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- PDB-6wg3: Cryo-EM structure of human Cohesin-NIPBL-DNA complex -

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Basic information

Entry
Database: PDB / ID: 6wg3
TitleCryo-EM structure of human Cohesin-NIPBL-DNA complex
Components
  • (DNA (51-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
KeywordsCELL 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 / gallbladder development / external genitalia morphogenesis / uterus morphogenesis / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / regulation of developmental growth / regulation of hair cycle / forelimb morphogenesis ...eye morphogenesis / gallbladder development / external genitalia morphogenesis / uterus morphogenesis / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / regulation of developmental growth / regulation of hair cycle / forelimb morphogenesis / cohesin loader activity / response to DNA damage checkpoint signaling / mitotic cohesin complex / maintenance of mitotic sister chromatid cohesion / embryonic viscerocranium morphogenesis / negative regulation of mitotic metaphase/anaphase transition / meiotic cohesin complex / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / cohesin complex / establishment of meiotic sister chromatid cohesion / positive regulation of sister chromatid cohesion / embryonic digestive tract morphogenesis / embryonic forelimb morphogenesis / negative regulation of glial cell apoptotic process / replication-born double-strand break repair via sister chromatid exchange / positive regulation of multicellular organism growth / chromo shadow domain binding / positive regulation of neuron migration / negative regulation of G2/M transition of mitotic cell cycle / metanephros development / cellular response to X-ray / mediator complex binding / establishment of mitotic sister chromatid cohesion / establishment of protein localization to chromatin / chromatin looping / lateral element / face morphogenesis / positive regulation of ossification / digestive tract development / integrator complex / reciprocal meiotic recombination / mitotic sister chromatid cohesion / microtubule motor activity / sister chromatid cohesion / negative regulation of interleukin-1 beta production / somatic stem cell population maintenance / mitotic spindle pole / lncRNA binding / outflow tract morphogenesis / regulation of DNA replication / mitotic sister chromatid segregation / dynein complex binding / positive regulation of interleukin-10 production / regulation of embryonic development / negative regulation of tumor necrosis factor production / developmental growth / mitotic spindle assembly / chromosome, centromeric region / heart morphogenesis / fat cell differentiation / SUMOylation of DNA damage response and repair proteins / beta-tubulin binding / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / sensory perception of sound / brain development / chromosome segregation / promoter-specific chromatin binding / meiotic cell cycle / response to radiation / cognition / histone deacetylase binding / kinetochore / nuclear matrix / spindle pole / intracellular protein localization / transcription corepressor activity / Separation of Sister Chromatids / double-strand break repair / mitotic cell cycle / chromosome / double-stranded DNA binding / DNA recombination / Estrogen-dependent gene expression / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / response to hypoxia / nuclear body / chromatin remodeling / protein heterodimerization activity / cell division / DNA repair / chromatin binding / apoptotic process / regulation of transcription by RNA polymerase II / DNA damage response
Similarity search - Function
HEAT repeat associated with sister chromatid cohesion protein / Sister chromatid cohesion C-terminal domain / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / Smc1, ATP-binding cassette domain / STAG ...HEAT repeat associated with sister chromatid cohesion protein / Sister chromatid cohesion C-terminal domain / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / Smc1, ATP-binding cassette domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / 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 / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Double-strand-break repair protein rad21 homolog / 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: 5.3 Å
AuthorsShi, Z.B. / Gao, H. / Bai, X.C. / Yu, H.
Funding support United States, 2items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT) United States
Welch Foundation United States
CitationJournal: 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
DepositionApr 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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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 (51-MER)
G: DNA (51-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)723,4489
Polymers722,4367
Non-polymers1,0122
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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-1A / Sb1.8


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
#2: Protein Structural maintenance of chromosomes protein 3 / SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / Chondroitin sulfate ...SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / Chondroitin sulfate proteoglycan 6 / Chromosome-associated polypeptide / hCAP


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

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Protein , 3 types, 3 molecules CDE

#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: 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 Nipped-B-like protein / Delangin / SCC2 homolog


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

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DNA chain , 2 types, 2 molecules FG

#6: DNA chain DNA (51-MER)


Mass: 15928.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#7: DNA chain DNA (51-MER)


Mass: 15468.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 2 molecules

#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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

ComponentName: Human Cohesin-NIPBL-DNA Complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: 0.82 MDa / Experimental 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
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5796
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
1RELION3particle selection
4GctfCTF correction
7UCSF Chimera1.14model fitting
9PHENIX1.17.1-3660model refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 510507
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6857 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 59.17 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005932441
ELECTRON MICROSCOPYf_angle_d1.165944129
ELECTRON MICROSCOPYf_chiral_restr0.06364987
ELECTRON MICROSCOPYf_plane_restr0.00675266
ELECTRON MICROSCOPYf_dihedral_angle_d28.70745016

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