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- PDB-8tll: CDCA7 (Mouse) Binds Non-B-form 26-mer DNA oligo -

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Basic information

Entry
Database: PDB / ID: 8tll
TitleCDCA7 (Mouse) Binds Non-B-form 26-mer DNA oligo
Components
  • Cell division cycle-associated protein 7
  • DNA (26-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: 2.58 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. / Zhou, J. / Horton, J.R. / Bramble, M.D. / Liu, B. / Lu, Y. / Liu, B. / Coletta, L.D. / Shen, J. / 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
Revision 1.2Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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 (26-MER)
B: Cell division cycle-associated protein 7
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,46913
Polymers48,8984
Non-polymers5719
Water28816
1
A: Cell division cycle-associated protein 7
X: DNA (26-MER)
hetero molecules

A: Cell division cycle-associated protein 7
X: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,64716
Polymers48,8984
Non-polymers74912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8880 Å2
ΔGint-75 kcal/mol
Surface area15070 Å2
MethodPISA
2
B: Cell division cycle-associated protein 7
C: DNA (26-MER)
hetero molecules

B: Cell division cycle-associated protein 7
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,29010
Polymers48,8984
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7120 Å2
ΔGint-31 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.710, 60.724, 84.106
Angle α, β, γ (deg.)90.000, 113.960, 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-102-

MG

21C-101-

HOH

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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 (26-MER)


Mass: 7996.127 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, 25 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / 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.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MgCl2, 0.1 M Tris pH 8.5, 23%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: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→48.4 Å / Num. obs: 12207 / % possible obs: 93.6 % / Redundancy: 7 % / Biso Wilson estimate: 49.07 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.072 / Net I/σ(I): 8.7
Reflection shellResolution: 2.58→2.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 814 / CC1/2: 0.702 / Rpim(I) all: 0.444

