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

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Basic information

Entry
Database: PDB / ID: 8tlk
TitleCDCA7 (Human) 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 speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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
X: DNA (32-MER)
B: Cell division cycle-associated protein 7
C: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,29115
Polymers52,5664
Non-polymers72511
Water1,17165
1
A: Cell division cycle-associated protein 7
X: DNA (32-MER)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)53,31516
Polymers52,5664
Non-polymers74912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11060 Å2
ΔGint-31 kcal/mol
Surface area19340 Å2
MethodPISA
2
B: Cell division cycle-associated protein 7
C: DNA (32-MER)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)53,26714
Polymers52,5664
Non-polymers70110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10160 Å2
ΔGint-30 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.479, 31.538, 94.566
Angle α, β, γ (deg.)90.000, 110.180, 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 ABXC

#1: Protein Cell division cycle-associated protein 7 / Protein JPO1


Mass: 16418.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA7, JPO1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codon-plus (DE3)-RIL / References: UniProt: Q9BWT1
#2: DNA chain DNA (32-MER)


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

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Non-polymers , 5 types, 76 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 0.1 M Bis-Tris pH6.0, 25%PEG3350

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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: 2.99→43.06 Å / Num. obs: 8135 / % possible obs: 79.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.07 / Net I/σ(I): 6.1
Reflection shellResolution: 2.99→3.09 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 772 / CC1/2: 0.777 / Rpim(I) all: 0.333 / % possible all: 75.8

