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- PDB-6wmi: ZNF410 zinc fingers 1-5 with 17 mer blunt DNA Oligonucleotide -

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Basic information

Entry
Database: PDB / ID: 6wmi
TitleZNF410 zinc fingers 1-5 with 17 mer blunt DNA Oligonucleotide
Components
  • DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*CP*AP*TP*AP*AP*TP*AP*AP*TP*G)-3')
  • DNA (5'-D(*CP*AP*TP*TP*AP*TP*TP*AP*TP*GP*GP*GP*AP*TP*GP*TP*G)-3')
  • Zinc finger protein 410
KeywordsTRANSCRIPTION/DNA / transcription factor / Zinc finger / Complex / DNA / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


transcription coregulator activity / sequence-specific double-stranded DNA binding / chromosome / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger protein 410
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsRen, R. / Horton, J.R. / Cheng, X.
CitationJournal: Mol.Cell / Year: 2021
Title: ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression.
Authors: Lan, X. / Ren, R. / Feng, R. / Ly, L.C. / Lan, Y. / Zhang, Z. / Aboreden, N. / Qin, K. / Horton, J.R. / Grevet, J.D. / Mayuranathan, T. / Abdulmalik, O. / Keller, C.A. / Giardine, B. / ...Authors: Lan, X. / Ren, R. / Feng, R. / Ly, L.C. / Lan, Y. / Zhang, Z. / Aboreden, N. / Qin, K. / Horton, J.R. / Grevet, J.D. / Mayuranathan, T. / Abdulmalik, O. / Keller, C.A. / Giardine, B. / Hardison, R.C. / Crossley, M. / Weiss, M.J. / Cheng, X. / Shi, J. / Blobel, G.A.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein 410
D: Zinc finger protein 410
B: DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*CP*AP*TP*AP*AP*TP*AP*AP*TP*G)-3')
C: DNA (5'-D(*CP*AP*TP*TP*AP*TP*TP*AP*TP*GP*GP*GP*AP*TP*GP*TP*G)-3')
E: DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*CP*AP*TP*AP*AP*TP*AP*AP*TP*G)-3')
F: DNA (5'-D(*CP*AP*TP*TP*AP*TP*TP*AP*TP*GP*GP*GP*AP*TP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,91518
Polymers56,1366
Non-polymers77812
Water2,468137
1
A: Zinc finger protein 410
E: DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*CP*AP*TP*AP*AP*TP*AP*AP*TP*G)-3')
F: DNA (5'-D(*CP*AP*TP*TP*AP*TP*TP*AP*TP*GP*GP*GP*AP*TP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4579
Polymers28,0683
Non-polymers3896
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-32 kcal/mol
Surface area13140 Å2
MethodPISA
2
D: Zinc finger protein 410
B: DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*CP*AP*TP*AP*AP*TP*AP*AP*TP*G)-3')
C: DNA (5'-D(*CP*AP*TP*TP*AP*TP*TP*AP*TP*GP*GP*GP*AP*TP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4579
Polymers28,0683
Non-polymers3896
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-33 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.257, 186.257, 46.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Zinc finger protein 410 / Another partner for ARF 1 / Zinc finger protein APA-1


Mass: 17656.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF410, APA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86VK4

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*CP*AP*TP*AP*AP*TP*AP*AP*TP*G)-3')


Mass: 5139.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*TP*TP*AP*TP*GP*GP*GP*AP*TP*GP*TP*G)-3')


