTV YVYLEKFMTF QMSLRREDVW LP LMSYRNS LLAGGDDDTM SVISGISSRG STVRSKKSKP STGKRKVVEG MQLSLTEESS SSDSMWLSRE QTLHTPVMMQ TPQ LTSTIM REPKRLRPED SFMSVYPMQT EHHQTPLDYN RRGTSLMEDD EEPIVEDVMM SSEGRIEDLN EGMDFDTMDI DLPP SKNRR ERTELKPDFF DPASIMDESV LGVSMFSSLA EENLYFQSWS HPQFEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Cohesin subunit SA-2

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Macromolecule #2: Double-strand-break repair protein rad21 homolog

MacromoleculeName: Double-strand-break repair protein rad21 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.693211 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DITVKETKAK RKRKLIVDSV KELDSKTIRA QLSDYSDIVT TLDLAPPTKK LMMWKETGGV EKLFSLPAQP LWNNRLLKLF TRCLTPLVP EDLRKRRKGG EADNLDEFLK EFENPEVPRE DQQQQHQQRD VIDEPIIEEP SRLQESVMEA SRTNIDESAM P PPPPQGVK ...String:
DITVKETKAK RKRKLIVDSV KELDSKTIRA QLSDYSDIVT TLDLAPPTKK LMMWKETGGV EKLFSLPAQP LWNNRLLKLF TRCLTPLVP EDLRKRRKGG EADNLDEFLK EFENPEVPRE DQQQQHQQRD VIDEPIIEEP SRLQESVMEA SRTNIDESAM P PPPPQGVK RKAGQIDPEP VMPPQQVEQM EIPPVELPPE EPPNICQLIP ELELLPEKEK EKEKEKEDDE EEEDEDASGG DQ D

