[English] 日本語
Yorodumi
- EMDB-10951: Condensin complex from S.cerevisiae ATP-free apo non-engaged stat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10951
TitleCondensin complex from S.cerevisiae ATP-free apo non-engaged state: overall map
Map dataoverall
Sample
  • Complex: Condensin
    • Protein or peptide: Structural maintenance of chromosomes protein 2,Structural maintenance of chromosomes protein 2,Smc2
    • Protein or peptide: Structural maintenance of chromosomes protein 4
    • Protein or peptide: Condensin complex subunit 2,Condensin complex subunit 2,Brn1
    • Protein or peptide: Condensin complex subunit 1,Condensin complex subunit 1,Ycs4
Keywordsessential for the functional organization of genomes / CELL CYCLE
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / synaptonemal complex assembly ...negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / synaptonemal complex assembly / nucleophagy / condensed chromosome, centromeric region / mitotic chromosome condensation / chromosome condensation / silent mating-type cassette heterochromatin formation / mitotic sister chromatid segregation / minor groove of adenine-thymine-rich DNA binding / condensed chromosome / histone binding / double-stranded DNA binding / cell division / chromatin binding / chromatin / nucleolus / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Condensin subunit 1 / Condensin complex subunit 1, N-terminal / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / non-SMC mitotic condensation complex subunit 1 / Smc2, ATP-binding cassette domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Structural maintenance of chromosomes protein ...Condensin subunit 1 / Condensin complex subunit 1, N-terminal / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / non-SMC mitotic condensation complex subunit 1 / Smc2, ATP-binding cassette domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Condensin complex subunit 2 / Structural maintenance of chromosomes protein 2 / Condensin complex subunit 1 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsLee B-G / Cawood C / Gutierrez-Escribano P / Nakane T / Merkel F / Hassler M / Haering CH / Aragon L / Lowe J
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC-A652-5PY00 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism.
Authors: Byung-Gil Lee / Fabian Merkel / Matteo Allegretti / Markus Hassler / Christopher Cawood / Léa Lecomte / Francis J O'Reilly / Ludwig R Sinn / Pilar Gutierrez-Escribano / Marc Kschonsak / Sol ...Authors: Byung-Gil Lee / Fabian Merkel / Matteo Allegretti / Markus Hassler / Christopher Cawood / Léa Lecomte / Francis J O'Reilly / Ludwig R Sinn / Pilar Gutierrez-Escribano / Marc Kschonsak / Sol Bravo / Takanori Nakane / Juri Rappsilber / Luis Aragon / Martin Beck / Jan Löwe / Christian H Haering /
Abstract: Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The ...Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities.
History
DepositionApr 28, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6yvu
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10951.png

Downloads & links

-
Map

FileDownload / File: emd_10951.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoverall
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 380 pix.
= 456. Å		1.2 Å/pix.
x 380 pix.
= 456. Å		1.2 Å/pix.
x 380 pix.
= 456. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.07728881 - 0.20011097
Average (Standard dev.)0.000036547728 (±0.0061781285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 456.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z456.000456.000456.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0770.2000.000

-
Supplemental data

-
Supplemental map: emd 10951 additional 1.map

Fileemd_10951_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: emd 10951 additional 2.map

Fileemd_10951_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Condensin

EntireName: Condensin
Components
  • Complex: Condensin
    • Protein or peptide: Structural maintenance of chromosomes protein 2,Structural maintenance of chromosomes protein 2,Smc2
    • Protein or peptide: Structural maintenance of chromosomes protein 4
    • Protein or peptide: Condensin complex subunit 2,Condensin complex subunit 2,Brn1
    • Protein or peptide: Condensin complex subunit 1,Condensin complex subunit 1,Ycs4

-
Supramolecule #1: Condensin

SupramoleculeName: Condensin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: complex of 5 protein subunits: Smc2; Smc4; Brn1; Ycs4; Ycg1
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 500 MDa

-
Macromolecule #1: Structural maintenance of chromosomes protein 2,Structural mainte...

