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- PDB-8tlj: CDCA7 (Mouse) Binds Non-B-form 32-mer DNA oligo Containing a 5mC -

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Basic information

Entry
Database: PDB / ID: 8tlj
TitleCDCA7 (Mouse) Binds Non-B-form 32-mer DNA oligo Containing a 5mC
Components
  • Cell division cycle-associated protein 7
  • DNA (32-MER)
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN / zinc fingers / chromatin architecture / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of cell population proliferation / regulation of DNA-templated transcription / apoptotic process / nucleoplasm / nucleus / cytosol
Similarity search - Function
Zinc-finger domain of monoamine-oxidase A repressor R1 / CDCA7/CDA7L / Zinc-finger domain of monoamine-oxidase A repressor R1
Similarity search - Domain/homology
DNA / DNA (> 10) / Cell division cycle-associated protein 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHorton, J.R. / Ren, R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: Sci Adv / Year: 2024
Title: The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA
Authors: Hardikar, S. / Ren, R. / Ying, Z. / Horton, J.R. / Bramble, M.D. / Liu, B. / Lu, Y. / Dan, J. / Zhang, X. / Cheng, X. / Chen, T.
History
DepositionJul 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division cycle-associated protein 7
X: DNA (32-MER)
B: Cell division cycle-associated protein 7
C: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,60019
Polymers52,6344
Non-polymers96615
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.874, 31.533, 91.823
Angle α, β, γ (deg.)90.000, 110.750, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11X-101-

MG

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Components

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Protein / DNA chain , 2 types, 4 molecules ABXC

#1: Protein Cell division cycle-associated protein 7


Mass: 16452.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdca7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codon-plus (DE3)-RIL / References: UniProt: Q9D0M2
#2: DNA chain DNA (32-MER)


Mass: 9864.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: n vitro SELEX screening / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 5 types, 125 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MgCl2, 0.1 M Bis-Tris pH 6.2, 25% PGE3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.3→45.03 Å / Num. obs: 19726 / % possible obs: 95.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 49.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.038 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1408 / CC1/2: 0.832 / Rpim(I) all: 0.321 / % possible all: 69

