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- PDB-6wg4: Crystal structure of human SMC1-SMC3 hinge domain heterodimer in ... -

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Basic information

Entry
Database: PDB / ID: 6wg4
TitleCrystal structure of human SMC1-SMC3 hinge domain heterodimer in south-open conformation
Components
  • Structural maintenance of chromosomes protein
  • Structural maintenance of chromosomes protein 3
KeywordsCELL CYCLE / ATPase / DNA-binding protein / Genome organization / Sister chromatid cohesion / Transcription regulation
Function / homology
Function and homology information


response to DNA damage checkpoint signaling / cohesin loader activity / meiotic cohesin complex / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / lateral element / mediator complex binding ...response to DNA damage checkpoint signaling / cohesin loader activity / meiotic cohesin complex / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / lateral element / mediator complex binding / establishment of mitotic sister chromatid cohesion / sister chromatid cohesion / mitotic sister chromatid cohesion / microtubule motor activity / dynein complex binding / stem cell population maintenance / beta-tubulin binding / mitotic spindle pole / mitotic sister chromatid segregation / somatic stem cell population maintenance / regulation of DNA replication / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / meiotic cell cycle / condensed nuclear chromosome / response to radiation / kinetochore / nuclear matrix / Separation of Sister Chromatids / mitotic cell cycle / chromosome / double-stranded DNA binding / Estrogen-dependent gene expression / protein heterodimerization activity / cell division / DNA repair / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Structural maintenance of chromosomes protein 1A, metazoan / 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 / Structural maintenance of chromosomes protein 1A / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsShi, Z.B. / 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 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Structural maintenance of chromosomes protein 3


Theoretical massNumber of molelcules
Total (without water)42,9242
Polymers42,9242
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.291, 119.612, 127.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-596-

ARG

21B-791-

HOH

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Components

#1: Protein Structural maintenance of chromosomes protein


Mass: 20161.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC1A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8JLG1, UniProt: Q14683*PLUS
#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: 22762.137 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.47 Å3/Da / Density % sol: 64.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2% 1,4-dioxane, 0.1 Tris pH 8.0, 15% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21541 / % possible obs: 98.5 % / Redundancy: 12.3 % / Biso Wilson estimate: 29.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.015 / Rrim(I) all: 0.055 / Net I/σ(I): 43.6
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 751 / CC1/2: 0.768 / CC star: 0.932 / Rpim(I) all: 0.389 / Rrim(I) all: 1.18 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WD5