MacromoleculeName: Structural maintenance of chromosomes protein 2,Structural maintenance of chromosomes protein 2,Smc2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 134.80675 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKVEELIIDG FKSYATRTVI TDWDPQFNAI TGLNGSGKSN ILDAICFVLG IASMSTVRAS SLQDLIYKRG QAGVTKASVT IVFDNTDKS NSPIGFTNSP QISVTRQVVL GGTSKYLING HRAPQQSVLQ LFQSVQLNIN NPNFLIMQGK ITKVLNMKPS E ILSLIEEA ...String:
MKVEELIIDG FKSYATRTVI TDWDPQFNAI TGLNGSGKSN ILDAICFVLG IASMSTVRAS SLQDLIYKRG QAGVTKASVT IVFDNTDKS NSPIGFTNSP QISVTRQVVL GGTSKYLING HRAPQQSVLQ LFQSVQLNIN NPNFLIMQGK ITKVLNMKPS E ILSLIEEA AGTKMFEDRR EKAERTMSKK ETKLQENRTL LTEEIEPKLE KLRNEKRMFL EFQSTQTDLE KTERIVVSYE YY NIKHKHT SIRETLENGE TRMKMLNEFV KKTSEEIDSL NEDVEEIKLQ KEKELHKEGT ISKLENKENG LLNEISRLKT SLS IKVENL NDTTEKSKAL ESEIASSSAK LIEKKSAYAN TEKDYKMVQE QLSKQRDLYK RKEELVSTLT TGISSTGAAD GGYN AQLAK AKTELNEVSL AIKKSSMKME LLKKELLTIE PKLKEATKDN ELNVKHVKQC QETCDKLRAR LVEYGFDPSR IKDLK QRED KLKSHYYQTC KNSEYLKRRV TNLEFNYTKP YPNFEASFVH GVVGQLFQID NDNIRYATAL QTCAGGRLFN VVVQDS QTA TQLLERGRLR KRVTIIPLDK IYTRPISSQV LDLAKKIAPG KVELAINLIR FDESITKAME FIFGNSLICE DPETAKK IT FHPKIRARSI TLQGDVYDPE GTLSGGSRNT SESLLVDIQK YNQIQKQIET IQADLNHVTE ELQTQYATSQ KTKTIQSD L NLSLHKLDLA KRNLDANPSS QIIARNEEIL RDIGECENEI KTKQMSLKKC QEEVSTIEKD MKEYDSDKGS KLNELKKEL KLLAKELEEQ ESESERKYDL FQNLELETEQ LSSELDSNKT LLHNHLKSIE SLKLENSDLE GKIRGVEDDL VTVQTELNEE KKRLMDIDD ELNELETLIK KKQDEKKSSE LELQKLVHDL NKYKSNTNNM EKIIEDLRQK HEFLEDFDLV RNIVKQNEGI D LDTYRERS KQLNEKFQEL RKKVNPNIMN MIENVEKKEA ALKTMIKTIE KDKMKIQETI SKLNEYKRET LVKTWEKVTL DF GNIFADL LPNSFAKLVP CEGKDVTQGL EVKVKLGNIW KESLIELSGG QRSLIALSLI MALLQFRPAP MYILDEVDAA LDL SHTQNI GHLIKTRFKG SQFIVVSLKE GMFANANRVF RTRFQDGTSV VSIM(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

