+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 / cohesin loader activity / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / regulation of hair cycle / response to DNA damage checkpoint signaling ...eye morphogenesis / cohesin loader activity / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / regulation of hair cycle / response to DNA damage checkpoint signaling / forelimb morphogenesis / maintenance of mitotic sister chromatid cohesion / negative regulation of mitotic metaphase/anaphase transition / embryonic viscerocranium morphogenesis / positive regulation of sister chromatid cohesion / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / uterus morphogenesis / embryonic digestive tract morphogenesis / negative regulation of G2/M transition of mitotic cell cycle / establishment of protein localization to chromatin / regulation of developmental growth / positive regulation of neuron migration / negative regulation of glial cell apoptotic process / cellular response to X-ray / integrator complex / digestive tract development / chromo shadow domain binding / lateral element / replication-born double-strand break repair via sister chromatid exchange / developmental growth / mediator complex binding / establishment of mitotic sister chromatid cohesion / positive regulation of multicellular organism growth / metanephros development / positive regulation of ossification / chromatin looping / embryonic forelimb morphogenesis / reciprocal meiotic recombination / face morphogenesis / lncRNA binding / sister chromatid cohesion / negative regulation of interleukin-1 beta production / microtubule motor activity / stem cell population maintenance / mitotic sister chromatid cohesion / dynein complex binding / fat cell differentiation / mitotic spindle pole / beta-tubulin binding / outflow tract morphogenesis / regulation of DNA replication / somatic stem cell population maintenance / mitotic sister chromatid segregation / regulation of embryonic development / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / heart morphogenesis / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / condensed nuclear chromosome / meiotic cell cycle / cognition / chromosome segregation / promoter-specific chromatin binding / sensory perception of sound / brain development / response to radiation / kinetochore / histone deacetylase binding / spindle pole / nuclear matrix / Separation of Sister Chromatids / transcription corepressor activity / double-strand break repair / protein localization / mitotic cell cycle / chromosome / double-stranded DNA binding / midbody / 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 / DNA damage response 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
Summary document | 6wg3_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6wg3_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6wg3_validation.xml.gz | 101.1 KB | Display | |
Data in CIF | 6wg3_validation.cif.gz | 156.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/6wg3 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wg3 | HTTPS FTP |
-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 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 |
-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 | ||||||||||||||||||||||||
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