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Open data
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Basic information
Entry | Database: PDB / ID: 6wg3 | |||||||||
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Title | Cryo-EM structure of human Cohesin-NIPBL-DNA complex | |||||||||
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![]() | CELL CYCLE/DNA / Protein-DNA complex / ATPase / DNA-binding protein / Genome organization / Sister chromatid cohesion / Transcription regulation / CELL CYCLE / CELL CYCLE-DNA complex | |||||||||
Function / homology | ![]() 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 / 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 / cohesin loader activity / embryonic viscerocranium morphogenesis / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / uterus morphogenesis / establishment of protein localization to chromatin / negative regulation of glial cell apoptotic process / regulation of developmental growth / embryonic digestive tract morphogenesis / replication-born double-strand break repair via sister chromatid exchange / cellular response to X-ray / integrator complex / lateral element / positive regulation of neuron migration / mediator complex binding / chromo shadow domain binding / 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 / lncRNA binding / sister chromatid cohesion / face morphogenesis / negative regulation of interleukin-1 beta production / microtubule motor activity / mitotic sister chromatid cohesion / stem cell population maintenance / dynein complex binding / beta-tubulin binding / fat cell differentiation / mitotic spindle pole / 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 / chromosome, centromeric region / negative regulation of tumor necrosis factor production / mitotic spindle assembly / developmental growth / localization / SUMOylation of DNA damage response and repair proteins / heart morphogenesis / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / meiotic cell cycle / condensed nuclear chromosome / chromosome segregation / promoter-specific chromatin binding / sensory perception of sound / response to radiation / protein localization / brain development / cognition / kinetochore / nuclear matrix / histone deacetylase binding / spindle pole / Separation of Sister Chromatids / transcription corepressor activity / double-strand break repair / chromosome / mitotic cell cycle / midbody / double-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / nuclear body / response to hypoxia / chromatin remodeling / protein heterodimerization activity / cell division / intracellular membrane-bounded organelle / DNA repair Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å | |||||||||
![]() | Shi, Z.B. / Gao, H. / Bai, X.C. / Yu, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the human cohesin-NIPBL-DNA complex. Authors: Zhubing Shi / Haishan Gao / Xiao-Chen Bai / Hongtao Yu / ![]() ![]() Abstract: As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How ...As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How cohesin executes these fundamental DNA transactions is not understood. Using cryo-electron microscopy (cryo-EM), we determined the structure of human cohesin bound to its loader NIPBL and DNA at medium resolution. Cohesin and NIPBL interact extensively and together form a central tunnel to entrap a 72-base pair DNA. NIPBL and DNA promote the engagement of cohesin's ATPase head domains and ATP binding. The hinge domains of cohesin adopt an "open washer" conformation and dock onto the STAG1 subunit. Our structure explains the synergistic activation of cohesin by NIPBL and DNA and provides insight into DNA entrapment by cohesin. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 774.1 KB | Display | ![]() |
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PDB format | ![]() | 578.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 101.1 KB | Display | |
Data in CIF | ![]() | 156.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 21658MC ![]() 6wg4C ![]() 6wg6C ![]() 6wgeC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 143484.109 Da / Num. of mol.: 1 / Mutation: E1157Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 141770.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein , 3 types, 3 molecules CDE
#3: Protein | Mass: 71556.102 Da / Num. of mol.: 1 / Mutation: R172A, D279A, R450A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#4: Protein | Mass: 146075.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Protein | Mass: 188151.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-DNA chain , 2 types, 2 molecules FG
#6: DNA chain | Mass: 15928.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#7: DNA chain | Mass: 15468.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 1 types, 2 molecules ![](data/chem/img/ANP.gif)
#8: Chemical |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human Cohesin-NIPBL-DNA Complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Molecular weight | Value: 0.82 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5796 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 510507 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6857 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.17 Å2 | ||||||||||||||||||||||||
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