UniProtKB: Structural maintenance of chromosomes protein 2

-
Macromolecule #2: Structural maintenance of chromosomes protein 4

MacromoleculeName: Structural maintenance of chromosomes protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 162.435812 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDSPLSKRQ KRKSAQEPEL SLDQGDAEED SQVENRVNLS ENTPEPDLPA LEASYSKSYT PRKLVLSSGE NRYAFSQPTN STTTSLHVP NLQPPKTSSR GRDHKSYSQS PPRSPGRSPT RRLELLQLSP VKNSRVELQK IYDRHQSSSK QQSRLFINEL V LENFKSYA ...String:
MSDSPLSKRQ KRKSAQEPEL SLDQGDAEED SQVENRVNLS ENTPEPDLPA LEASYSKSYT PRKLVLSSGE NRYAFSQPTN STTTSLHVP NLQPPKTSSR GRDHKSYSQS PPRSPGRSPT RRLELLQLSP VKNSRVELQK IYDRHQSSSK QQSRLFINEL V LENFKSYA GKQVVGPFHT SFSAVVGPNG SGKSNVIDSM LFVFGFRANK MRQDRLSDLI HKSEAFPSLQ SCSVAVHFQY VI DESSGTS RIDEEKPGLI ITRKAFKNNS SKYYINEKES SYTEVTKLLK NEGIDLDHKR FLILQGEVEN IAQMKPKAEK ESD DGLLEY LEDIIGTANY KPLIEERMGQ IENLNEVCLE KENRFEIVDR EKNSLESGKE TALEFLEKEK QLTLLRSKLF QFKL LQSNS KLASTLEKIS SSNKDLEDEK MKFQESLKKV DEIKAQRKEI KDRISSCSSK EKTLVLERRE LEGTRVSLEE RTKNL VSKM EKAEKTLKST KHSISEAENM LEELRGQQTE HETEIKDLTQ LLEKERSILD DIKLSLKDKT KNISAEIIRH EKELEP WDL QLQEKESQIQ LAESELSLLE ETQAKLKKNV ETLEEKILAK KTHKQELQDL ILDLKKKLNS LKDERSQGEK NFTSAHL KL KEMQKVLNAH RQRAMEARSS LSKAQNKSKV LTALSRLQKS GRINGFHGRL GDLGVIDDSF DVAISTACPR LDDVVVDT V ECAQHCIDYL RKNKLGYARF ILLDRLRQFN LQPISTPENV PRLFDLVKPK NPKFSNAFYS VLRDTLVAQN LKQANNVAY GKKRFRVVTV DGKLIDISGT MSGGGNHVAK GLMKLGTNQS DKVDDYTPEE VDKIERELSE RENNFRVASD TVHEMEEELK KLRDHEPDL ESQISKAEME ADSLASELTL AEQQVKEAEM AYVKAVSDKA QLNVVMKNLE RLRGEYNDLQ SETKTKKEKI K GLQDEIMK IGGIKLQMQN SKVESVCQKL DILVAKLKKV KSASKKSGGD VVKFQKLLQN SERDVELSSD ELKVIEEQLK HT KLALAEN DTNMNETLNL KVELKEQSEQ LKEQMEDMEE SINEFKSIEI EMKNKLEKLN SLLTYIKSEI TQQEKGLNEL SIR DVTHTL GMLDDNKMDS VKEDVKNNQE LDQEYRSCET QDESEIKDAE TSCDNYHPMN IDETSDEVSR GIPRLSEDEL RELD VELIE SKINELSYYV EETNVDIGVL EEYARRLAEF KRRKLDLNNA VQKRDEVKEQ LGILKKKRFD EFMAGFNIIS MTLKE MYQM ITMGGNAELE LVDSLDPFSE GVTFSVMPPK KSWRNITNLS GGEKTLSSLA LVFALHKYKP TPLYVMDEID AALDFR NVS IVANYIKERT KNAQFIVISL RNNMFELAQQ LVGVYKRDNR TKSTTIKNID ILNRT

UniProtKB: Structural maintenance of chromosomes protein 4

-
Macromolecule #3: Condensin complex subunit 2,Condensin complex subunit 2,Brn1

MacromoleculeName: Condensin complex subunit 2,Condensin complex subunit 2,Brn1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 87.940234 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTTQLRYENN DDDERVEYNL FTNRSTMMAN FEEWIKMATD NKINSRNSWN FALIDYFYDL DVLKDGENNI NFQKASATLD GCIKIYSSR VDSVTTETGK LLSGLAQRKT NGASNGDDSN GGNGEGLGGD SDEANIEIDP LTGMPISNDP DVNNTRRRVY N RVLETTLV ...String:
MTTQLRYENN DDDERVEYNL FTNRSTMMAN FEEWIKMATD NKINSRNSWN FALIDYFYDL DVLKDGENNI NFQKASATLD GCIKIYSSR VDSVTTETGK LLSGLAQRKT NGASNGDDSN GGNGEGLGGD SDEANIEIDP LTGMPISNDP DVNNTRRRVY N RVLETTLV EFETIKMKEL DQELIIDPLF KKALVDFDEG GAKSLLLNTL NIDNTARVIF DASIKDTQNV GQGKLQRKEE EL IERDSLV DDENEPSQSL ISTRNDSTVN DSVISAPSME DEILSLGMDF IKFDQIAVCE ISGSIEQLRN VVEDINQAKD FIE NVNNRF DNFLTEEELQ AAVPDNAEDD SDGFDMGMQQ ELCYPDENHD NTSHDEQDDD NVNSTTGSIF EKDLMAYFDE NLNR NWRGR EHWKVRNFKK ANLVNKESDL LEETRTTIGD TTDKNTTDDK SMDTKKKHKQ KKVLEIDFFK TDDSFEDKVF ASKGR TKID MPIKNRKNDT HYLLPDDFHF STDRITRLFI KPGQKMSLFS HRKHTRGDVS SGLFEKSTVS ANHSNNDIPT IADEHF WAD NYERKEQEEK EKEQSKEVGD VVGGALDNPF EDDMDGVDFN QAFEGTDDNE EASVKLDLQD DEDHKFPIRE NKVTYSR VS KKVDVRRLKK NVWRSINNLI QEHDSRKNRE QSSNDSETHT EDESTKELKF SDIIQGISKM YSDDTLKDIS TSFCFICL L HLANEHGLQI THTENYNDLI VNYEDLATTQ AAS(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

