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- PDB-6wge: Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 -

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Basic information

Entry
Database: PDB / ID: 6wge
TitleCryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1
Components
  • (DNA (43-MER)) x 2
  • (Structural maintenance of chromosomes protein ...) x 2
  • 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 / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / regulation of hair cycle / response to DNA damage checkpoint signaling / maintenance of mitotic sister chromatid cohesion / forelimb morphogenesis ...eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / regulation of hair cycle / response to DNA damage checkpoint signaling / maintenance of mitotic sister chromatid cohesion / forelimb morphogenesis / negative regulation of mitotic metaphase/anaphase transition / embryonic viscerocranium morphogenesis / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin loader activity / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / uterus morphogenesis / negative regulation of G2/M transition of mitotic cell cycle / regulation of developmental growth / negative regulation of glial cell apoptotic process / establishment of protein localization to chromatin / embryonic digestive tract morphogenesis / cellular response to X-ray / positive regulation of neuron migration / chromo shadow domain binding / lateral element / replication-born double-strand break repair via sister chromatid exchange / mediator complex binding / establishment of mitotic sister chromatid cohesion / integrator complex / positive regulation of multicellular organism growth / metanephros development / chromatin looping / positive regulation of ossification / embryonic forelimb morphogenesis / reciprocal meiotic recombination / digestive tract development / face morphogenesis / microtubule motor activity / sister chromatid cohesion / negative regulation of interleukin-1 beta production / mitotic sister chromatid cohesion / stem cell population maintenance / lncRNA binding / mitotic spindle pole / dynein complex binding / beta-tubulin binding / fat cell differentiation / outflow tract morphogenesis / regulation of DNA replication / mitotic sister chromatid segregation / regulation of embryonic development / positive regulation of interleukin-10 production / somatic stem cell population maintenance / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / developmental growth / SUMOylation of DNA damage response and repair proteins / heart morphogenesis / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / sensory perception of sound / promoter-specific chromatin binding / response to radiation / brain development / kinetochore / cognition / histone deacetylase binding / nuclear matrix / spindle pole / transcription corepressor activity / Separation of Sister Chromatids / intracellular protein localization / 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 / chromatin remodeling / protein heterodimerization activity / cell division / DNA repair / intracellular membrane-bounded organelle / apoptotic process / 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 / Smc1, ATP-binding cassette domain / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal ...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 / Smc1, ATP-binding cassette domain / : / 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 / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 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 5, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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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
E: Nipped-B-like protein
F: DNA (43-MER)
G: DNA (43-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,10810
Polymers570,0476
Non-polymers1,0614
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 / Mutation: E1144Q
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 , 2 types, 2 molecules CE

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


Mass: 186778.250 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

#5: DNA chain DNA (43-MER)


Mass: 13422.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (43-MER)


Mass: 13035.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 4 molecules

#7: 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
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / 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

ComponentName: Human Cohesin-NIPBL-DNA Complex without STAG1 / Type: COMPLEX / Entity ID: #1-#6 / 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
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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
12RELION33D reconstruction
13PHENIX1.17.1-3660model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 510507
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68161 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 80.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007120708
ELECTRON MICROSCOPYf_angle_d0.975728246
ELECTRON MICROSCOPYf_chiral_restr0.05663199
ELECTRON MICROSCOPYf_plane_restr0.00573286
ELECTRON MICROSCOPYf_dihedral_angle_d30.66123353

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