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- EMDB-12887: Folded elbow of cohesin -

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Basic information

Entry
Database: EMDB / ID: EMD-12887
TitleFolded elbow of cohesin
Map data
Sample
  • Complex: Cohesin
    • Protein or peptide: Structural maintenance of chromosomes protein 1
    • Protein or peptide: Structural maintenance of chromosomes protein 3
KeywordsCohesin / Elbow / Hinge / Smc1 / Smc3 / coiled coil / DNA / CELL CYCLE
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / DNA secondary structure binding / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / DNA secondary structure binding / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / reciprocal meiotic recombination / sister chromatid cohesion / mitotic sister chromatid cohesion / mitotic sister chromatid segregation / minor groove of adenine-thymine-rich DNA binding / G2/M transition of mitotic cell cycle / double-strand break repair / double-stranded DNA binding / cell division / protein kinase binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Smc1, ATP-binding cassette domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 1 / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsGonzalez Llamazares A / Lee B-G / Collier J / Nasmyth KA / Lowe J
CitationJournal: Elife / Year: 2021
Title: Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes.
Authors: Naomi J Petela / Andres Gonzalez Llamazares / Sarah Dixon / Bin Hu / Byung-Gil Lee / Jean Metson / Heekyo Seo / Antonio Ferrer-Harding / Menelaos Voulgaris / Thomas Gligoris / James Collier ...Authors: Naomi J Petela / Andres Gonzalez Llamazares / Sarah Dixon / Bin Hu / Byung-Gil Lee / Jean Metson / Heekyo Seo / Antonio Ferrer-Harding / Menelaos Voulgaris / Thomas Gligoris / James Collier / Byung-Ha Oh / Jan Löwe / Kim A Nasmyth /
Abstract: Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 ...Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 and ATP-dependent engagement of cohesin's Smc1 and Smc3 head domains. Scc2's replacement by Pds5 abrogates cohesin's ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50-nm-long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the form of cohesin that reveals the structure of folded and zipped-up coils in unprecedented detail and shows that Scc2 can associate with Smc1's ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific crosslinking, we show that cohesin's coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation () within Smc1's hinge that alters how Scc2 and Pds5 interact with Smc1's hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin's hinge, which in turn requires coiled coil folding.
History
DepositionMay 7, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ogt
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12887.png

Downloads & links

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Map

FileDownload / File: emd_12887.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 200 pix.
= 392. Å		1.96 Å/pix.
x 200 pix.
= 392. Å		1.96 Å/pix.
x 200 pix.
= 392. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.016028393 - 0.101499714
Average (Standard dev.)0.0002021191 (±0.002916396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 392.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.961.961.96
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z392.000392.000392.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0160.1010.000

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Supplemental data

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Sample components

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Entire : Cohesin

EntireName: Cohesin
Components
  • Complex: Cohesin
    • Protein or peptide: Structural maintenance of chromosomes protein 1
    • Protein or peptide: Structural maintenance of chromosomes protein 3

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Supramolecule #1: Cohesin

SupramoleculeName: Cohesin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Structural maintenance of chromosomes protein 1

MacromoleculeName: Structural maintenance of chromosomes protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 141.491781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGRLVGLELS NFKSYRGVTK VGFGESNFTS IIGPNGSGKS NMMDAISFVL GVRSNHLRSN ILKDLIYRGV LNDENSDDYD NEGAASSNP QSAYVKAFYQ KGNKLVELMR IISRNGDTSY KIDGKTVSYK DYSIFLENEN ILIKAKNFLV FQGDVEQIAA Q SPVELSRM ...String:
MGRLVGLELS NFKSYRGVTK VGFGESNFTS IIGPNGSGKS NMMDAISFVL GVRSNHLRSN ILKDLIYRGV LNDENSDDYD NEGAASSNP QSAYVKAFYQ KGNKLVELMR IISRNGDTSY KIDGKTVSYK DYSIFLENEN ILIKAKNFLV FQGDVEQIAA Q SPVELSRM FEEVSGSIQY KKEYEELKEK IEKLSKSATE SIKNRRRIHG ELKTYKEGIN KNEEYRKQLD KKNELQKFQA LW QLYHLEQ QKEELTDKLS ALNSEISSLK GKINNEMKSL QRSKSSFVKE SAVISKQKSK LDYIFKDKEK LVSDLRLIKV PQQ AAGKRI SHIEKRIESL QKDLQRQKTY VERFETQLKV VTRSKEAFEE EIKQSARNYD KFKLNENDLK TYNCLHEKYL TEGG SILEE KIAVLNNDKR EIQEELERFN KRADISKRRI TEELSITGEK LDTQLNDLRV SLNEKNALHT ERLHELKKLQ SDIES ANNQ EYDLNFKLRE TLVKIDDLSA NQRETMKERK LRENIAMLKR FFPGVKGLVH DLCHPKKEKY GLAVSTILGK NFDSVI VEN LTVAQECIAF LKKQRAGTAS FIPLDTIETE LPTLSLPDSQ DYILSINAID YEPEYEKAMQ YVCGDSIICN TLNIAKD LK WKKGIRGKLV TIEGALIHKA GLMTGGISGD ANNRWDKEEY QSLMSLKDKL LIQIDELSNG QRSNSIRARE VENSVSLL N SDIANLRTQV TQQKRSLDEN RLEIKYHNDL IEKEIQPKIT ELKKKLDDLE NTKDNLVKEK EALQNNIFKE FTSKIGFTI KEYENHSGEL MRQQSKELQQ LQKQILTVEN KLQFETDRLS TTQRRYEKAQ KDLENAQVEM KSLEEQEYAI EMKIGSIESK LEEHKNHLD ELQKKFVTKQ SELNSSEDIL EDMNSNLQVL KRERDGIKED IEKFDLERVT ALKNCKISNI NIPISSETTI D DLPISSTD NEAITISNSI DINYKGLPKK YKENNTDSAR KELEQKIHEV EEILNELQPN ARALERYDEA EGRFEVINNE TE QLKAEEK KILNQFLKIK KKRKELFEKT FDYVSDHLDA IYRELTKNPN SNVELAGGNA SLTIEDEDEP FNAGIKYHAT PPL KRFKDM EYLSGGEKTV AALALLFAIN SYQPSPFFVL DEVDAALDIT NVQRIAAYIR RHRNPDLQFI VISLKNTMFE KSDA LVGVY RQQQENSSKI ITLDLSNYAE

