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- PDB-8tlf: CDCA7 (Mouse) Binds Non-B-form DNA oligo 36-mer (sg C2-Form 2) -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8tlf
TitleCDCA7 (Mouse) Binds Non-B-form DNA oligo 36-mer (sg C2-Form 2)
Components
  • Cell division cycle-associated protein 7
  • ssDNA
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: 1.64 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: Biorxiv / Year: 2023
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. / Liu, B. / 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
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
B: Cell division cycle-associated protein 7
X: ssDNA
Y: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,95619
Polymers55,0964
Non-polymers86015
Water4,450247
1
A: Cell division cycle-associated protein 7
X: ssDNA
hetero molecules

A: Cell division cycle-associated protein 7
X: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25124
Polymers55,0964
Non-polymers1,15520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9200 Å2
ΔGint-68 kcal/mol
Surface area18770 Å2
MethodPISA
2
B: Cell division cycle-associated protein 7
Y: ssDNA
hetero molecules

B: Cell division cycle-associated protein 7
Y: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,66114
Polymers55,0964
Non-polymers56510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8620 Å2
ΔGint-46 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.400, 31.492, 133.324
Angle α, β, γ (deg.)90.000, 95.750, 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

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Components

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Protein / DNA chain , 2 types, 4 molecules ABXY

