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- EMDB-17331: Human Cohesin ATPase module -

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Basic information

Entry
Database: EMDB / ID: EMD-17331
TitleHuman Cohesin ATPase module
Map datacryo-EM map of the engaged human Cohesin ATPase module
Sample
  • Complex: Human Cohesin ATP-engaged ATPase module
    • Protein or peptide: Structural maintenance of chromosomes protein 1A
    • Protein or peptide: Structural maintenance of chromosomes protein 3
    • Protein or peptide: 64-kDa C-terminal product
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywords3D genome organization / Chromatin / Cohesin / ATPase activity / ATPase cycle / Cell cycle / DNA binding / DNA BINDING PROTEIN
Function / homology
Function and homology information


response to DNA damage checkpoint signaling / negative regulation of mitotic metaphase/anaphase transition / positive regulation of sister chromatid cohesion / 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 G2/M transition of mitotic cell cycle ...response to DNA damage checkpoint signaling / negative regulation of mitotic metaphase/anaphase transition / positive regulation of sister chromatid cohesion / 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 G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process / lateral element / replication-born double-strand break repair via sister chromatid exchange / mediator complex binding / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / microtubule motor activity / negative regulation of interleukin-1 beta production / lncRNA binding / mitotic sister chromatid cohesion / stem cell population maintenance / dynein complex binding / mitotic spindle pole / beta-tubulin binding / regulation of DNA replication / mitotic sister chromatid segregation / somatic stem cell population maintenance / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / response to radiation / kinetochore / spindle pole / nuclear matrix / Separation of Sister Chromatids / double-strand break repair / mitotic cell cycle / chromosome / midbody / double-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / protein heterodimerization activity / cell division / DNA repair / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / Smc1, ATP-binding cassette domain / 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 / Structural maintenance of chromosomes protein ...Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / Smc1, ATP-binding cassette domain / 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 / 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
Double-strand-break repair protein rad21 homolog / Structural maintenance of chromosomes protein 1A / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsLandwerlin P / Durand A / Diebold-Durand M-L / Romier C
Funding support France, 7 items
OrganizationGrant numberCountry
Fondation ARCARCPJA20181208268 France
Fondation ARCARCPJA2021060003715 France
Fondation ARCDOC20180507150 France
Agence Nationale de la Recherche (ANR)ANR-10-LABX-030-INRT France
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0023 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-0005-01 France
CitationJournal: To Be Published
Title: Human Cohesin ATPase module
Authors: Landwerlin P / Durand A / Diebold-Durand M-L / Romier C
History
DepositionMay 10, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17331.png

Downloads & links

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Map

FileDownload / File: emd_17331.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of the engaged human Cohesin ATPase module
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 256 pix.
= 230.656 Å		0.9 Å/pix.
x 256 pix.
= 230.656 Å		0.9 Å/pix.
x 256 pix.
= 230.656 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.901 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.8474728 - 1.1834729
Average (Standard dev.)-0.00033437883 (±0.022528132)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 230.656 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human Cohesin ATP-engaged ATPase module

EntireName: Human Cohesin ATP-engaged ATPase module
Components
  • Complex: Human Cohesin ATP-engaged ATPase module
    • Protein or peptide: Structural maintenance of chromosomes protein 1A
    • Protein or peptide: Structural maintenance of chromosomes protein 3
    • Protein or peptide: 64-kDa C-terminal product
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human Cohesin ATP-engaged ATPase module

SupramoleculeName: Human Cohesin ATP-engaged ATPase module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Structural maintenance of chromosomes protein 1A