Mass: 5272.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 149 molecules

#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 4.18 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium formate, 20% 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: Mar 10, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→41.92 Å / Num. obs: 47241 / % possible obs: 99.93 % / Redundancy: 11.1 % / Biso Wilson estimate: 51.45 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.07 / Net I/σ(I): 12.3
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 10 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4697 / CC1/2: 0.498 / CC star: 0.815 / Rpim(I) all: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→41.92 Å / SU ML: 0.3211 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5442
RfactorNum. reflection% reflection
Rfree0.1941 2365 5.01 %
Rwork0.1591 --
obs0.1609 47202 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.47 Å2
Refinement stepCycle: LAST / Resolution: 2.75→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 1382 18 137 3803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473882
X-RAY DIFFRACTIONf_angle_d0.6835508
X-RAY DIFFRACTIONf_chiral_restr0.0384583
X-RAY DIFFRACTIONf_plane_restr0.004475
X-RAY DIFFRACTIONf_dihedral_angle_d23.47471506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.810.33241300.30552599X-RAY DIFFRACTION99.85
2.81-2.870.31151380.28292643X-RAY DIFFRACTION99.89
2.87-2.940.32721340.28312725X-RAY DIFFRACTION100
2.94-3.010.30411370.27022542X-RAY DIFFRACTION99.96
3.01-3.090.38091380.2732665X-RAY DIFFRACTION100
3.09-3.180.23481380.20282626X-RAY DIFFRACTION99.96
3.18-3.280.17481420.15932644X-RAY DIFFRACTION100
3.28-3.40.18341360.13792661X-RAY DIFFRACTION100
3.4-3.540.24041460.15032641X-RAY DIFFRACTION100
3.54-3.70.27141440.16772629X-RAY DIFFRACTION100
3.7-3.890.16241400.1462668X-RAY DIFFRACTION100
3.89-4.140.19051420.13732598X-RAY DIFFRACTION100
4.14-4.460.1681420.12812635X-RAY DIFFRACTION99.96
4.46-4.90.15631460.13522643X-RAY DIFFRACTION99.96
4.9-5.610.15561380.12162638X-RAY DIFFRACTION99.93
5.61-7.060.15981370.13662644X-RAY DIFFRACTION99.86
7.07-41.920.11321370.12842636X-RAY DIFFRACTION99.46
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)
12.056962846660.873549621372-5.259000762126.396960960750.3517464242417.43043701045-0.2335951190180.651985586995-0.424790419428-1.05996308216-0.180386393352-0.644448458560.4554021475560.5738422641240.3394916506240.4241274299470.1023629765780.05573667046790.801444041236-0.02544287848360.38631032636-20.858911893266.4672728273-19.0451996392
22.98227209208-1.42573798873-0.9649902696887.297668014311.644987810145.735511304150.1053681227930.4002951566930.381950911084-0.416816972893-0.0091511683385-0.907208693294-0.6675317368670.718845763292-0.008142355477320.324035252066-0.1555340531960.04691904294640.7129919534750.03362858688130.354889943112-20.203367318986.1376974389-8.68987755431
32.05676020114.23433806236-5.600082517555.55437083646-3.273880927972.017933136860.1823766884-0.1548881771820.4434832248960.2918063188320.3138369719550.195106490686-0.3304441002830.0277866555524-0.6166351367090.314324130814-0.0829404966446-0.02662323117090.629540644935-0.01702942484370.321944695063-26.035801752583.304239633912.6136287444
44.64499769406-4.03149875512-0.9387155749542.099326014790.6496229099682.10724622785-0.513055734887-0.305895294586-0.7183301348090.2054805812720.486482733930.108726312790.694449586124-0.0607203502703-0.06953138173330.486993358457-0.006425332662720.01524520304090.6070185874820.04880987106050.410325153968-17.833616882666.406067744513.3891248386
59.99249195734-0.623093079629-4.956973125042.009375022032.959100434697.25553008308-0.465458087620.64054897744-1.70370538819-0.736308578997-0.188474635103-1.317442417241.03148186951.115504976580.6127553874950.5617519347020.1865428524740.09021781107391.0544009544-0.01307594686670.728244877871-7.697612378664.20591561577.30734315634