#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 ssDNA


Mass: 11095.103 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, 262 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Zn
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.69 Å3/Da / Density % sol: 27.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris pH8.5, 25%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→29.9 Å / Num. obs: 72067 / % possible obs: 89.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.049 / Net I/σ(I): 13.6
Reflection shellResolution: 1.64→1.71 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4182 / CC1/2: 0.867 / Rpim(I) all: 0.343 / % possible all: 65.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUI1.20.1_4487data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→29.9 Å / SU ML: 0.1698 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.0218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2184 3484 4.84 %
Rwork0.1916 68499 -
obs0.1929 71983 81.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 1.64→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 1052 34 247 3001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232906
X-RAY DIFFRACTIONf_angle_d0.4774141
X-RAY DIFFRACTIONf_chiral_restr0.0358446
X-RAY DIFFRACTIONf_plane_restr0.0051364
X-RAY DIFFRACTIONf_dihedral_angle_d19.52521187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.67000.29581249X-RAY DIFFRACTION35.63
1.67-1.690.31591380.29031597X-RAY DIFFRACTION49.12
1.69-1.720.28741470.27851791X-RAY DIFFRACTION55.67
1.72-1.74000.28032236X-RAY DIFFRACTION62.27
1.74-1.770.27521530.282117X-RAY DIFFRACTION65.23
1.77-1.80.31171610.28442287X-RAY DIFFRACTION70.04
1.8-1.830.25451670.2662480X-RAY DIFFRACTION74.69
1.83-1.87000.25622714X-RAY DIFFRACTION77.68
1.87-1.910.31111670.23632530X-RAY DIFFRACTION76.64
1.91-1.950.25651720.23192677X-RAY DIFFRACTION80.37
1.95-1.990.23421750.23242677X-RAY DIFFRACTION81.44
1.99-2.040.27361790.23762981X-RAY DIFFRACTION89.77
2.04-2.10.27121800.21023128X-RAY DIFFRACTION92.9
2.1-2.16000.22173317X-RAY DIFFRACTION94.77
2.16-2.230.25071900.21843139X-RAY DIFFRACTION95.36
2.23-2.310.23931890.20353106X-RAY DIFFRACTION94.63
2.31-2.40.261850.20253253X-RAY DIFFRACTION95.74
2.4-2.510.23351790.19693062X-RAY DIFFRACTION92.79
2.51-2.650.23681860.20713132X-RAY DIFFRACTION93.49
2.65-2.810.21681850.19812949X-RAY DIFFRACTION89.77
2.81-3.03000.20253326X-RAY DIFFRACTION95.88
3.03-3.330.19891890.17783239X-RAY DIFFRACTION96.75
3.33-3.810.18921840.14793241X-RAY DIFFRACTION96.83
3.81-4.80.16921780.13643148X-RAY DIFFRACTION94.92
4.8-29.90.15521800.15193123X-RAY DIFFRACTION93.41
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3124155256330.5675695333530.3606406013291.42431928962-0.6580531270715.32168052956-0.4027324606570.09679633377360.629937275651-0.1019911051670.145918735755-0.606434477796-0.4886410500180.5398837541540.3008813858620.298612778512-0.046105796762-0.09865916403250.359225481793-0.02590490008130.60088514918619.19965428687.7408776681213.3578263393
28.21318143911-2.740012612631.011609785845.63626904722-1.153381288471.80632086781-0.259637288027-0.335312528905-0.2464314337440.9907036111290.257892174552-0.259109851381-0.1108198240110.167746530772-0.01143903177160.2371962821930.0184001558161-0.06207329287060.170110641511-0.05064953334950.1666777744589.142013622145.1141563031726.9930543874
31.92863310801-0.841669420443-0.002482806090771.658101005730.8232728381362.21642179276-0.03417251801980.003838938181090.1890631499310.0562224596710.111713117582-0.333128537224-0.1139187127160.206989224682-0.06450505955540.1278339858320.0160479219498-0.02047561440440.085644059546-0.02447364425350.1465664575288.984888511784.6299151732317.9029909056
45.6913665872-3.942375087562.054488930455.12322106841-2.675620684151.396890563710.2531796053310.967308179597-0.303337223632-0.887067157122-0.29143699563-0.4234045324030.07177017337881.01983612566-0.02281942240850.2204915437540.02318720755010.08703584850940.382639395631-0.03464805980190.24385470025916.73618910530.4246648035683.19005337538
51.46948340767-1.094432668631.636122752994.00222136196-4.85878976966.74420775365-0.1361767655920.07752340380860.141821506308-0.2046510889010.0314580951548-0.0374437536925-0.36806954304-0.2305023024720.1319615145360.1898828968080.028349793687-0.02581417250170.157794053456-0.01170817576610.1657954607749.566701878821.4081409230810.5561992352
64.543898297432.93191831481-0.8782698658875.807034650533.003156112363.584359928810.358983647738-0.139117067166-0.143269830920.491558031206-0.0845596445757-0.5731622255070.3962017369410.207018924191-0.2517091777480.1818515678040.0437343325051-0.06012821388570.12795578237-0.01064228851480.21747788827210.9081013642-6.6383997381221.7011109289
73.160658005793.71069834676-1.70035880437.106558222970.09520884732952.490862480370.361620592948-0.238200202977-0.4949386443330.645225913731-0.148615200022-1.007030659530.3440002402030.678953026273-0.2325235970440.1882415335380.0769930393901-0.07926237657340.245989172218-0.04208364012020.33844466679718.6584248175-5.2860532389518.0900524459
86.861022964441.6550880.7223598973951.30406753656-0.7606167982031.10045941126-0.1005011887580.536865814897-0.482360533559-0.2058960122350.243627161329-0.6335589324260.4411075320690.566780473259-0.02116712804820.1569810386260.05197476532280.03093844303270.263873290078-0.09862413403790.29354783758415.3738473208-5.915035617039.46185878313
98.86346044569-2.32216844823-1.543367674476.9905634282-0.0863085693882.34974554665-0.00586251112431.27181862087-0.710736937378-0.987612665070.1054212186551.361940891941.10775027842-1.31744094993-0.04974073410080.313027769248-0.087723925903-0.07703213833940.31365106309-0.05664189351090.32619965837-0.813508335759-7.7212083139610.7694020288
101.994135950351.590018428850.2359618205165.19854393603-1.025265704854.25073180533-0.247564388422-0.5922041885990.6538403657510.347102875489-0.04698292226290.428879697019-0.749290188724-0.3679980208710.2930012702990.4236856206150.1347402500920.0326235841020.387673907684-0.1090496200260.369622774893-19.75826146615.6448667690760.7404187402