UniProtKB: Structural maintenance of chromosomes protein 1

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Macromolecule #2: Structural maintenance of chromosomes protein 3

MacromoleculeName: Structural maintenance of chromosomes protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 141.539984 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MYIKRVIIKG FKTYRNETII DNFSPHQNVI IGSNGSGKSN FFAAIRFVLS DDYSNLKREE RQGLIHQGSG GSVMSASVEI VFHDPDHSM ILPSGVLSRG DDEVTIRRTV GLKKDDYQLN DRNVTKGDIV RMLETAGFSM NNPYNIVPQG KIVALTNAKD K ERLQLLED ...String:
MYIKRVIIKG FKTYRNETII DNFSPHQNVI IGSNGSGKSN FFAAIRFVLS DDYSNLKREE RQGLIHQGSG GSVMSASVEI VFHDPDHSM ILPSGVLSRG DDEVTIRRTV GLKKDDYQLN DRNVTKGDIV RMLETAGFSM NNPYNIVPQG KIVALTNAKD K ERLQLLED VVGAKSFEVK LKASLKKMEE TEQKKIQINK EMGELNSKLS EMEQERKELE KYNELERNRK IYQFTLYDRE LN EVINQME RLDGDYNNTV YSSEQYIQEL DKREDMIDQV SKKLSSIEAS LKIKNATDLQ QAKLRESEIS QKLTNVNVKI KDV QQQIES NEEQRNLDSA TLKEIKSIIE QRKQKLSKIL PRYQELTKEE AMYKLQLASL QQKQRDLILK KGEYARFKSK DERD TWIHS EIEELKSSIQ NLNELESQLQ MDRTSLRKQY SAIDEEIEEL IDSINGPDTK GQLEDFDSEL IHLKQKLSES LDTRK ELWR KEQKLQTVLE TLLSDVNQNQ RNVNETMSRS LANGIINVKE ITEKLKISPE SVFGTLGELI KVNDKYKTCA EVIGGN SLF HIVVDTEETA TLIMNELYRM KGGRVTFIPL NRLSLDSDVK FPSNTTTQIQ FTPLIKKIKY EPRFEKAVKH VFGKTIV VK DLGQGLKLAK KHKLNAITLD GDRADKRGVL TGGYLDQHKR TRLESLKNLN ESRSQHKKIL EELDFVRNEL NDIDTKID Q VNGNIRKVSN DRESVLTNIE VYRTSLNTKK NEKLILEESL NAIILKLEKL NTNRTFAQEK LNTFENDLLQ EFDSELSKE EKERLESLTK EISAAHNKLN ITSDALEGIT TTIDSLNAEL ESKLIPQEND LESKMSEVGD AFIFGLQDEL KELQLEKESV EKQHENAVL ELGTVQREIE SLIAEETNNK KLLEKANNQQ RLLLKKLDNF QKSVEKTMIK KTTLVTRREE LQQRIREIGL L PEDALVND FSDITSDQLL QRLNDMNTEI SGLKNVNKRA FENFKKFNER RKDLAERASE LDESKDSIQD LIVKLKQQKV NA VDSTFQK VSENFEAVFE RLVPRGTAKL IIHRKNDNAN DHDESIDVDM DAESNESQNG KDSEIMYTGV SISVSFNSKQ NEQ LHVEQL SGGQKTVCAI ALILAIQMVD PASFYLFDEI DAALDKQYRT AVATLLKELS KNAQFICTTF RTDMLQVADK FFRV KYENK ISTVIEVNRE EAIGFIRGSN KFAEV

UniProtKB: Structural maintenance of chromosomes protein 3

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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

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63892
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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