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- PDB-7dg5: Crystal structure of mouse Smc1-Smc3 hinge domain containing a D5... -

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Basic information

Entry
Database: PDB / ID: 7dg5
TitleCrystal structure of mouse Smc1-Smc3 hinge domain containing a D574Y mutation
Components
  • Structural maintenance of chromosomes protein 1A
  • Structural maintenance of chromosomes protein 3
KeywordsDNA BINDING PROTEIN / cohesin / Smc1 / Smc3 / hinge
Function / homology
Function and homology information


Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / response to DNA damage checkpoint signaling / SUMOylation of DNA damage response and repair proteins / cohesin loader activity / meiotic cohesin complex / mitotic cohesin complex / cohesin complex / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids ...Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / response to DNA damage checkpoint signaling / SUMOylation of DNA damage response and repair proteins / cohesin loader activity / meiotic cohesin complex / mitotic cohesin complex / cohesin complex / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / synaptonemal complex / lateral element / mediator complex binding / sister chromatid cohesion / mitotic sister chromatid cohesion / stem cell population maintenance / dynein complex binding / beta-tubulin binding / mitotic spindle pole / regulation of DNA replication / somatic stem cell population maintenance / chromosome, centromeric region / basement membrane / mitotic spindle assembly / meiotic cell cycle / response to radiation / kinetochore / nuclear matrix / double-stranded DNA binding / protein heterodimerization activity / cell division / DNA repair / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Smc1, ATP-binding cassette domain / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 1A / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeo, H. / Noh, H. / Oh, B.-H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1A4A3079755 Korea, Republic Of
CitationJournal: Elife / Year: 2021
Title: Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes.
Authors: Naomi J Petela / Andres Gonzalez Llamazares / Sarah Dixon / Bin Hu / Byung-Gil Lee / Jean Metson / Heekyo Seo / Antonio Ferrer-Harding / Menelaos Voulgaris / Thomas Gligoris / James Collier ...Authors: Naomi J Petela / Andres Gonzalez Llamazares / Sarah Dixon / Bin Hu / Byung-Gil Lee / Jean Metson / Heekyo Seo / Antonio Ferrer-Harding / Menelaos Voulgaris / Thomas Gligoris / James Collier / Byung-Ha Oh / Jan Löwe / Kim A Nasmyth /
Abstract: Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 ...Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 and ATP-dependent engagement of cohesin's Smc1 and Smc3 head domains. Scc2's replacement by Pds5 abrogates cohesin's ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50-nm-long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the form of cohesin that reveals the structure of folded and zipped-up coils in unprecedented detail and shows that Scc2 can associate with Smc1's ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific crosslinking, we show that cohesin's coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation () within Smc1's hinge that alters how Scc2 and Pds5 interact with Smc1's hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin's hinge, which in turn requires coiled coil folding.
History
DepositionNov 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 1A
B: Structural maintenance of chromosomes protein 3
C: Structural maintenance of chromosomes protein 1A
D: Structural maintenance of chromosomes protein 3


Theoretical massNumber of molelcules
Total (without water)97,9424
Polymers97,9424
Non-polymers00
Water6,377354
1
A: Structural maintenance of chromosomes protein 1A
B: Structural maintenance of chromosomes protein 3


Theoretical massNumber of molelcules
Total (without water)48,9712
Polymers48,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-6 kcal/mol
Surface area18410 Å2
MethodPISA
2
C: Structural maintenance of chromosomes protein 1A
D: Structural maintenance of chromosomes protein 3


Theoretical massNumber of molelcules
Total (without water)48,9712
Polymers48,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-7 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.080, 60.851, 77.757
Angle α, β, γ (deg.)72.660, 88.430, 89.990
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Structural maintenance of chromosomes protein 1A / SMC-1A / Chromosome segregation protein SmcB / Sb1.8


Mass: 24631.336 Da / Num. of mol.: 2 / Mutation: D574Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smc1a, Sb1.8, Smc1, Smc1l1, Smcb / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9CU62
#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 segregation protein SmcD / Mad member-interacting protein 1


Mass: 24339.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smc3, Bam, Bmh, Cspg6, Mmip1, Smc3l1, Smcd / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9CW03
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium phosphate, Potassium phosphate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 52576 / % possible obs: 88.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.044 / Rrim(I) all: 0.078 / Χ2: 0.759 / Net I/σ(I): 7.3 / Num. measured all: 134894
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.031.90.17622790.8950.1390.2250.41276.6
2.03-2.0720.1722840.9120.1330.2170.44277.5
2.07-2.112.10.15924010.9320.120.2010.44981.1
2.11-2.152.30.15924500.9330.1170.1980.50383.3
2.15-2.22.30.14925390.9430.110.1860.49884.7
2.2-2.252.30.12725570.9620.0930.1580.48685.1
2.25-2.312.30.1225400.9660.0880.1490.49886.9
2.31-2.372.30.10726040.9690.0780.1330.53587.6
2.37-2.442.30.09925540.9740.0720.1230.56985.9
2.44-2.522.30.09425590.9760.0710.1190.63186
2.52-2.612.50.08626760.980.0620.1060.60490.1
2.61-2.712.60.08126620.9850.0560.0990.61390.8
2.71-2.842.70.07427590.9880.050.090.62592.9
2.84-2.992.80.06927590.9880.0470.0840.71292.7
2.99-3.172.70.06227750.9910.0420.0750.82193.3
3.17-3.422.80.05727760.9910.0390.070.89394.1
3.42-3.763.20.05328840.9930.0340.0630.98396.3
3.76-4.313.20.05128190.9940.0320.0611.09995.8
4.31-5.433.10.04728400.9940.0310.0571.14495.8
5.43-503.30.04928590.9940.0320.0591.2196.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WD5

2wd5


Resolution: 2→42.06 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2.18 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 2002 3.81 %
Rwork0.2187 50562 -
obs0.2207 52564 88.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.69 Å2 / Biso mean: 20.6405 Å2 / Biso min: 5.15 Å2
Refinement stepCycle: final / Resolution: 2→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5815 0 0 355 6170
Biso mean---22.65 -
Num. residues----738
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.29171220.2333049317175
2.05-2.10.331260.22073220334679
2.1-2.160.30681300.22143443357384
2.16-2.230.28611390.21233470360985
2.23-2.310.26471460.21043492363886
2.31-2.410.28021350.21243579371487
2.41-2.520.28591410.22013515365686
2.52-2.650.25911440.22443670381490
2.65-2.810.2891550.23873756391192
2.81-3.030.3031480.2373801394993
3.03-3.340.27881510.22953827397894
3.34-3.820.25471500.20713909405996
3.82-4.810.21541530.19533900405396
4.81-42.060.26111620.22713931409396

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