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- EMDB-4616: Structural basis of cohesin ring opening -

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Basic information

Entry
Database: EMDB / ID: EMD-4616
TitleStructural basis of cohesin ring opening
Map data
Sample
  • Complex: Cohesin ATPase head module
    • Complex: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
      • Protein or peptide: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
    • Complex: Sister chromatid cohesion protein 1, Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
      • Protein or peptide: Sister chromatid cohesion protein 1
      • Protein or peptide: Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
      • Protein or peptide: Sister chromatid cohesion protein 1,Structural maintenance of chromosomes protein
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / cohesin loader activity / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / SUMOylation of DNA damage response and repair proteins / synaptonemal complex assembly / meiotic sister chromatid cohesion ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / cohesin loader activity / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / SUMOylation of DNA damage response and repair proteins / synaptonemal complex assembly / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / reciprocal meiotic recombination / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / condensed nuclear chromosome / double-strand break repair / mitotic cell cycle / double-stranded DNA binding / cell division / apoptotic process / DNA damage response / chromatin binding / protein kinase binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus
Similarity search - Function
Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge ...Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / 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 / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein / Structural maintenance of chromosomes protein 3 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPanne D / Muir KW / Li Y / Weis F
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: The structure of the cohesin ATPase elucidates the mechanism of SMC-kleisin ring opening.
Authors: Kyle W Muir / Yan Li / Felix Weis / Daniel Panne /
Abstract: Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring- ...Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring-shaped complex that can topologically engage chromatin to regulate chromatin structure. Release from chromatin involves opening of the ring at the Smc3-Scc1 interface in a reaction that is controlled by acetylation and engagement of the Smc ATPase head domains. To understand the underlying molecular mechanisms, we have determined the 3.2-Å resolution cryo-electron microscopy structure of the ATPγS-bound, heterotrimeric cohesin ATPase head module and the 2.1-Å resolution crystal structure of a nucleotide-free Smc1-Scc1 subcomplex from Saccharomyces cerevisiae and Chaetomium thermophilium. We found that ATP-binding and Smc1-Smc3 heterodimerization promote conformational changes within the ATPase that are transmitted to the Smc coiled-coil domains. Remodeling of the coiled-coil domain of Smc3 abrogates the binding surface for Scc1, thus leading to ring opening at the Smc3-Scc1 interface.
History
DepositionFeb 15, 2019-
Header (metadata) releaseApr 3, 2019-
Map releaseFeb 5, 2020-
UpdateMar 18, 2020-
Current statusMar 18, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qpw
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4616.png

Downloads & links

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Map

FileDownload / File: emd_4616.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.05741336 - 0.10685454
Average (Standard dev.)0.00004681285 (±0.0011952366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 283.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z283.500283.500283.500
α/β/γ90.00090.00090.000
start NX/NY/NZ29921935
NX/NY/NZ271234450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0570.1070.000

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Supplemental data

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Sample components

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Entire : Cohesin ATPase head module

EntireName: Cohesin ATPase head module
Components
  • Complex: Cohesin ATPase head module
    • Complex: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
      • Protein or peptide: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
    • Complex: Sister chromatid cohesion protein 1, Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
      • Protein or peptide: Sister chromatid cohesion protein 1
      • Protein or peptide: Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
      • Protein or peptide: Sister chromatid cohesion protein 1,Structural maintenance of chromosomes protein
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: Cohesin ATPase head module

SupramoleculeName: Cohesin ATPase head module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Structural maintenance of chromosomes protein,Structural maintena...

SupramoleculeName: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #3: Sister chromatid cohesion protein 1, Structural maintenance of ch...

SupramoleculeName: Sister chromatid cohesion protein 1, Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Structural maintenance of chromosomes protein,Structural maintena...