2wd5


Resolution: 2.31→43.56 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.8758
RfactorNum. reflection% reflection
Rfree0.2354 2000 9.29 %
Rwork0.1829 --
obs0.1877 21536 81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.06 Å2
Refinement stepCycle: LAST / Resolution: 2.31→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 209 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782817
X-RAY DIFFRACTIONf_angle_d1.05183800
X-RAY DIFFRACTIONf_chiral_restr0.0533421
X-RAY DIFFRACTIONf_plane_restr0.0068496
X-RAY DIFFRACTIONf_dihedral_angle_d28.0029387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.2606530.1988455X-RAY DIFFRACTION27.06
2.37-2.430.2594550.2212581X-RAY DIFFRACTION34.1
2.43-2.50.2588730.2255711X-RAY DIFFRACTION42.04
2.5-2.580.3394840.2016929X-RAY DIFFRACTION53.74
2.58-2.680.26511470.21641364X-RAY DIFFRACTION81.24
2.68-2.780.28281650.21891680X-RAY DIFFRACTION98.03
2.78-2.910.26741840.21081708X-RAY DIFFRACTION99.68
2.91-3.060.28731680.21311692X-RAY DIFFRACTION99.09
3.06-3.250.26511860.19951695X-RAY DIFFRACTION99.26
3.26-3.510.20951690.16841724X-RAY DIFFRACTION100
3.51-3.860.20641770.16841727X-RAY DIFFRACTION99.63
3.86-4.420.21221760.14661709X-RAY DIFFRACTION98.64
4.42-5.560.19391840.15621746X-RAY DIFFRACTION99.9
5.56-43.560.24231790.19621815X-RAY DIFFRACTION98.13
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.185266443910.424312903525-1.881663062546.91321215314-2.104504130016.244998120190.2545249915810.2336673498630.283666238307-0.2733031603890.3203367441240.683127802739-0.579199854051-0.637715233224-0.5859045981160.820622133986-0.1666508389570.07178286971270.9476447449870.4721869909220.758586211559-3.83725282912-22.7646713494-30.9934366808
21.058915069911.24629784823-1.257170483412.49576163932-1.216424038061.56079455261-0.06121652134060.1652284071240.0401320731183-0.3496337145470.126808747749-0.0173479473339-0.186189532153-0.106848434216-0.06149510020160.466209923949-0.07843747214060.06143798217830.69519951740.3357827140670.385042793049-14.0122968772-40.0781572543-29.7655890897
33.2915245941.23182518038-0.9366309603356.95945197459-0.168122344452.961272923140.275810590033-0.1900595786070.3763783803680.679611285723-0.183629843714-0.0365649273023-0.7119631063870.282480368719-0.08514767695130.588124053772-0.1356939735380.0899600063890.8993546795830.453908364420.831653396126-3.42322816355-29.3408072802-20.580786166
43.937954655513.75877429463-4.244321674367.07541092466-1.475367881467.72794482732-0.5839427089330.0687555345546-1.22637646186-0.4247204326850.230845163952-1.420769956540.8517155837720.8636580626930.3446475065220.5054796481920.03627541097610.08737339741380.8196557222710.008146099564590.688061511921-10.9644719121-59.1327039885-25.6772603453
52.06796249070.759214454534-0.7907793066352.24314315241.72486591944.71685211227-0.1777027297250.371240274941-0.0193316465018-0.989317662790.213818239783-0.632442103324-0.4297703881340.0870137428827-0.03978166298130.573217876014-0.07750535882450.1942839517880.8675213174710.3023629369650.534648768557-5.34946123675-44.0769982151-28.4116808461
63.433464451761.67997054651-2.171884536582.34353986155-1.170238842953.33529734931-0.2971404927270.236052336113-0.255430214886-0.3233850953880.0843996735914-0.2002165736060.41660984268-0.03969285004410.3041921471440.196759499406-0.04411568243940.05765736834820.4699615650170.2362150540070.306336632826-20.9218871716-54.2994905454-19.3460476808
72.034513465680.309679052407-1.322226085530.3667620982240.01628585491631.007530482530.1739438064570.2094145130030.231299369827-0.216366637313-0.247997204438-0.298648856234-0.6437875576550.4222464134280.07555734495850.632593201126-0.0495961436677-0.03410212895141.000782758510.5338886640970.767382241036-24.0925925095-37.7193399377-29.9794945199
80.260757442581-0.9828879999870.7246611085968.82317143528-0.146030962963.319609311880.1318061069470.5273258793850.520540090732-0.882901118912-0.347831981708-0.737611805441-1.071832017950.7802111596340.2220095960681.24143687227-0.1001883842910.06131521509621.416893306440.6551238678481.06797375039-17.2298690006-31.2536979242-42.1288621544
91.12239901404-0.110215191580.5263428070621.14676029808-0.3382716353230.905138274302-0.06981201113750.1515179888460.215665989665-0.118535741204-0.0422363021173-0.0341334723641-0.1223868123510.1056068622720.08985009483080.3000858660260.06602367372-0.1176307276410.3036092214510.2456577673380.428591811851-38.9731219404-40.0922903716-16.4762648792
104.223384242782.639316024073.956861571145.194377884952.482459907716.02139223336-0.0618171477967-0.1314012893750.5087795083470.0718164582644-0.191204803960.0145404278112-0.238021157829-0.1579275097810.2298008087060.09337926801990.0253735980832-0.02711120205550.1219149052260.05557897719820.302807586305-37.8358088216-46.4101312684-5.64832252784
111.013248195521.127543482170.03565213966051.66369085480.8462551451311.58915121850.0953681735161-0.02797590847120.3579960982750.0991032039475-0.07558609001230.275277072765-0.4617312923690.194152754698-0.01641150148890.426906767232-0.151218137308-0.1338311608130.2604380463550.1165045354540.716047037466-26.0535083818-34.06401263750.0718302893115
120.470989213259-0.331325943260.5677595240972.38630173395-1.200397577792.51396315405-0.01412397043410.1793318371860.132531925339-0.297043569742-0.01225520260240.03104895188720.00596300606549-0.00728385008539-0.05650109712750.1407105609330.01128804163510.004726176317250.2804007907360.2784941527280.275589610197-31.9688019521-49.2083370737-15.5076835363
136.209585705493.211438893183.128088787815.394457778016.261430760017.373383396940.223226239563-0.613007449344-0.03693543096781.183149434870.187783915151-1.015054613870.8662957335690.953303720546-0.4167306310020.5784556843620.0294898705082-0.1919100664470.7578804082940.1155653167990.621873062208-15.4461852047-47.28143107399.15132630052
145.633056096591.83891103517-0.6557019273962.581940455310.7599387328291.874602008420.0057358540171-0.2670551941790.1810957979820.212869643268-0.021413844272-0.382327780073-0.1385401110970.370447737953-0.0291328320760.127014656795-0.0396399850094-0.1078352864230.1448371758620.08415972152640.349257838469-27.2662971179-45.70442243784.17780091886
155.71793816031.526110754722.126441252870.7019773675561.59151007964.348046655680.0601601259805-0.6490941916870.4278118906740.2667807028270.319667932553-1.02770524163-0.4173844089761.19223849041-0.4125217763940.517342897244-0.293942551028-0.2418627029840.8735183008880.04780086791431.04094855591-11.556412932-36.43057896527.97767130313
164.60523250338-5.86611085236-4.111630853657.605908081035.890986781826.874182449970.199253766525-0.3830679362021.05662613794-0.7422487949270.58585599054-1.68336599293-1.089156570211.39254984231-0.8130334387280.803655631678-0.394059772884-0.1816873105270.7785468381820.01009995093671.15188635545-12.141340148-32.92559630731.7997376711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 499 through 514 )
2X-RAY DIFFRACTION2chain 'A' and (resid 515 through 543 )
3X-RAY DIFFRACTION3chain 'A' and (resid 544 through 582 )
4X-RAY DIFFRACTION4chain 'A' and (resid 583 through 594 )
5X-RAY DIFFRACTION5chain 'A' and (resid 595 through 613 )
6X-RAY DIFFRACTION6chain 'A' and (resid 614 through 655 )
7X-RAY DIFFRACTION7chain 'A' and (resid 656 through 666 )
8X-RAY DIFFRACTION8chain 'A' and (resid 667 through 674 )
9X-RAY DIFFRACTION9chain 'B' and (resid 500 through 522 )
10X-RAY DIFFRACTION10chain 'B' and (resid 523 through 543 )
11X-RAY DIFFRACTION11chain 'B' and (resid 544 through 559 )
12X-RAY DIFFRACTION12chain 'B' and (resid 560 through 594 )
13X-RAY DIFFRACTION13chain 'B' and (resid 595 through 605 )
14X-RAY DIFFRACTION14chain 'B' and (resid 606 through 627 )
15X-RAY DIFFRACTION15chain 'B' and (resid 628 through 652 )
16X-RAY DIFFRACTION16chain 'B' and (resid 653 through 664 )

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