+Open data
-Basic information
Entry | Database: PDB / ID: 6wg3 | |||||||||
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Title | Cryo-EM structure of human Cohesin-NIPBL-DNA complex | |||||||||
Components |
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Keywords | 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 | 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 / 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 / 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 / positive regulation of neuron migration / cellular response to X-ray / lateral element / chromo shadow domain binding / mediator complex binding / establishment of mitotic sister chromatid cohesion / chromatin looping / positive regulation of multicellular organism growth / metanephros development / digestive tract development / lncRNA binding / positive regulation of ossification / reciprocal meiotic recombination / 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 / regulation of embryonic development / positive regulation of interleukin-10 production / chromosome, centromeric region / mitotic spindle assembly / negative regulation of tumor necrosis factor production / 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 / brain development / response to radiation / protein localization / kinetochore / cognition / nuclear matrix / spindle pole / histone deacetylase binding / transcription corepressor activity / 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 / nuclear body / chromatin remodeling / protein heterodimerization activity / cell division / DNA repair / intracellular membrane-bounded organelle Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å | |||||||||
Authors | Shi, Z.B. / Gao, H. / Bai, X.C. / Yu, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2020 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wg3.cif.gz | 774.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wg3.ent.gz | 578.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/6wg3 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wg3 | HTTPS FTP |
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-Related structure data
Related structure data | 21658MC 6wg4C 6wg6C 6wgeC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: SMC1A, DXS423E, KIAA0178, SB1.8, SMC1, SMC1L1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14683 |
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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.) Homo sapiens (human) / Gene: SMC3, BAM, BMH, CSPG6, SMC3L1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UQE7 |
-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.) Homo sapiens (human) / Gene: RAD21, HR21, KIAA0078, NXP1, SCC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60216 |
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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.) Homo sapiens (human) / Gene: STAG1, SA1, SCC3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WVM7 |
#5: Protein | Mass: 188151.688 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 |
-DNA chain , 2 types, 2 molecules FG
#6: DNA chain | Mass: 15928.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#7: DNA chain | Mass: 15468.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 1 types, 2 molecules
#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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
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 |
-Processing
Software |
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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 | ||||||||||||||||||||||||
Refine LS restraints |
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