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- EMDB-17820: Human Cohesin ATPase module with an open DNA exit gate -

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Basic information

Entry
Database: EMDB / ID: EMD-17820
TitleHuman Cohesin ATPase module with an open DNA exit gate
Map dataCryo-EM map of the human open engaged Cohesin ATPase module
Sample
  • Complex: Human Cohesin ATP-open-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
Keywords3D genome organization / Chromatin / Cohesin / ATPase activity / ATPase cycle / Cell cycle / DNA binding / DNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of mitotic metaphase/anaphase transition / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / 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 ...negative regulation of mitotic metaphase/anaphase transition / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / 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 / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / lncRNA binding / sister chromatid cohesion / negative regulation of interleukin-1 beta production / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / condensed nuclear chromosome / chromosome segregation / spindle pole / nuclear matrix / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / cell division / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / DNA binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
: / 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 / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 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: Conformational dynamics of the human Cohesin ATPase module
Authors: Vitoria Gomes M / Landwerlin P / Durand A / Diebold-Durand M-L / Romier C
History
DepositionJul 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_17820.png

Downloads & links

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Map

FileDownload / File: emd_17820.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the human open engaged 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: 0.0025
Minimum - Maximum-0.009291739 - 0.018769456
Average (Standard dev.)0.000035225745 (±0.0004571225)
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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Half map: Half map 2

Fileemd_17820_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_17820_half_map_2.map
AnnotationHalf map 1
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 Cohesin ATP-open-engaged ATPase module

EntireName: Human Cohesin ATP-open-engaged ATPase module
Components
  • Complex: Human Cohesin ATP-open-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

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Supramolecule #1: Human Cohesin ATP-open-engaged ATPase module

SupramoleculeName: Human Cohesin ATP-open-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

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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

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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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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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 144721
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 modelPDB ID:

8p0a


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8pq5:
Human Cohesin ATPase module with an open DNA exit gate

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