UniProtKB: Condensin complex subunit 2

-
Macromolecule #4: Condensin complex subunit 1,Condensin complex subunit 1,Ycs4

MacromoleculeName: Condensin complex subunit 1,Condensin complex subunit 1,Ycs4
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 133.88275 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSGFSLSEYL TKFQTTDRES YPRLQDPSRE LNVIIDQLAV SPEQIDASPD SLEALIDLCH DFPHLTPKLQ TQLSYLISSS LSNLSKDIK ANLSSNVNFT EIGGLIPQWK RHLEEYGYLI QVLLTFLQDE LHKVSSQSTN LNRSAKNSKN DSANVELFKR D CNQMENLL ...String:
MSGFSLSEYL TKFQTTDRES YPRLQDPSRE LNVIIDQLAV SPEQIDASPD SLEALIDLCH DFPHLTPKLQ TQLSYLISSS LSNLSKDIK ANLSSNVNFT EIGGLIPQWK RHLEEYGYLI QVLLTFLQDE LHKVSSQSTN LNRSAKNSKN DSANVELFKR D CNQMENLL ESITKLLEIN LSKIFQTTPE KDLFIGLFTR PLFVLLEIEP VTKVSSLKMF IQRILAMCVK NHGQSSSIQS SL MTNLTYF LHLSVFNAEL LKLLNDEYNY PQLTEDILKE ISTRVFNAKD TTGPKAISNF LIKLSELSPG IMLRQMNLVI TLL NNSSIT LRCSVVEACG NIVAELAQDP QTMEHYKQQI AVLIELLEER FQDSNPYVRT KAIQGCSKIC DLSSKFNKSK AKFT SLAVR SLQDRSSLVR RNSVKLLSKL LLKHPFKAIH GSQLRLSEWE EYLKGSESQL NSTLKKVESQ ETLNDTIERS LIEEE VEQD EGQCRTELEG SFNKSAELSR IENEVENINA TNTSVLMKLK LMIVYYKDAI SFIKEIHKSI ELISNLLFSK NRNEVL ESM DFLVLADAFD IELSEFGIKK MLHLVWMKGT NDEGTSISVH LIECYKQLFL TAPDSCNMQE KAAHIAKNLI NLSIGAS IA DLASLEQLLG MMYEQKLIDQ HVINILWAIY NSASKASMQK EQNVNNRDSE KGFSKEQIHG SIIILGMLSL ADNEIALK G LESLLNIGLG AVGLKDLTLC RYSCLALERM VPKRSTIITK AINQELEDVA VKKLYAIIIN YTKDNEYYPM CEQALSALF TISSKPDILA TDLIREKTMM TFGKPEEEDS ILSLEQSSRV VSLSQLLFIV GQVAIKTLVY LEKCEAEFKK RKIEAETRNG KVKNQGADV TNTTQDNGGD KELEMIGGTN EDDFTDAIQF VKENELLFGE KSILGKFCPI VEEIVSNSSR FSDPMLQRTA T LCLEKLMC LSSKYCEKSL PLLITVMEKS PDPTIRSNAV LGLGDMAVCF NNLVDENTDY LYRRLHDENL MVQRTCLMTV TF LILAGQV KVKGQLGEMA KCLDNPDQGI SDMCRLFFTE LASKDNAIYN GFIDIFSNLS SDDLLGKESF KKIIKFLLTF IDK ERHQKQ LNEKLVGRLR KCETQKQWDD IAFVLNNLPY KNEDVTALLE QGFKVVSAKE (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

UniProtKB: Condensin complex subunit 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5 / Component - Name: Tris
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number grids imaged: 1 / #0 - Number real images: 10000 / #0 - Average exposure time: 10.0 sec. / #0 - Average electron dose: 45.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Image recording ID1
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 100388
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION

-
Atomic model buiding 1

Initial model
PDB IDChain

4rsi

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

4rsi

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

6qj2

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

6qj2

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

6cj3

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

6c63

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

6q6e

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

PDB-6yvu:
Condensin complex from S.cerevisiae ATP-free apo non-engaged state

+
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