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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: 2.99→43.06 Å / SU ML: 0.4844 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3018 400 5 %
Rwork0.2426 7604 -
obs0.2454 8004 78.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.88 Å2
Refinement stepCycle: LAST / Resolution: 2.99→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 1308 27 65 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263136
X-RAY DIFFRACTIONf_angle_d0.48664517
X-RAY DIFFRACTIONf_chiral_restr0.0325492
X-RAY DIFFRACTIONf_plane_restr0.0048374
X-RAY DIFFRACTIONf_dihedral_angle_d22.09321288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.420.36141250.29462387X-RAY DIFFRACTION74.94
3.42-4.310.35041310.28892497X-RAY DIFFRACTION78.03
4.31-43.060.22311440.17682720X-RAY DIFFRACTION81.46
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)
11.49002885507-1.903267504471.065116519332.46771891358-1.7424360813.996113477720.10169847042-0.1378467836210.220358475111-0.7814918748470.976768716871-0.307712803963-0.3520538486020.0650573467858-0.828039028530.603977087734-0.1580149733260.03510316915040.5846043714-0.1611350276860.380318692834-9.822-3.99512.158
22.889877538980.197841237614-0.1966813076223.087771570680.5604772575961.996054093640.500476627233-0.1720975809910.1681931508260.02911554311060.366796916627-0.0710133926729-0.9180160957050.531490135518-0.8760918513760.4045291423060.09690070549340.06512257345590.569029126021-0.1630899594750.648599005469-24.773-5.7219.311
31.445270159790.6838459881513.28371959095.17102324271.682350815217.452804878370.6932949093230.2335690130230.0715872819970.6300036946430.316667087326-0.2517369257560.164774157059-0.89593047489-0.8569371890010.216556777995-0.0507325005213-0.04225000786940.5158571113180.0962552490950.533759759507-31.222-11.4244.014
41.15270259276-0.0368428078466-0.4796956777261.21252833445-0.226113953470.8395899591790.098255195750.0243678880676-0.4259485652750.081205649366-0.2911532798840.6676881373140.0849356390725-0.06040213833050.104259514380.2145556444750.007034355863640.04076718582620.275031729188-0.09855046871840.669394746753-20.919-5.9443.515
54.82948031030.3978369326810.5710214097152.173899060370.2144941736240.941144725628-0.380874911129-0.127956536945-1.136351330750.01464661195830.45093324672-0.1588310748090.1768427056570.126229288505-0.07980173990730.3931781877010.0172649303244-0.0646423312410.239394524269-0.03164926390540.449078674699-17.377-14.85910.618
65.02594419814-1.74917810692-0.1894464781492.642508088940.5890698609880.143769394594-0.433701792428-1.28989233674-0.3398271449960.8949195211290.165304708067-0.1731900611480.466369549396-0.129827449170.1631399059880.5047664532790.03399959389770.2669725803540.518332843116-0.02432137929010.560428127638-13.159-16.87615.469
77.272771078320.4044664820165.178239338823.422948895862.07377178645.729314114110.4162614488240.681348794108-1.2280521696-0.1711141145230.133273217691.836827830850.2145869452710.412139599102-0.1052460436610.3807622966030.0197492895746-0.01700077800380.282956525197-0.03603602305370.820876084743-11.462-19.5380.926
83.22428690683-2.2040350576-3.36682862422.098791763531.056484425576.220918027940.45973807967-1.095414924470.3277177130320.7338691897621.0663371529-0.711367933840.3545819123551.26188197847-0.8150185598520.7054318283720.138985916943-0.4289719045750.8914448167430.1002541254371.3710454339235.967-22.5697.981
92.13750917591-0.525141435826-0.8307992040291.30623667962-0.1558404897850.3916080917650.06843686090540.07039094618140.076535861478-0.23367244435-0.0008722532613760.1921294935020.155662311652-0.180297858056-0.07191442765280.31461567031-0.0543621728871-0.05505811993410.5646715024730.1883538942530.334564314366-11.715-14.262-2.82
102.265943017920.229055919256-2.133363378322.243887675230.2661103031332.878348639980.263422097493-0.2754378596460.38235197210.1868853222680.537599328163-0.0419429124678-1.302281061070.0120467695811-0.7733039386550.4396687098760.0887029300278-0.02917148669820.371267322071-0.04577516378650.662226401967-8.138.66332.808
111.653674839560.3053830351340.9481136211970.2015348852330.2662172898880.61432006143-0.22417415590.07082371863770.536982021136-0.0819573797191-0.107395613194-0.0530828740052-0.1129228696180.1233874010590.03412190609160.566999603528-0.360482287770.2687712474980.592465583696-0.005450960352950.4711318808196.3066.68523.235
124.62338352266-0.6106934474391.927199302272.939735680630.694624958388.7070586767-0.19603990358-0.5655910203350.598593528597-0.7538521406640.201254046058-0.0280282724774-0.1464579999630.1459078197520.01740152410580.341811780647-0.148594620438-0.05864670656890.329983011492-0.1080396039640.5134257058714.2580.87737.953
131.260340865650.6243062151320.1005252303242.70964857729-1.36347652711.5915517121-0.35501537742-0.2315188752710.5718805919050.408925834830.197858333374-0.206408460468-0.399631124595-0.07749687426560.1215639763430.3506432651640.00994819579131-0.06165407555230.199525673420.03375600926960.5368860708484.4666.71741.529
141.62077847832-0.8970335085361.34807199931.45517602085-0.4112373114213.07214533978-0.1765335223190.2101877750890.349237897272-0.487629552398-0.2162518852270.4300597642410.01232851167890.3942099963940.3274439721390.2852804743530.0390018176826-0.06340626269350.1784885188690.03691089744110.4776770289340.865-0.69133.395
150.2529588844550.04853696863970.2730501118510.2872076671710.09654525295530.293300638904-0.2992196759350.1492901474340.205224971187-0.21921584869-0.1270197418020.1529847945650.0955260301462-0.1619522285530.1499432563570.26445074396-0.270229120375-0.1093342155360.4122194180050.0789798664510.313928029643-4.676-4.78428.347
164.03000796931-2.489041145522.342986769315.474335317472.190218605074.70713975538-0.280268609965-0.425396847761-0.6820984451240.5110398607860.004418473629270.5867386629070.303235111279-0.58446011371-0.05318268486260.438582147363-0.135514328364-0.06596273988620.2279892238940.1482546678740.535068788692-5.376-8.57644.076
170.3378400281650.5800692853690.8186158908355.94044774369-2.130464651274.498636684840.0694991659158-0.0116868097356-0.668218592456-0.7066878201060.4667827405530.465498546932-0.0588383956213-0.470029463432-0.4823420326850.74321962612-0.176123747887-0.1242252797861.00382095439-0.07853124019121.90550576546-54.302-6.97131.786
180.838011415001-0.252145870867-0.2839667047821.12669029196-0.1278198314960.9843597372890.0009825783612780.3139271318570.17444779194-0.3684459883320.183727545070.003658543062030.309329791692-0.485388720785-0.03115882828570.101995348299-0.401332380386-0.09928146007770.337687507921-0.271363377520.895383111415-40.451-4.83640.743
190.346394475896-0.06384774815850.1359600863280.8394382815220.2192135380920.1468521800720.128099990251-0.2656807410730.3036339107010.3481473478150.2298118183080.50687799685-0.287903145285-0.376045434098-0.02721695822340.1788281384830.112269314719-0.02239546639530.5518800559080.04771271159270.486463425575-2.4184.8547.353
203.867301006930.7465780324344.856073395790.14378527550.9322432474336.084628874680.231184417191-1.27083744036-1.177874717950.9629006825680.75472133262-2.201157742620.8700424077680.918116743647-0.8309467217740.6809731252930.238802852512-0.2176135643540.9699513967790.1000335616921.3610494598619.196-14.28555.353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 233:241 )B233 - 241
2X-RAY DIFFRACTION2( CHAIN B AND RESID 242:252 )B242 - 252
3X-RAY DIFFRACTION3( CHAIN B AND RESID 253:259 )B253 - 259
4X-RAY DIFFRACTION4( CHAIN B AND RESID 260:284 )B260 - 284
5X-RAY DIFFRACTION5( CHAIN B AND RESID 285:313 )B285 - 313
6X-RAY DIFFRACTION6( CHAIN B AND RESID 314:324 )B314 - 324
7X-RAY DIFFRACTION7( CHAIN B AND RESID 325:333 )B325 - 333
8X-RAY DIFFRACTION8( CHAIN C AND RESID 3:12 )C3 - 12
9X-RAY DIFFRACTION9( CHAIN C AND RESID 13:34 )C13 - 34
10X-RAY DIFFRACTION10( CHAIN A AND RESID 232:241 )A232 - 241
11X-RAY DIFFRACTION11( CHAIN A AND RESID 242:252 )A242 - 252
12X-RAY DIFFRACTION12( CHAIN A AND RESID 253:259 )A253 - 259
13X-RAY DIFFRACTION13( CHAIN A AND RESID 260:274 )A260 - 274
14X-RAY DIFFRACTION14( CHAIN A AND RESID 275:313 )A275 - 313
15X-RAY DIFFRACTION15( CHAIN A AND RESID 314:324 )A314 - 324
16X-RAY DIFFRACTION16( CHAIN A AND RESID 325:335 )A325 - 335
17X-RAY DIFFRACTION17( CHAIN X AND RESID 3:7 )X3 - 7
18X-RAY DIFFRACTION18( CHAIN X AND RESID 8:18 )X8 - 18
19X-RAY DIFFRACTION19( CHAIN X AND RESID 19:28 )X19 - 28
20X-RAY DIFFRACTION20( CHAIN X AND RESID 29:34 )X29 - 34

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