MacromoleculeName: Structural maintenance of chromosomes protein 1A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.443246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGFLKLIEIE NFKSYKGRQI IGPFQRFTAI IGPNGSGKSN LMDAISFVLG EKTSNLRVKT LRDLIHGAPV GKPAANRAFV SMVYSEEGA EDRTFARVIV GGSSEYKINN KVVQLHEYSE ELEKLGILIK ARNFLVFQGA VESIAMKNPK ERTALFEEIS R SGELAQEY ...String:
MGFLKLIEIE NFKSYKGRQI IGPFQRFTAI IGPNGSGKSN LMDAISFVLG EKTSNLRVKT LRDLIHGAPV GKPAANRAFV SMVYSEEGA EDRTFARVIV GGSSEYKINN KVVQLHEYSE ELEKLGILIK ARNFLVFQGA VESIAMKNPK ERTALFEEIS R SGELAQEY DKRKKEMVKA EEDTQFNYHR KKNIAAERKE AKESSKHPTS LVPRGSDAQA EEEIKQEMNT LQQKLNEQQS VL QRIAAPN MKAMEKLESV RDKFQETSDE FEAARKRAKK AKQAFEQIKK ERFDRFNACF ESVATNIDEI YKALSRNSSA QAF LGPENP EEPYLDGINY NCVAPGKRFR PMDNLSGGEK TVAALALLFA IHSYKPAPFF VLDQIDAALD NTNIGKVANY IKEQ STCNF QAIVISLKEE FYTKAESLIG VYPEQGDCVI SKVLTFDLTK YPDANPNPNE Q

UniProtKB: Structural maintenance of chromosomes protein 1A, Structural maintenance of chromosomes protein 1A

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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: Homo sapiens (human)
Molecular weightTheoretical: 52.391367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYIKQVIIQG FRSYRDQTIV DPFSSKHNVI VGRNGSGKSN FFYAIQFVLS DEFSHLRPEQ RLALLHEGTG PRVISAFVEI IFDNSDNRL PIDKEEVSLR RVIGAKKDQY FLDKKMVTKN DVMNLLESAG FSRSNPYYIV KQGKINQMAT APDSQRLKLL R EVAGTRVY ...String:
MYIKQVIIQG FRSYRDQTIV DPFSSKHNVI VGRNGSGKSN FFYAIQFVLS DEFSHLRPEQ RLALLHEGTG PRVISAFVEI IFDNSDNRL PIDKEEVSLR RVIGAKKDQY FLDKKMVTKN DVMNLLESAG FSRSNPYYIV KQGKINQMAT APDSQRLKLL R EVAGTRVY DERKEESISL MKETEGKREK INELLKYIEE RLHTLEEEKE ELAGSGSLVP RGSGSYSHVN KKALDQFVNF SE QKEKLIK RQEELDRGYK SIMELMNVLE LRKYEAIQLT FKQVSKNFSE VFQKLVPGGK ATLVMKKGDV EGSQSQDEGE GSG ESERGS GSQSSVPSVD QFTGVGIRVS FTGKQGEMRE MQQLSGGQKS LVALALIFAI QKCDPAPFYL FDQIDQALDA QHRK AVSDM IMELAVHAQF ITTTFRPELL ESADKFYGVK FRNKVSHIDV ITAEMAKDFV EDDTTHG

UniProtKB: Structural maintenance of chromosomes protein 3, Structural maintenance of chromosomes protein 3

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Macromolecule #3: 64-kDa C-terminal product

MacromoleculeName: 64-kDa C-terminal product / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.203648 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKRTQQMLHG LQRALAKTGA ESISLLELCR NTNRKQAAAK FYSFLVLKKQ QAIELTQEEP YSDIIATPGP RFHGSLEVLF Q

UniProtKB: Double-strand-break repair protein rad21 homolog

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation #1

Preparation ID1
BufferpH: 8.2
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Sample preparation #2

Preparation ID2
BufferpH: 8.2
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Sample preparation #3

Preparation ID3
BufferpH: 8.2
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy #1

Microscopy ID1
MicroscopeTFS GLACIOS
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4146 / Average electron dose: 44.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS GLACIOS
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5574 / Average electron dose: 63.85 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Electron microscopy #1~~

Microscopy ID1
MicroscopeTFS GLACIOS
Image recordingImage recording ID: 3 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1593 / Average electron dose: 43.61 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Image recording ID1
DetailsAll three data sets processed together.
Particle selectionNumber selected: 7098916
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 174054
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8a6y
PDB Unreleased entry

source_name: PDB, initial_model_type: experimental model

8a8a
PDB Unreleased entry

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

PDB-8p0a:
Human Cohesin ATPase module

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