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- PDB-5j70: The Chd1 DNA-binding domain in complex with 17mer DNA duplex -

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Basic information

Entry
Database: PDB / ID: 5j70
TitleThe Chd1 DNA-binding domain in complex with 17mer DNA duplex
Components
  • Chromo domain-containing protein 1
  • DNA (5'-D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3')
Keywordschromatin-binding protein/DNA / DNA-bound complex / SANT domain / SLIDE domain / chromatin-binding protein-DNA complex
Function / homology
Function and homology information


nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / : / helicase activity / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
Helix Hairpins - #1440 / Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. ...Helix Hairpins - #1440 / Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helix Hairpins / Homeodomain-like / Helix non-globular / Special / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Chromo domain-containing protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.956 Å
AuthorsBowman, G.D. / Jenkins, K.R. / Hauk, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-R01-084192 United States
CitationJournal: To Be Published
Title: Chd1 domains communicate across the DNA gyres of the nucleosome
Authors: Nodelman, I.M. / Jenkins, K.R. / Ren, R. / Horvath, K.C. / Hauk, G. / Bowman, G.D.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Chromo domain-containing protein 1
B: Chromo domain-containing protein 1
W: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3')
X: DNA (5'-D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')
Y: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3')
Z: DNA (5'-D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)81,8416
Polymers81,8416
Non-polymers00
Water00
1
A: Chromo domain-containing protein 1
W: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3')
X: DNA (5'-D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)40,9213
Polymers40,9213
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-26 kcal/mol
Surface area19340 Å2
MethodPISA
2
B: Chromo domain-containing protein 1
Y: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3')
Z: DNA (5'-D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)40,9213
Polymers40,9213
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-24 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.076, 57.099, 99.493
Angle α, β, γ (deg.)90.00, 103.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chromo domain-containing protein 1 / ATP-dependent helicase CHD1


Mass: 30505.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CHD1, YER164W, SYGP-ORF4 / Plasmid: pDEST17 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P32657, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3')


Mass: 5227.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')


Mass: 5187.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.91 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.5
Details: 14% PEG 4000, 0.2M ammonium acetate, 0.01M CaCl2, 0.05 M Na cacodylate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.956→96.553 Å / Num. obs: 19925 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.44 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.3
Reflection shellResolution: 2.956→3.14 Å / Redundancy: 7.48 % / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 1.89 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TED