62.031711378420.203032484769-1.795864446670.0633876864127-0.261086276711.76157369023-0.6669798243390.954670858887-0.565385169935-0.377248442987-0.109907144269-0.904571641424-0.009878539499680.4518136308920.6828467427820.4317240833810.0753233417671-0.01324509656011.712604312090.1709233720441.378850891285.2823352963772.15486054973.26850304012
70.425175738423-2.01106615306-1.107293979.512074611945.251304620562.89722412704-0.7662429776661.02900830027-0.677922995709-0.2547871582951.08486751997-3.11720379418-1.46173176412.25592521937-0.3305210996770.756200095259-0.386656274524-0.21310288681.871037418640.303768647781.413812372985.4601811980980.72051867326.97501462239
88.623927796725.46267252319-5.358026187262.08189254489-4.106796289533.634654762340.0792615488407-0.437411723517-0.5017238991590.684855126853-0.238559038488-0.1202339895830.2288709144580.006562335240180.1829826321140.575985808108-0.0627791575463-5.19534236507E-50.53809690075-0.004751029204550.281447916213-40.930454552257.026786779529.2131831746
97.20409851667-5.003281283563.003080785556.68898037484-3.426768903477.49732401630.0103387630544-0.35269857177-0.4239187927470.2208254167180.250334757950.5836212706390.0587932163143-0.749007698785-0.2371718220690.321524583203-0.1930018811250.04105808357570.445822886531-0.05274892005140.301508365206-56.968562728868.261737595718.5968940219
109.760818115241.42002073219-2.261459655765.836775962760.3862997392957.557464473210.3074561517660.2635041288570.711730838169-0.760273383545-0.331560257856-0.0518812774645-0.8059575415480.01504885261940.01819367584830.354519080124-0.0699929879662-0.0592481104090.4997028249430.1476078956940.381323564201-49.64087375572.168610084-2.38280238645
117.34221589529-4.75736377712-2.579971309919.636147823571.88670163025.75027214309-0.1497692136520.243184843564-0.349848737764-0.1257247003190.0134211656042-0.1284822697640.6300296049210.3680626482210.113996031370.365953950718-0.1505795307820.009777433690060.440946268424-0.06383239840770.268330725936-44.164417628857.2078474055-2.76972608316
122.027704006894.71912592683-7.473587370824.4642264599-5.522441375427.24806484266-0.549792613282-0.838884728669-1.573710913360.127998318175-0.4461279621580.7422299454781.53983820606-0.1142135159920.8140973398471.06525894337-0.2408720120810.15712149120.6641602729080.006784423658061.06355246997-54.384115001541.72641014595.45124489874
132.00088490059-2.586351089228.494394326527.522369195291.246027072856.820486792080.627484408424-1.77478583258-3.07099870393-0.165428631392-0.7292468325450.4714542882661.3724330142-2.880074820760.08783997507721.07278004167-0.4996403419680.21037048841.37765188278-0.3938717169961.3974604661-67.72669732544.34999672323.59338560233
146.317506872733.127867520412.533808603067.191950021251.457138504051.023147202840.077013745290.135555639369-1.588408302030.838018808217-0.07531897972440.2908193523741.81681871244-0.679780816972-0.02992588418651.31583691197-0.438088157093-0.04123426991370.771149523142-0.2644563105470.912720561019-55.388041565744.4728678505-4.14168099097
154.09284760041-1.36869397538-0.3995268294890.399263470525-0.145370309357.373700740480.0160058826735-0.480643737210.497656332609-0.0790833216432-0.0449083427123-0.1241501873780.488498073276-0.125913494949-0.006178640615930.304065465102-0.0512703803884-0.006000024199620.23604499414-0.0563433349080.367884860808-45.221399149163.09002558812.7551377703
168.92974701299-0.1487806493793.342277066157.324691239864.99513770038.774459046290.180697222335-0.461360843729-0.09855566714070.2437158757180.462902813653-0.5092842027850.589990567057-0.571686208096-0.6788837168140.377115882346-0.141555687613-0.06841903978570.472779152011-0.01625432173660.336797483145-41.89798708572.813577050220.6080147791
173.42350941556-1.904891250423.412104323382.01259472628-0.8761631279413.88208451566-0.05554463175050.284508223719-0.45483695551-0.8678090265250.3470716907710.06801599158360.462718917060.252358608038-0.2208842478010.39744875343-0.05990695622160.04471998200330.376556843454-0.1079263036770.347229337723-44.596732988957.799702190910.0703514492
