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- PDB-7w1m: Cryo-EM structure of human cohesin-CTCF-DNA complex -

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Basic information

Entry
Database: PDB / ID: 7w1m
TitleCryo-EM structure of human cohesin-CTCF-DNA complex
Components
  • (DNA (118-MER)) x 2
  • (Structural maintenance of chromosomes protein ...) x 2
  • Cohesin subunit SA-1
  • Double-strand-break repair protein rad21 homolog
  • Nipped-B-like protein
  • Transcriptional repressor CTCF
KeywordsDNA BINDING PROTEIN/DNA / 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
Function and homology information


eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / response to DNA damage checkpoint signaling / regulation of hair cycle / negative regulation of mitotic metaphase/anaphase transition ...eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / response to DNA damage checkpoint signaling / regulation of hair cycle / negative regulation of mitotic metaphase/anaphase transition / cohesin loader activity / 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 / integrator complex / embryonic viscerocranium morphogenesis / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / regulation of centromeric sister chromatid cohesion / uterus morphogenesis / establishment of protein localization to chromatin / negative regulation of glial cell apoptotic process / regulation of developmental growth / embryonic digestive tract morphogenesis / genomic imprinting / replication-born double-strand break repair via sister chromatid exchange / cellular response to X-ray / lateral element / positive regulation of neuron migration / mediator complex binding / chromo shadow domain binding / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / chromatin looping / negative regulation of gene expression via chromosomal CpG island methylation / positive regulation of multicellular organism growth / metanephros development / digestive tract development / positive regulation of ossification / reciprocal meiotic recombination / lncRNA binding / embryonic forelimb morphogenesis / sister chromatid cohesion / face morphogenesis / negative regulation of interleukin-1 beta production / mitotic sister chromatid cohesion / microtubule motor activity / : / dynein complex binding / stem cell population maintenance / beta-tubulin binding / fat cell differentiation / mitotic spindle pole / outflow tract morphogenesis / mitotic sister chromatid segregation / somatic stem cell population maintenance / regulation of DNA replication / positive regulation of interleukin-10 production / regulation of embryonic development / chromosome, centromeric region / negative regulation of tumor necrosis factor production / mitotic spindle assembly / developmental growth / localization / SUMOylation of DNA damage response and repair proteins / epigenetic regulation of gene expression / heart morphogenesis / condensed chromosome / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / meiotic cell cycle / condensed nuclear chromosome / male germ cell nucleus / chromosome segregation / promoter-specific chromatin binding / transcription coregulator binding / sensory perception of sound / brain development / response to radiation / protein localization / kinetochore / cognition / nuclear matrix / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle pole / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / Separation of Sister Chromatids / transcription corepressor activity / double-strand break repair / mitotic cell cycle / chromosome / midbody
Similarity search - Function
: / Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein ...: / Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / 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 / Stromalin conservative domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative (SCD) domain profile. / 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 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Double-strand-break repair protein rad21 homolog / Transcriptional repressor CTCF / Structural maintenance of chromosomes protein 1A / Nipped-B-like protein / Cohesin subunit SA-1 / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsShi, Z.B. / Bai, X.C. / Yu, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124096, GM143158, GM136976 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP160667-P2, RP160082 United States
Welch FoundationI-1441, I-1944 United States
CitationJournal: Mol Cell / Year: 2023
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
DepositionNov 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_3d_fitting_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 1A
B: Structural maintenance of chromosomes protein 3
C: Double-strand-break repair protein rad21 homolog
D: Cohesin subunit SA-1
E: Nipped-B-like protein
F: DNA (118-MER)
G: DNA (118-MER)
H: Transcriptional repressor CTCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)826,70323
Polymers824,9978
Non-polymers1,70615
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Sucrose gradient ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AB

#1: Protein Structural maintenance of chromosomes protein 1A / SMC protein 1A / SMC-1-alpha / SMC-1A / Sb1.8


Mass: 143485.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC1A, DXS423E, KIAA0178, SB1.8, SMC1, SMC1L1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14683
#2: Protein Structural maintenance of chromosomes protein 3 / SMC protein 3 / SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / ...SMC protein 3 / SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / Chondroitin sulfate proteoglycan 6 / Chromosome-associated polypeptide / hCAP


Mass: 141771.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC3, BAM, BMH, CSPG6, SMC3L1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UQE7

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Protein , 4 types, 4 molecules CDEH

#3: Protein Double-strand-break repair protein rad21 homolog / hHR21 / Nuclear matrix protein 1 / NXP-1 / SCC1 homolog


Mass: 71556.102 Da / Num. of mol.: 1 / Mutation: R172A, D279A, R450A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD21, HR21, KIAA0078, NXP1, SCC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60216
#4: Protein Cohesin subunit SA-1 / / SCC3 homolog 1 / Stromal antigen 1


Mass: 144616.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAG1, SA1, SCC3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WVM7
#5: Protein Nipped-B-like protein / Delangin / SCC2 homolog


Mass: 167830.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NIPBL, IDN3, SCC2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6KC79
#8: Protein Transcriptional repressor CTCF / 11-zinc finger protein / CCCTC-binding factor / CTCFL paralog


Mass: 82928.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49711

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DNA chain , 2 types, 2 molecules FG

#6: DNA chain DNA (118-MER)


Mass: 36202.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#7: DNA chain DNA (118-MER)


Mass: 36605.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 15 molecules

#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#10: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human cohesin-NIPBL-CTCF-DNA complexCOMPLEX#1-#80MULTIPLE SOURCES
2Human cohesin-NIPBL-CTCFCOMPLEX#1-#5, #81RECOMBINANT
3DNACOMPLEX#6-#71RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameCategory
4GctfCTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2185704
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42704 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16WGE

6wge

16WGE1PDBexperimental model
25T0U

5t0u

15T0U2PDBexperimental model
35YEF

5yef

15YEF3PDBexperimental model
45YEL

5yel

15YEL4PDBexperimental model
56QNX

6qnx

16QNX5PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 236.05 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004835295
ELECTRON MICROSCOPYf_angle_d1.076248464
ELECTRON MICROSCOPYf_chiral_restr0.05865438
ELECTRON MICROSCOPYf_plane_restr0.00725436
ELECTRON MICROSCOPYf_dihedral_angle_d22.88186172

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