3ted


Resolution: 2.956→46.985 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1967 5.21 %RANDOM
Rwork0.2307 ---
obs0.2318 37734 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.956→46.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 1382 0 0 5055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045286
X-RAY DIFFRACTIONf_angle_d0.6627399
X-RAY DIFFRACTIONf_dihedral_angle_d18.7962967
X-RAY DIFFRACTIONf_chiral_restr0.041815
X-RAY DIFFRACTIONf_plane_restr0.004706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.956-3.030.52971350.53822396X-RAY DIFFRACTION92
3.03-3.11190.43341530.41672537X-RAY DIFFRACTION98
3.1119-3.20340.3491370.35732526X-RAY DIFFRACTION96
3.2034-3.30680.36471200.35042429X-RAY DIFFRACTION94
3.3068-3.42490.33661120.32722547X-RAY DIFFRACTION97
3.4249-3.5620.31931650.30572588X-RAY DIFFRACTION99
3.562-3.72410.33621150.27162551X-RAY DIFFRACTION99
3.7241-3.92030.2991730.27012549X-RAY DIFFRACTION100
3.9203-4.16580.30031410.25052611X-RAY DIFFRACTION100
4.1658-4.48720.26611520.22272626X-RAY DIFFRACTION100
4.4872-4.93830.26661390.21852614X-RAY DIFFRACTION100
4.9383-5.65190.23021220.20422626X-RAY DIFFRACTION100
5.6519-7.11680.23891360.20032646X-RAY DIFFRACTION100
7.1168-46.9910.15611670.14532521X-RAY DIFFRACTION99
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)
16.10042.14120.02595.40340.78082.8818-0.1354-1.5562-1.27821.72870.2317-1.62110.67830.5324-0.30611.47830.1943-0.32811.4304-0.06740.617727.0786-13.632725.6614
20.96141.63381.01323.08721.971.19070.55861.1341-0.8870.27140.1163-1.07581.85490.22081.2211.3353-0.28920.07482.08490.00010.32810.1225-16.65813.038
36.69710.43014.03244.30881.92293.0769-0.22191.06171.3275-0.3050.14080.4562-1.2368-0.7896-0.36871.3263-0.18720.04682.14960.23160.6997-2.5923-1.9951-11.6457
48.0396-0.6274.13617.8131-2.1096.74350.3185-0.88940.16860.6331-0.01840.00010.6148-1.3022-0.49171.2384-0.1199-0.12211.5592-0.070.615512.1358-11.44814.8172
54.08160.52670.955.9139-0.01874.16370.06251.1297-0.1157-0.58980.2617-1.44920.06970.7033-0.36580.83180.03940.05431.3833-0.31910.83736.0645-0.0468.9876
65.04191.79451.28872.52050.45682.0886-0.01431.47750.461-1.68670.5486-1.0006-0.47290.2279-0.02351.07470.1122-0.10041.5018-0.11090.778327.81414.54536.9285
76.60931.2252-1.27254.0912-1.0677.79670.3334-0.9685-0.56750.46260.03851.24980.2908-0.9176-0.39681.3531-0.0380.33881.38960.29140.946838.093916.103146.4088
86.0264.3126-2.42386.6086-4.37695.94020.68760.3461.21880.37140.49961.4389-1.3952-0.7774-1.22911.62090.20930.44780.8548-0.01030.982149.657236.499730.2724
94.94223.2154-1.59785.0833-3.32333.38130.4546-0.72470.66540.8673-0.16130.6077-1.66740.8914-0.23641.9862-0.12410.30161.0986-0.2640.907862.537238.35431.9317
107.72352.5649-0.48472.19960.22619.06461.07351.78280.7339-0.47470.19990.7932-0.4798-1.2961-1.12881.32890.1412-0.07780.86420.07180.836445.754816.908831.6341
111.3775-0.0096-0.94140.6391-0.06820.6559-1.022-0.63241.06110.7684-0.1673-0.3078-1.59220.72240.48341.9093-0.3603-0.48811.3408-0.17031.371142.13220.334725.6422
126.37622.5485-1.24515.2915-0.3126.3358-0.07160.1533-1.4408-0.31690.2001-0.50651.73520.7289-0.1391.55180.4859-0.12811.0729-0.09490.815557.08344.656132.9653
137.26760.0488-4.56956.04610.37293.60630.245-1.17350.5162.07050.23680.7701-0.622-0.6485-0.01342.27430.04770.21022.3385-0.03370.494310.68135.013826.6784
142.1436-0.93051.43654.0446-0.34382.3880.0333-0.98770.23150.9756-0.5448-0.3852-0.90690.1851-0.00841.0317-0.0722-0.0071.62370.06760.443810.39282.887810.1367
154.0099-0.3075-2.84365.03220.58759.1380.6646-0.13760.5989-1.6817-0.0204-0.4519-0.9004-0.6207-0.5381.25270.09520.2611.45180.0640.720616.511912.8895-8.0216
163.9092-0.64890.95893.8120.05195.8290.81650.92180.4594-0.8028-0.621-0.36850.4203-1.137-0.14281.17550.20880.13141.62450.03040.657513.95589.8044-3.5248
170.97031.2332-1.20981.61-1.80343.0838-0.1167-1.0845-0.42751.41830.0537-0.04331.1231-0.09970.53571.81890.03810.05851.9730.01820.47118.44991.155321.5246
184.126-2.47153.35299.82692.49645.1540.4119-2.26990.22181.64070.66040.07460.83042.1774-0.1842.1772-0.05770.41012.3093-0.09260.825560.007921.795356.3238
191.6014-0.91041.97115.5927-1.50913.03520.0792-0.2633-0.40620.561-0.7950.1158-1.43492.08230.36381.5449-0.20780.30751.4525-0.13790.763563.701326.519640.8083
201.11911.0108-2.74624.8665-1.22327.09060.6506-0.0520.2140.6857-0.8848-0.4630.63261.9850.07721.53460.39010.19842.2696-0.06680.759878.077721.180325.1379
210.52610.6268-1.0743.1269-2.43642.97050.6754-0.11190.11660.1441-0.8245-0.1285-0.95780.8722-0.56931.58910.3520.15532.4902-0.2610.77679.294327.963623.733
222.0342-0.2742-1.8945.53550.46121.77181.18331.2211-0.7926-0.2094-0.00980.23510.50941.0464-0.04411.54280.17050.21262.3195-0.19520.858669.357519.344934.5776
230.9121-0.86690.1730.91480.0391.6446-0.0227-0.7098-0.03420.73910.03230.3464-0.0549-0.27650.22542.125-0.23340.41692.1421-0.20040.697259.021226.704951.5847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1007 through 1045 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1046 through 1091 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1092 through 1113 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1114 through 1129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1130 through 1209 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1210 through 1266 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1007 through 1045 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1046 through 1091 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1092 through 1129 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1130 through 1144 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1145 through 1154 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1155 through 1266 )
13X-RAY DIFFRACTION13chain 'W' and (resid 1 through 5 )
14X-RAY DIFFRACTION14chain 'W' and (resid 6 through 10 )
15X-RAY DIFFRACTION15chain 'W' and (resid 11 through 17 )
16X-RAY DIFFRACTION16chain 'X' and (resid 1 through 10 )
17X-RAY DIFFRACTION17chain 'X' and (resid 11 through 17 )
18X-RAY DIFFRACTION18chain 'Y' and (resid 1 through 5 )
19X-RAY DIFFRACTION19chain 'Y' and (resid 6 through 10 )
20X-RAY DIFFRACTION20chain 'Y' and (resid 11 through 17 )
21X-RAY DIFFRACTION21chain 'Z' and (resid 1 through 5 )
22X-RAY DIFFRACTION22chain 'Z' and (resid 6 through 10 )
23X-RAY DIFFRACTION23chain 'Z' and (resid 11 through 17 )

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