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Processing

Software
NameVersionClassification
SERGUI1.20.1_4487data collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→48.4 Å / SU ML: 0.4547 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.8956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2821 598 4.99 %
Rwork0.235 11381 -
obs0.2374 11979 92.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.67 Å2
Refinement stepCycle: LAST / Resolution: 2.58→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 807 17 16 2416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382521
X-RAY DIFFRACTIONf_angle_d0.58213587
X-RAY DIFFRACTIONf_chiral_restr0.0395394
X-RAY DIFFRACTIONf_plane_restr0.0067333
X-RAY DIFFRACTIONf_dihedral_angle_d21.3754985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.840.35051160.31032212X-RAY DIFFRACTION72.43
2.84-3.250.31391590.293026X-RAY DIFFRACTION98.85
3.25-4.090.29331600.22013039X-RAY DIFFRACTION99.13
4.09-48.40.25091630.21183104X-RAY DIFFRACTION99.33
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)
14.22554235260.469004686333-0.2063199025545.135181670380.003318518724170.8216557374250.3541647601860.1900036817870.5173293292860.4088431829510.0416382223505-0.126538401404-0.700740881925-0.357506375388-0.4769206220760.6021377604680.05100452187280.05697760965610.5449717473910.1344522745730.2352859356364.983585082710.638688643429.4343772598
26.113851215732.82353374206-2.88416383296.61870995443-0.6045895286191.5907521360.164243320851-0.08742665714680.0320298446526-0.111164397112-0.4887797793810.344204770737-0.0293985166795-0.437312577830.3046078297490.3762693148520.0296956459646-0.06017165820340.433058837359-0.02900031725170.2442681722081.183806440979.3942730870736.4699222288
35.561744227950.247679081186-1.934892062385.19092825189-2.202982888062.66851779306-0.3168119004490.435797762805-0.291925214661-0.566181284463-0.0532925058648-0.2900968554280.301798682009-0.4126461945010.319994748860.5440612476520.03679423631490.02961050365030.468071293618-0.06590283208630.2705853614232.808975506350.29961763857331.426066688
48.05936401321-0.2471277348026.973903637914.050621078893.605155010449.64988045471-0.49603044379-1.18118380329-0.4393100706390.578763188296-0.09148115736860.4736254389790.504624038418-2.689656347490.3702886016410.649568858341-0.1479276409820.1061223277260.6184222331790.08221334551770.387729195148-3.92973811366-5.2744866436142.1501697554
56.832272497914.076766540420.1800221446942.8157602462-1.6490665037.62855409119-0.1944632753430.787599329646-0.356456137883-0.8714727315370.3939561764820.02676415165011.339185666560.140827302206-0.03797925876990.711741039979-0.00289879369314-0.04697687078440.546642737924-0.05045841258230.410812317984-37.07560365081.7007610627327.3181423223
65.532348938334.561720266036.142685368657.050007524665.658962241286.827434534580.2108530893061.01743489029-0.711389649174-1.062874538890.578574135495-0.89201163695-1.3882323563.12440135055-1.083610791910.619049249657-0.1295135839780.07050658405710.890024179074-0.02202265080430.572040302789-18.08527243487.5495154576531.4313766289
75.84321907721-4.316856757042.249182692947.50654555887-3.562034651645.95269024981-0.638853469022-0.842969753815-0.5016737772931.614279648470.7864229658230.819311535976-0.177862227334-0.574369006696-0.1956659336310.728875243194-0.0163313355260.0335657492950.659451404217-0.02699517441260.327931830309-0.2941939885179.3599229735149.5934652464
85.74966326625-3.176072840010.2104057485244.850533415240.4188415933430.107181751088-0.594602306082-0.5836059257251.063201027831.237291254460.189606515783-0.5500485317990.293985886780.1078644722650.2504677255080.612007551635-0.104467015717-0.01797597369780.500556769732-0.1989490012460.608327498852-18.838272914324.756087472511.5757795765
92.4551133302-2.05853034686-2.49850949289.49697720824-0.2105525732385.10236522784-0.03019792719560.1213873376710.328519908712-0.3600417115610.06370181886131.112603656620.797995471707-0.311951338440.000487731626560.3254477007440.03548968715940.009614568602060.4097533434450.06566993414630.605630010441-24.23288040523.9693334899-2.12486470105
103.160192241071.944159535331.196424119158.15555048128-3.282155795072.823882773120.157160217689-0.05464260012780.4756865085060.5999580944970.03967736837850.649460736366-0.715336822961-0.355078815565-0.1230531159340.2753330899270.05841203081690.002855396039950.473168630981-0.1194014784170.518938977355-21.098512331922.8160544784-0.497160589179
113.246556202330.862714499479-0.6865426834395.86400939913-5.256687549688.958125373710.198616015442-1.411443331291.029884831271.19742373061-0.887004299106-0.8682564308180.219669115743-0.3012738129040.5012693874180.663338849413-0.0578094308999-0.09355180770010.546206168436-0.02827457159650.420750551613-10.743613723417.142810800310.3719242678
120.9935349827542.4193280871-0.515978066146.04849907464-0.1899139443777.701984306210.5803447012020.2800588851580.2040767279281.73721810643-0.02943290444560.3405829480220.368844669898-1.193293107050.007725705323830.419084593311-0.0233266037756-0.0123909385367-0.148440803691-0.148443777721.12658576999-22.089693525214.47090662321.81717300711
136.31399168442-1.91973412277-0.1129391016666.047666896811.251166171210.2879317754270.243179318331-0.61331074641-0.2766079216690.712140637754-0.20200203776-0.1406344714730.6898357036030.0802686670263-0.01871139553290.842632406441-0.0451098517210.04691439760550.3940248134830.114692773560.340307314446-20.591186664312.309605196410.4978281401
149.756554276883.197735965621.808227852714.89776343465-5.433131959869.7440150883-0.1238827879771.54470254535-0.3580309978110.28745848137-0.1349593728430.4164686533771.46722180023-0.04580196457760.08428563251890.4182593706450.05864561364190.0449436222670.3490240113-0.1315844640730.54786915335-13.13846479347.70193610363-3.51644226191
152.780620664082.821022718062.568359882084.700706941930.7218512816877.546235750970.135012723287-0.204002705534-0.9472810713580.744238597393-1.13604988479-0.638812251360.2563292681250.5929991890380.5991390643080.481353145103-0.016851547773-0.1083977504640.4238046955130.1377655748460.48554276815419.963987049614.495045221411.20420065
168.82173242022-5.407230252388.538470195753.95138758308-5.602915955459.137518302640.617993794498-0.92622981753-1.154781323740.2947437364750.9432195044380.7363790449790.2780580154680.422787191918-1.27058482490.3267594734940.008292328695950.08876099160170.7056057953820.05263935752970.5217179835040.98662994429120.57720302737.06801768973
178.913600270861.892212988167.501715192667.031996316383.93163894847.574143090060.0512495302725-0.6838952550730.75885432398-0.788508406037-0.6452513931830.502446073577-0.203295889831-1.143572350770.6612627155850.3999579796020.1102838473720.02338166298290.4450670136810.039395291880.453580780241-18.540603779320.6611515639-11.4130330429
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 270 )AA244 - 2701 - 27
22chain 'A' and (resid 271 through 300 )AA271 - 30028 - 57
33chain 'A' and (resid 301 through 335 )AA301 - 33558 - 92
44chain 'A' and (resid 336 through 346 )AA336 - 34693 - 103
55chain 'X' and (resid 12 through 16 )XC12 - 16
66chain 'X' and (resid 17 through 21 )XC17 - 21
77chain 'X' and (resid 22 through 28 )XC22 - 28
88chain 'B' and (resid 244 through 263 )BE244 - 2631 - 20
99chain 'B' and (resid 264 through 283 )BE264 - 28321 - 40
1010chain 'B' and (resid 284 through 293 )BE284 - 29341 - 50
1111chain 'B' and (resid 294 through 303 )BE294 - 30351 - 60
1212chain 'B' and (resid 304 through 315 )BE304 - 31561 - 72
1313chain 'B' and (resid 316 through 335 )BE316 - 33573 - 92
1414chain 'B' and (resid 336 through 346 )BE336 - 34693 - 103
1515chain 'C' and (resid 12 through 16 )CF12 - 16
1616chain 'C' and (resid 17 through 21 )CF17 - 21
1717chain 'C' and (resid 22 through 29 )CF22 - 29

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