116.29245292074-2.40293846892-1.823856274757.800708950061.329601226185.349905060610.4231583288680.1693097977310.96001596982-0.0719944883716-0.03083764903891.20290345502-0.74110873666-1.65564585969-0.4569537661410.2740217544770.0795113894557-0.02845289171940.694582258374-0.09237321831680.836423992438-33.12718318323.9892131230348.0425502911
129.34822547572.510966402370.1908038687195.390209272491.878921671216.83492650426-0.2163627905890.576348270596-0.34724609497-0.8508320539910.2118833703080.344083280152-0.292510105923-0.1681583252820.01410319209770.2542552289140.0244255521561-0.01616998661220.1863148091340.0129502522490.202365348412-16.93456960533.0502596619740.1813955217
133.263886439820.2831716305180.9520278808984.19490016391-0.8713505920772.92570490349-0.07675894441720.05802580723710.123389198267-0.005252149523010.03411111558970.238438444992-0.348073336493-0.1966088789040.01625231386310.1828492573730.01038380818490.03926267692150.1098637472370.004024367313290.126858134748-16.71027142181.6963840131848.94554978
147.326770439121.676222034991.676550738946.659012308841.52571224240.5942483411510.124856138014-0.481618741416-0.2026318385850.576839767895-0.3947900262340.0587991866380.145457745501-0.8487107626970.16809500140.2865869720490.03889921991490.2030108262870.4489994818130.001926185265480.367714637298-23.6574422889-2.8661495186763.9408988892
151.672925206951.740716235252.162184917422.940442889843.183072876213.55702092548-0.260815860039-0.130968363520.04354514827840.146193528571-0.03601582000270.04324061561030.2336465133430.2212463316520.2618832853950.2599772588720.02049425917330.06310016325280.201638825882-0.01061591564250.181784847696-16.8684459423-1.7173003346156.2532047543
164.70070477444-2.004306682940.6446372487642.00347715771-2.162595206398.097755705090.2580298171890.187797084036-0.241077204842-0.286366431122-0.009048387018970.5339901547190.309977074685-0.559723690813-0.1717709122770.147717474487-0.008949799820090.007136802765790.183336094621-0.03976042028380.248998413379-18.9262063405-9.4271170703144.9914679064
174.45666691696-5.48236127772-0.9534566710296.781261685540.8839994013192.079460494160.1366195556070.0771381297709-0.516128866410.14704021666-0.04323706255551.285793002360.234158421512-0.842059635441-0.09780507150460.175717054944-0.04072162223690.05104506099070.3420642513110.02574368423440.417730532111-26.4080184-8.047859423849.0066446197
184.35930119146-1.424675703941.06845563443.434416221570.8296025256620.735653134513-0.124235544146-0.377485577562-0.2854254466480.6355905939130.1354478679920.5554588199320.530700090496-0.745186254391-0.04557857736440.2674257681-0.04704364225870.1014179270230.357113696620.05273989255140.264001293456-21.9690490229-9.0451657448557.1507826159
194.115570709693.107603323352.168360029482.765205851690.4173497947084.752814367510.358089450257-1.45181420291-1.24542931511.346264498120.143345786295-1.376258552982.156693659621.65663965454-0.5278897048890.6325188484730.164677251711-0.1412501696540.5666555581280.03726676566030.486615026808-5.77328491471-11.234485100656.5405587669
208.96200510449-4.99832600364-2.826178324119.361411963455.751205396783.577507903960.04051910466421.09844618705-0.943906531896-0.756567009189-0.7429611358231.27543969059-0.0376069402498-0.5881280001140.6816831455040.4380185884460.0136594118201-0.1024073691210.41910753695-0.08246030044350.32340805237-5.99583725848-15.0279402076-35.787075444
210.915594182615-0.750647019768-1.124304445731.298878748960.4847824816562.405886585310.0612831706296-0.229898624625-0.04085920394810.0968696943290.0587776445078-0.07688175190050.0983459439760.317155060974-0.1063979972280.138173387628-0.0191160171716-0.002800615424890.1677958434240.03225975409240.08674085469314.134192163481.04108522215-12.5458314723
220.7046283817320.067919747352-0.05132323729173.33882460583-0.6857653257470.438697570631-0.0461779257292-0.00487132314662-0.07780387795390.2515212441980.1037019103080.1129566582060.041585555271-0.0955973026301-0.02041629119540.1748253557390.0173704202357-0.001108982634760.152901902132-0.01920319037320.132747681805-2.40062220798-3.452281846723.4061196925
230.5376052678050.03546381462580.4125302807951.79494063258-2.068731276445.282535266730.07818868227920.0265192854486-0.204486357452-0.09033654067690.06239585081070.009128401733290.0378270323733-0.190991394648-0.09329770511070.1283079828380.00320846567550.04737646420020.2100057669580.01164057152960.147718385698-6.24937534812-6.4427592054886.9851899352
240.971424254263-0.137627461333-0.3207026769323.795301171782.16698816184.81638024501-0.1238001847460.174408245847-0.193678610861-0.08066177464640.199167942613-0.269385338209-0.06632625742630.515641166146-0.0525352555420.169795268392-0.02072855107920.04001523636570.262951954148-0.06644523510.18002345506-5.4418869062-4.4486146377842.4850741767
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 243 through 262 )AA243 - 2621 - 20
22chain 'A' and (resid 263 through 275 )AA263 - 27521 - 33
33chain 'A' and (resid 276 through 295 )AA276 - 29534 - 53
44chain 'A' and (resid 296 through 300 )AA296 - 30054 - 58
55chain 'A' and (resid 301 through 308 )AA301 - 30859 - 66
66chain 'A' and (resid 309 through 315 )AA309 - 31567 - 73
77chain 'A' and (resid 316 through 324 )AA316 - 32474 - 82
88chain 'A' and (resid 325 through 339 )AA325 - 33983 - 97
99chain 'A' and (resid 340 through 346 )AA340 - 34698 - 104
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 295 )BD276 - 29534 - 53
1414chain 'B' and (resid 296 through 300 )BD296 - 30054 - 58
1515chain 'B' and (resid 301 through 308 )BD301 - 30859 - 66
1616chain 'B' and (resid 309 through 315 )BD309 - 31567 - 73
1717chain 'B' and (resid 316 through 324 )BD316 - 32474 - 82
1818chain 'B' and (resid 325 through 340 )BD325 - 34083 - 98
1919chain 'B' and (resid 341 through 346 )BD341 - 34699 - 104
2020chain 'X' and (resid 7 through 11 )XE7 - 11
2121chain 'X' and (resid 12 through 21 )XE12 - 21
2222chain 'X' and (resid 22 through 32 )XE22 - 32
2323chain 'Y' and (resid 7 through 21 )YH7 - 21
2424chain 'Y' and (resid 22 through 32 )YH22 - 32

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