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.03 Å / SU ML: 0.3391 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2114
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 987 5 %
Rwork0.1846 18739 -
obs0.1868 19726 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 1308 42 110 3090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283155
X-RAY DIFFRACTIONf_angle_d0.54564534
X-RAY DIFFRACTIONf_chiral_restr0.036492
X-RAY DIFFRACTIONf_plane_restr0.0051367
X-RAY DIFFRACTIONf_dihedral_angle_d23.3581271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.32591030.29071947X-RAY DIFFRACTION68.42
2.42-2.570.32481370.26932602X-RAY DIFFRACTION94.16
2.57-2.770.32011470.26512786X-RAY DIFFRACTION99.42
2.77-3.050.34331470.25332802X-RAY DIFFRACTION99.66
3.05-3.490.23391490.19292828X-RAY DIFFRACTION99.7
3.49-4.40.20831480.15732837X-RAY DIFFRACTION99.57
4.4-45.030.17181560.1452937X-RAY DIFFRACTION99.13
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)
16.25658539507-2.095346118030.9614012730133.492507137710.05394540474354.38148572558-0.370473748637-1.573454648130.7398011132680.5100630795440.614909613079-1.046406486880.6000998231590.943655534519-0.1685571755960.4963986557190.101239910704-0.1338709749750.835815667478-0.03338362936990.85495422000527.5973694974-19.07911704499.06514246886
23.52834329554-1.749244043750.09228763021415.427342292230.0587660336017.16919998105-0.1169050262961.191958209380.348450812701-0.5069805056060.2442679859020.1312277384880.1496901194990.0315884109296-0.08818957800780.338074607464-0.01063750932660.008941126797450.5874091131690.01764872779290.491718125053-21.3241741254-15.7416162968-7.76726735673
33.486869163493.217673030022.465265877567.23137194529-0.159682959988.183839463010.0831709016210.09700399272070.548865945366-0.2922477208650.1168888703910.520433376986-0.194102137649-0.752444354161-0.1796769492490.5637298235060.1185959170340.02829612886910.4214239714240.09239977887870.5461628545-9.030779362659.48494113530.9846744956
48.54628709028-1.360350665946.988850722586.95176789248-0.3457139406696.48917883427-0.3080073366610.7810938128481.05403169592-1.16825213898-0.196572384314-0.904904277191-0.3905681962140.453584351130.4808944271850.790914328644-0.09339285154490.2677169393040.6567428750760.09948649214090.5046587029974.903306227697.3833327662920.0638227038
58.374681137340.7366631232161.071012722948.993720410551.75141433087.145290875190.0583596158169-0.081312500808-0.015410377179-0.2297619665530.00599687002312-1.57747974557-0.1718425454041.19577431164-0.122285606860.310970793971-0.03811449962330.04389251089790.4442048389690.01975430411190.74336302185711.351657236.2558954418336.0559882911
63.265874680880.00632862176316-0.1500558542335.40668654066-0.4167747874843.48893545999-0.008436952686070.3800843380070.0449200464804-0.6525795675940.0693681196635-0.3976031909450.161542451855-0.0212388015509-0.06974421286410.351266568249-0.02102493341650.04379888024710.2854513545940.0005596103199930.295259236198-0.828642796663-0.008473737064931.4075937251
73.632595573583.128166331956.185939588783.763751809276.283204249172.02131221813-0.114885535062-0.805202454579-0.8571793277530.629273458122-0.05299704824180.46788456060.721526880333-1.256778643890.2335099509050.491910178614-0.03564719516520.04253568060160.4440064759180.07340264625990.485743497738-5.33395546324-7.5691613965342.6067738763
89.627365960980.05143672411144.942674385466.130361707691.675983128076.500476096160.15415720150.61859583901-0.481470054184-0.7140682747910.1757053857080.985898650695-0.121545138285-1.34538455869-0.2937467893140.569326265396-0.103346959486-0.03777894962260.785323611252-0.0264915594660.940506418396-52.8207813159-8.6706086777239.4644825685
93.050908402910.359805658212-1.378792893572.25327928494-0.2529220426450.637162355855-0.0504828996767-0.2264068661090.3097299697830.245420770893-0.0316121156674-0.3749700234790.2499667507890.2769864274650.01989743159130.3506322024230.0569274877412-0.03754947560860.417322899081-0.07944280311410.229051313914-4.41846516673-0.90470478337944.3931757876
102.96581834060.800024754343-0.06081529413594.9674545931-3.898029929197.57749984548-0.7448261379610.2970274762440.328546286383-0.4229351379180.275828464189-0.2732087641650.248317924261-0.4671100891670.4342362184270.827287533543-0.126510914103-0.0843339198270.615112419487-0.1212984780030.547300673001-9.67313844439-4.2987421615711.2882819669
111.39803497681-0.54289070449-1.14598306862.85191829873-1.011506304671.72142988120.248103420704-0.3893704875860.7809336422130.417400573470.3670494292510.184543842804-0.1036774547970.0919273251342-0.5423966424991.01875040739-0.2473792164020.3414701890790.870639556113-0.168490721360.648556334146-25.0760885532-6.1901354948319.6938600652
129.465055874796.161598627161.948920940316.553850423651.200653498398.942039672520.541828671819-0.1555694240260.9836835955490.281343593783-0.6323548586581.925303086560.106464935465-0.7529382973260.09620257160980.4902103092480.03578332636140.002276336632990.457737649101-0.1195198990570.85153515436-28.5470359925-7.311067940012.40853381039
131.59438647946-0.9807662295690.2664589894144.679167403450.5500602313843.20212125324-0.0775624424731-0.1155478365080.3793883398720.549359573953-0.2283083223170.0930124130987-0.11050834408-0.06003438023980.3333607659980.481419857998-0.0978455484215-0.06101445759550.456704790459-0.01389674540990.640431093494-17.4472859551-9.141798719957.09810449679
147.54243371911-0.647321351350.8355844505543.705299470110.115230814643.539101982450.271174072984-0.554527323816-0.5086456129660.527000003509-0.216037432306-0.6632554970810.200048425088-0.106969729973-0.101696349920.570139696598-0.0969168216147-0.1274288511020.368432122608-0.02471248417460.644784625021-18.2894601994-15.73137661266.49159813452
156.94963874653-0.396399076568-0.5594037761833.961282764320.5735401285596.343058180280.693030750095-1.04450132025-0.5695353090461.36152143215-0.376521069836-0.1456085568320.3962423011020.116884857943-0.3952420252270.847884210483-0.164229004708-0.08256481382860.5147525104340.005065694873260.580959312489-17.4571302663-17.504842640215.2935064386
168.552164646733.36079071133.63338667083.76867786438-2.254703832226.997493865590.2943067759490.233847228941-0.314820345405-0.93199909170.0794191440963-0.733484044811.061722990260.610411217342-0.3427880240580.6994179962030.0871863721458-0.1517847383460.45346734065-0.01849250519930.762284973721-11.5689399314-21.4860413819-0.563089205603
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 3 through 18 )CE3 - 18
22chain 'C' and (resid 19 through 34 )CE19 - 34
33chain 'A' and (resid 243 through 252 )AA243 - 2521 - 10
44chain 'A' and (resid 253 through 262 )AA253 - 26211 - 20
55chain 'A' and (resid 263 through 275 )AA263 - 27521 - 33
66chain 'A' and (resid 276 through 335 )AA276 - 33534 - 93
77chain 'A' and (resid 336 through 346 )AA336 - 34694 - 104
88chain 'X' and (resid 3 through 12 )XB3 - 12
99chain 'X' and (resid 13 through 34 )XB13 - 34
1010chain 'B' and (resid 243 through 252 )BD243 - 2521 - 10
1111chain 'B' and (resid 253 through 262 )BD253 - 26211 - 20
1212chain 'B' and (resid 263 through 275 )BD263 - 27521 - 33
1313chain 'B' and (resid 276 through 300 )BD276 - 30034 - 58
1414chain 'B' and (resid 301 through 316 )BD301 - 31659 - 74
1515chain 'B' and (resid 317 through 335 )BD317 - 33575 - 93
1616chain 'B' and (resid 336 through 346 )BD336 - 34694 - 104

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