187.7607811051-2.16068611041.940198410788.950950433368.592487199952.012208607260.2885866057340.163748489455-1.31879846763-1.54719081636-0.2326438654420.953792077028-0.23703316477-2.36994938755-0.09726000681570.752401170967-0.278471689954-0.1133354094060.824186589851-0.07781699133610.561500931629-59.697913860653.2236543249-0.400485790907
194.50931469169-0.30628793081-3.679024451131.499058205833.632076089362.0025937149-0.1524472736830.4949744945170.243078655491-1.120083152030.109661776078-0.0214876537207-0.7933086984630.1522724576390.05341185751241.48020661916-0.411603335330.004107682558520.971172364147-0.5159692574260.968761987272-58.484243564845.3281961532-12.9709786818
208.028915444766.32995513142.083652903746.67210708111.175866633340.6735441317750.6651551309510.534156118071-0.675016236610.0456558092469-0.976435450387-2.072332578760.3164658381561.377580854230.2896400933330.4860612021860.0916011730622-0.2528656624961.387722635070.04440983928791.08377781659-2.197516166771.004003537414.5432697092
211.276868171011.574317738290.759864544254.018052579741.155480485254.50746574686-0.2658862407190.1770147675780.365937518375-0.185774902220.1866031572610.343185771140.001970287922470.3750110251090.07360447354980.206954296795-0.01550995006-0.02893779376080.5146559840180.03149539664310.355955493031-23.109927835474.1020419815-2.44421435452
229.34809157986-2.642466852356.920427307515.78122317143-1.457160345135.27448083270.03259746697360.000704187014634-0.351118774826-0.5792768688310.6309489909980.1753310243410.1599914267850.505810263129-0.7375674062680.355122737134-0.0651301857481-0.05221796928030.623643877331-0.1039296541050.339244024524-32.88498101477.2626173304-10.2954007654
232.00641665854-3.265731767986.037416378748.760431182681.330536904166.88303847194-0.0471343428221-0.4758904483630.02467131388230.1205613649220.621195688593-0.3918126063190.4941786979730.302324798625-0.5816852115220.311630868015-0.0165711777871-0.0485936463150.635058618910.007324681079080.31279434234-19.290879493170.43113502830.363278286068
244.39071650232-2.09754413327.779981080062.02551179368-3.935028835332.01275741387-0.785577813298-0.465910267116-0.1058140499690.9450926240360.476092684391-1.82097416059-1.926301236750.6349419056960.2863229658050.65168791982-0.151640659525-0.2024562907911.25752473098-0.1752170644890.712577575134-6.4522667637279.807599098610.663261428
256.727963412342.8513294776-0.3329828913986.08488785127-5.07770347348.79874710318-0.785427527662-1.29689612464-0.005733380788351.587179674950.12332904033-0.969187829511-0.973730569234-0.5263117631120.5637096932190.7496848613380.214326256496-0.4764359676041.82606695672-0.008308329313610.975455907284-0.87131755235774.201352542423.2346034558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 244 )
2X-RAY DIFFRACTION2chain 'A' and (resid 245 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 292 )
4X-RAY DIFFRACTION4chain 'A' and (resid 293 through 322 )
5X-RAY DIFFRACTION5chain 'A' and (resid 323 through 334 )
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 350 )
7X-RAY DIFFRACTION7chain 'A' and (resid 351 through 362 )
8X-RAY DIFFRACTION8chain 'D' and (resid 217 through 244 )
9X-RAY DIFFRACTION9chain 'D' and (resid 245 through 274 )
10X-RAY DIFFRACTION10chain 'D' and (resid 275 through 284 )
11X-RAY DIFFRACTION11chain 'D' and (resid 285 through 322 )
12X-RAY DIFFRACTION12chain 'D' and (resid 323 through 350 )
13X-RAY DIFFRACTION13chain 'D' and (resid 351 through 362 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1 through 5 )
15X-RAY DIFFRACTION15chain 'B' and (resid 6 through 17 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 5 )
17X-RAY DIFFRACTION17chain 'C' and (resid 6 through 10 )
18X-RAY DIFFRACTION18chain 'C' and (resid 11 through 15 )
19X-RAY DIFFRACTION19chain 'C' and (resid 16 through 17 )
20X-RAY DIFFRACTION20chain 'E' and (resid 1 through 5 )
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 17 )
22X-RAY DIFFRACTION22chain 'F' and (resid 1 through 5 )
23X-RAY DIFFRACTION23chain 'F' and (resid 6 through 10 )
24X-RAY DIFFRACTION24chain 'F' and (resid 11 through 15 )
25X-RAY DIFFRACTION25chain 'F' and (resid 16 through 17 )

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