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Open data
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Basic information
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Title | Cryo-EM structure of human cohesin-CTCF-DNA complex | ||||||||||||
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![]() | Cohesin / NIPBL / CTCF / DNA / chromosome folding / topologically associating domain / chromatin loops / DNA loop extrusion / sister chromatid cohesion / complex / ATPase / HEAT repeat protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | ![]() eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / cohesin loader activity / response to DNA damage checkpoint signaling / regulation of hair cycle ...eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / cohesin loader activity / response to DNA damage checkpoint signaling / regulation of hair cycle / chromatin loop anchoring activity / negative regulation of mitotic metaphase/anaphase transition / chromatin insulator sequence binding / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / maintenance of mitotic sister chromatid cohesion / Establishment of Sister Chromatid Cohesion / forelimb morphogenesis / embryonic viscerocranium morphogenesis / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / uterus morphogenesis / regulation of centromeric sister chromatid cohesion / negative regulation of glial cell apoptotic process / establishment of protein localization to chromatin / regulation of developmental growth / genomic imprinting / embryonic digestive tract morphogenesis / replication-born double-strand break repair via sister chromatid exchange / cellular response to X-ray / lateral element / positive regulation of neuron migration / integrator complex / mediator complex binding / chromo shadow domain binding / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / positive regulation of multicellular organism growth / metanephros development / chromatin looping / positive regulation of ossification / digestive tract development / reciprocal meiotic recombination / embryonic forelimb morphogenesis / sister chromatid cohesion / face morphogenesis / lncRNA binding / negative regulation of interleukin-1 beta production / microtubule motor activity / mitotic sister chromatid cohesion / negative regulation of gene expression via chromosomal CpG island methylation / stem cell population maintenance / dynein complex binding / mitotic spindle pole / fat cell differentiation / beta-tubulin binding / outflow tract morphogenesis / regulation of DNA replication / mitotic sister chromatid segregation / somatic stem cell population maintenance / positive regulation of interleukin-10 production / regulation of embryonic development / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / developmental growth / SUMOylation of DNA damage response and repair proteins / heart morphogenesis / condensed chromosome / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / epigenetic regulation of gene expression / condensed nuclear chromosome / meiotic cell cycle / male germ cell nucleus / transcription coregulator binding / chromosome segregation / promoter-specific chromatin binding / sensory perception of sound / response to radiation / brain development / kinetochore / cognition / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle pole / histone deacetylase binding / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Separation of Sister Chromatids / transcription corepressor activity / sequence-specific double-stranded DNA binding / double-strand break repair / protein localization / mitotic cell cycle / chromosome / midbody Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||||||||
![]() | Shi ZB / Bai XC | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: CTCF and R-loops are boundaries of cohesin-mediated DNA looping. Authors: Hongshan Zhang / Zhubing Shi / Edward J Banigan / Yoori Kim / Hongtao Yu / Xiao-Chen Bai / Ilya J Finkelstein / ![]() ![]() Abstract: Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, ...Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging, we demonstrate that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping. The cryo-EM structure of the cohesin-CTCF complex reveals that this CTCF motif ahead of zinc fingers can only reach its binding site on the STAG1 cohesin subunit when the N terminus of CTCF faces cohesin. Remarkably, a C-terminally oriented CTCF accelerates DNA compaction by cohesin. DNA-bound Cas9 and Cas12a ribonucleoproteins are also polar cohesin barriers, indicating that stalling may be intrinsic to cohesin itself. Finally, we show that RNA-DNA hybrids (R-loops) block cohesin-mediated DNA compaction in vitro and are enriched with cohesin subunits in vivo, likely forming TAD boundaries. | ||||||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 104.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.9 KB 29.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 63.1 KB | ||
Filedesc metadata | ![]() | 11.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w1mMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.44 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Human cohesin-NIPBL-CTCF-DNA complex
+Supramolecule #1: Human cohesin-NIPBL-CTCF-DNA complex
+Supramolecule #2: Human cohesin-NIPBL-CTCF
+Supramolecule #3: DNA
+Macromolecule #1: Structural maintenance of chromosomes protein 1A
+Macromolecule #2: Structural maintenance of chromosomes protein 3
+Macromolecule #3: Double-strand-break repair protein rad21 homolog
+Macromolecule #4: Cohesin subunit SA-1
+Macromolecule #5: Nipped-B-like protein
+Macromolecule #8: Transcriptional repressor CTCF
+Macromolecule #6: DNA (118-MER)
+Macromolecule #7: DNA (118-MER)
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #10: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||||||
Output model | ![]() PDB-7w1m: |