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- PDB-8tlg: CDCA7 (Mouse) Binds Non-B-form 34-mer DNA oligo -

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Basic information

Entry
Database: PDB / ID: 8tlg
TitleCDCA7 (Mouse) Binds Non-B-form 34-mer DNA oligo
Components
  • Cell division cycle-associated protein 7
  • DNA (34-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: 2.09 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 (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2668
Polymers26,9222
Non-polymers3456
Water1,18966
1
A: Cell division cycle-associated protein 7
X: DNA (34-MER)
hetero molecules

A: Cell division cycle-associated protein 7
X: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,53216
Polymers53,8434
Non-polymers68912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9390 Å2
ΔGint-55 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.491, 60.562, 53.229
Angle α, β, γ (deg.)90.000, 123.100, 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-103-

MG

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Components

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Protein / DNA chain , 2 types, 2 molecules AX

#1: Protein Cell division cycle-associated protein 7


Mass: 16452.814 Da / Num. of mol.: 1
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 (34-MER)


Mass: 10468.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: n vitro SELEX screening / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 4 types, 72 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M MgCl2, 0.1 M Tris pH8.5 and 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: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→30.28 Å / Num. obs: 11460 / % possible obs: 83.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 39.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.037 / Net I/σ(I): 15.5
Reflection shellResolution: 2.09→2.16 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 653 / CC1/2: 0.827 / Rpim(I) all: 0.257

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→30.28 Å / SU ML: 0.2534 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.2186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 573 5 %
Rwork0.1856 10876 -
obs0.1874 11449 83.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.24 Å2
Refinement stepCycle: LAST / Resolution: 2.09→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 694 12 66 1585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291613
X-RAY DIFFRACTIONf_angle_d0.5222326
X-RAY DIFFRACTIONf_chiral_restr0.0352254
X-RAY DIFFRACTIONf_plane_restr0.0055186
X-RAY DIFFRACTIONf_dihedral_angle_d24.5438657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.30.3003980.24861849X-RAY DIFFRACTION57.18
2.3-2.640.2631550.23792948X-RAY DIFFRACTION91.08
2.64-3.320.27331590.21773036X-RAY DIFFRACTION93.5
3.32-30.280.18511610.15423043X-RAY DIFFRACTION92.2
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)
10.778614459768-0.0563272241554-0.5708586050695.79469560181-1.786936759662.04386367274-0.184914580407-0.198279352961-0.102248063573-0.27520599302-0.35976666464-0.2707749556080.809533065394-0.2623497539770.5217162298360.756731983330.0242988404297-0.03701877260220.5409464646570.000481770952230.70051855582217.8977428848-12.201580851712.7009138375
23.35421944924-0.022840192746-0.4943965369153.75645317749-0.6321794191163.274532791650.02712499804840.320196682181-0.0616334764678-0.402229088874-0.01595273936960.2776557262360.166303105516-0.313619305201-0.009565483784140.278450192523-0.00809606460959-0.03949364926880.254752782108-0.01925100605680.2684088315897.67578108375-6.8004231216417.0979470558
35.06342160598-0.436441541598-5.048863311728.57826842027-4.497170899977.879928970430.282979543671-0.8921729784040.6596919760990.375297187054-0.535752517371-0.779791566545-0.4865730341631.328771670870.2329748004070.314947168129-0.0495388527258-0.01615557565470.357105674995-0.0233391725010.42539883368915.84466470784.5669347976625.9079249966
41.11240023932-0.737651664855-2.585905919236.146841041941.424821129656.417507085720.4788777163961.0942438523-0.027611610277-1.32305068208-0.579104457674-0.822671283459-0.3829526297920.79579741769-0.1119787506151.46402460754-0.07446594665560.2259938031711.58508221748-0.05988913147321.410081632165.65430649592.728924293562.34705595236
51.960481001881.202570539780.8180825642682.990985452630.2963175269594.223770614750.1334006888660.5808879361580.537984240130.2186540588730.189108985781-1.10187548229-1.017670699671.0257818405-0.3039586529530.572654424311-0.1810001537210.1044763806570.6090848994460.04618273678850.8894390991161.88562709231.709510428616.069468956
62.609481350320.8545666319-0.1445801863020.904708793747-0.6019450565370.3709225350280.2867580132530.0953517054909-0.03503930548970.266637825829-0.1512079901680.0635033811582-0.459502182511-0.260781376666-0.1423456410710.4044118835470.06845782843330.02022638438460.3943219989690.03659505983620.25635762056216.8072906733-3.9054400496426.578352134
71.162414482212.50908209925-2.014516130555.50563774176-4.404415245423.54920117810.1433699019080.07496537384910.7497145043010.189878064861-0.542084763202-0.621854104347-0.7599838091880.820549933130.2392947726881.68248888443-0.1155407069340.3740683308421.814290558570.002049750510681.0769539443-8.778135221287.51589228252.5609845875
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 244 through 252 )AA244 - 2521 - 9
22chain 'A' and (resid 253 through 335 )AA253 - 33510 - 92
33chain 'A' and (resid 336 through 346 )AA336 - 34693 - 103
44chain 'X' and (resid 4 through 8 )XB4 - 8
55chain 'X' and (resid 9 through 13 )XB9 - 13
66chain 'X' and (resid 14 through 33 )XB14 - 33
77chain 'X' and (resid 34 through 35 )XB34 - 35

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