MacromoleculeName: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 27.570475 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGKLIRLELF NFKSYKGHHT LLFGDSYFTS IIGPNGSGKS NSMDAISFVL GIKSSHLRSS NLRDLIYRGR VMKTSKIQDD GTTAPATNG DVNGYENGDA GDDEDTSQRT SRNDPKTAWV MAVYEDDAGE LHRWKRTITA NGTSEYRIND RVVNAQQYNE A LEKENILI ...String:
MGKLIRLELF NFKSYKGHHT LLFGDSYFTS IIGPNGSGKS NSMDAISFVL GIKSSHLRSS NLRDLIYRGR VMKTSKIQDD GTTAPATNG DVNGYENGDA GDDEDTSQRT SRNDPKTAWV MAVYEDDAGE LHRWKRTITA NGTSEYRIND RVVNAQQYNE A LEKENILI KARNFLVFQG DVEAIASQSP QDLTRLIEQI SGSLEYKEEY ERLEEEVRQA TEEQAYKLQR RRAANSEIKQ YM EQ

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Macromolecule #2: Sister chromatid cohesion protein 1

MacromoleculeName: Sister chromatid cohesion protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 9.48994 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MASKAIVQMA KILRKELSEE KEVIFTDVLK SQANTEPENI TKREASRGFF DILSLATEGC IGLSQTEAFG NIKIDAKPAL FERFI

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Macromolecule #3: Structural maintenance of chromosomes protein 3,Structural mainte...

MacromoleculeName: Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 61.051789 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAYIKRVIIK GFKTYRNETI IDNFSPHQNV IIGSNGSGKS NFFAAIRFVL SDDYSNLKRE ERQGLIHQGS GGSVMSASVE IVFHDPDHS MILPSGVLSR GDDEVTIRRT VGLKKDDYQL NDRNVTKGDI VRMLETAGFS MNNPYNIVPQ GKIVALTNAK D KERLQLLE ...String:
MAYIKRVIIK GFKTYRNETI IDNFSPHQNV IIGSNGSGKS NFFAAIRFVL SDDYSNLKRE ERQGLIHQGS GGSVMSASVE IVFHDPDHS MILPSGVLSR GDDEVTIRRT VGLKKDDYQL NDRNVTKGDI VRMLETAGFS MNNPYNIVPQ GKIVALTNAK D KERLQLLE DVVGAKSFEV KLKASLKKME ETEQKKIQIN KEMGELNSKL SEMEQERKEL EKYNELERNR KIYQFTLYDR EL NEVINQM ERLDGDYNNT VYSSESSKHP TSLVPRGSDI TSDQLLQRLN DMNTEISGLK NVNKRAFENF KKFNERRKDL AER ASELDE SKDSIQDLIV KLKQQKVNAV DSTFQKVSEN FEAVFERLVP RGTAKLIIHR KNDNANDHDE SIDVDMDAES NESQ NGKDS EIMYTGVSIS VSFNSKQNEQ LHVEQLSGGQ KTVCAIALIL AIQMVDPASF YLFDEIDACL DKQYRTAVAT LLKEL SKNA QFICTTFRTD MLQVADKFFR VKYECKISTV IEVNREEAIG FIRGSNKFAE V

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Macromolecule #4: Sister chromatid cohesion protein 1,Structural maintenance of chr...

MacromoleculeName: Sister chromatid cohesion protein 1,Structural maintenance of chromosomes protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 42.292125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVTENPQRLT VLRLATNKGP LAQIWLASNM SNIPRGSVIQ THIAESAKEI AKASGSDDES GDNEYITLRT SGELLQGIVR VYSKQATFL LTDIKDTLTK ISMLFKTSQK MTSTVNRLNT VTRVHQLMLE DAVTEREVLV TPGLEFLDDT TIPVGLMAQE N PNLRAMDR ...String:
MVTENPQRLT VLRLATNKGP LAQIWLASNM SNIPRGSVIQ THIAESAKEI AKASGSDDES GDNEYITLRT SGELLQGIVR VYSKQATFL LTDIKDTLTK ISMLFKTSQK MTSTVNRLNT VTRVHQLMLE DAVTEREVLV TPGLEFLDDT TIPVGLMAQE N PNLRAMDR LDHVRKQLEQ TEQEFEASKA KLRQARESFQ AVKQKRLELF NKAFTHIQEQ ITHVYKELTR SEAYPLGGQA YL DIEEDTD TPFLSGVKYH AMPPCKRFRD MEHLSGGEKT MAALALLFAI HSYQPSPFFV LDEVDCALDN ANVEKIKKYI REH AGPGMQ FIVISLKPAL FQASESLIGV YRDQEANTSR TLTLDLRKYR HHHHHH

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 42.08 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b) / Number images used: 178162
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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