UniProtKB: Double-strand-break repair protein rad21 homolog

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Macromolecule #3: Separin

MacromoleculeName: Separin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: separase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 238.086344 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKSGPGGSG GSGGGSGGGS GENLYFQGGG SGGSGMRSFK RVNFGTLLSS QKEAEELLPD LKEFLSNPP AGFPSSRSDA ERRQACDAIL RACNQQLTAK LACPRHLGSL LELAELACDG YLVSTPQRPP LYLERILFVL L RNAAAQGS ...String:
MDYKDHDGDY KDHDIDYKDD DDKSGPGGSG GSGGGSGGGS GENLYFQGGG SGGSGMRSFK RVNFGTLLSS QKEAEELLPD LKEFLSNPP AGFPSSRSDA ERRQACDAIL RACNQQLTAK LACPRHLGSL LELAELACDG YLVSTPQRPP LYLERILFVL L RNAAAQGS PEVTLRLAQP LHACLVQCSR EAAPQDYEAV ARGSFSLLWK GAEALLERRA AFAARLKALS FLVLLEDEST PC EVPHFAS PTACRAVAAH QLFDASGHGL NEADADFLDD LLSRHVIRAL VGERGSSSGL LSPQRALCLL ELTLEHCRRF CWS RHHDKA ISAVEKAHSY LRNTNLAPSL QLCQLGVKLL QVGEEGPQAV AKLLIKASAV LSKSMEAPSP PLRALYESCQ FFLS GLERG TKRRYRLDAI LSLFAFLGGY CSLLQQLRDD GVYGGSSKQQ QSFLQMYFQG LHLYTVVVYD FAQGCQIVDL ADLTQ LVDS CKSTVVWMLE ALEGLSGQEL TDHMGMTASY TSNLAYSFYS HKLYAEACAI SEPLCQHLGL VKPGTYPEVP PEKLHR CFR LQVESLKKLG KQAQGCKMVI LWLAALQPCS PEHMAEPVTF WVRVKMDAAR AGDKELQLKT LRDSLSGWDP ETLALLL RE ELQAYKAVRA DTGQERFNII CDLLELSPEE TPAGAWARAT HLVELAQVLC YHDFTQQTNC SALDAIREAL QLLDSVRP E AQARDQLLDD KAQALLWLYI CTLEAKMQEG IERDRRAQAP GNLEEFEVND LNYEDKLQED RFLYSNIAFN LAADAAQSK CLDQALALWK ELLTKGQAPA VRCLQQTAAS LQILAALYQL VAKPMQALEV LLLLRIVSER LKDHSKAAGS SCHITQLLLT LGCPSYAQL HLEEAASSLK HLDQTTDTYL LLSLTCDLLR SQLYWTHQKV TKGVSLLLSV LRDPALQKSS KAWYLLRVQV L QLVAAYLS LPSNNLSHSL WEQLCAQGWQ TPEIALIDSH KLLRSIILLL MGSDILSTQK AAVETSFLDY GENLVQKWQV LS EVLSCSE KLVCHLGRLG SVSEAKAFCL EALKLTTKLQ IPRQCALFLV LKGELELARN DIDLCQSDLQ QVLFLLESCT EFG GVTQHL DSVKKVHLQK GKQQAQVPCP PQLPEEELFL RGPALELVAT VAKEPGPIAP STNSSPVLKT KPQPIPNFLS HSPT CDCSL CASPVLTAVC LRWVLVTAGV RLAMGHQAQG LDLLQVVLKG CPEAAERLTQ ALQASLNHKT PPSLVPSLLD EILAQ AYTL LALEGLNQPS NESLQKVLQS GLKFVAARIP HLEPWRASLL LIWALTKLGG LSCCTTQLFA SSWGWQPPLI KSVPGS EPS KTQGQKRSGR GRQKLASAPL SLNNTSQKGL EGRGLPCTPK PPDRIRQAGP HVPFTVFEEV CPTESKPEVP QAPRVQQ RV QTRLKVNFSD DSDLEDPVSA EAWLAEEPKR RGTASRGRGR ARKGLSLKTD AVVAPGSAPG NPGLNGRSRR AKKVASRH C EERRPQRASD QARPGGLEVL FQGPGSGDSS KKKLPSPCPD KESDKDLGPR LQLPSAPVAT GLSTLDSICD SLSVAFRGI SHCPPSGLYA HLCRFLALCL GHRDPYATAF LVTESVSITC RHQLLTHLHR QLSKAQKHRG SLEIADQLQG LSLQEMPGDV PLARIQRLF SFRALESGHF PQPEKESFQE RLALIPSGVT VCVLALATLQ PGTVGNTLLL TRLEKDSPPV SVQIPTGQNK L HLRSVLNE FDAIQKAQKE NSSCTDKREW WTGRLALDHR MEVLIASLEK SVLGCWKGLL LPSSEEPGPA QEASRLQELL QD CGWKYPD RTLLKIMLSG AGALTPQDIQ ALAYGLCPTQ PERAQELLNE AVGRLQGLTV PSNSHLVLVL DKDLQKLPWE SMP SLQALP VTRLPSFRFL LSYSIIKEYG ASPVLSQGVD PRSTFYVLNP HNNLSSTEEQ FRANFSSEAG WRGVVGEVPR PEQV QEALT KHDLYIYAGH GAGARFLDGQ AVLRLSCRAV ALLFGSSSAA LAVHGNLEGA GIVLKYIMAG CPLFLGNLWD VTDRD IDRY TEALLQGWLG AGPGAPLLYY VNQARQAPRL KYLIGAAPIA YGLPVSLRSS LAEENLYFQS WSHPQFEKGG GSGGGS GGG SWSHPQFEK

UniProtKB: Separin, Separin

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHepes2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
150.0 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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 16 / Number real images: 57012 / Average electron dose: 50.0 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 106898589 / Details: The particles were automatically selected
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Software - details: Non-uniform refinement was used / Number images used: 177878
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.4.0)

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Atomic model buiding 1

Initial model
PDB IDChain

7nj1

chain_id: A, source_name: PDB, initial_model_type: experimental model

4pju

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9hms:
Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2

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