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- PDB-5lux: Homeobox transcription factor CDX1 bound to methylated DNA -

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Basic information

Entry
Database: PDB / ID: 5lux
TitleHomeobox transcription factor CDX1 bound to methylated DNA
Components
  • DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
  • DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*C)-3')
  • DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3')
  • Homeobox protein CDX-1
KeywordsTRANSCRIPTION / transcription factor / methylated DNA
Function / homology
Function and homology information


regulation of somitogenesis / embryonic pattern specification / bone morphogenesis / methyl-CpG binding / digestive tract development / anterior/posterior axis specification / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific ...regulation of somitogenesis / embryonic pattern specification / bone morphogenesis / methyl-CpG binding / digestive tract development / anterior/posterior axis specification / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Caudal-like activation domain / : / Caudal like protein activation region / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...Caudal-like activation domain / : / Caudal like protein activation region / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein CDX-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsMorgunova, E. / Popov, A. / Taipale, J.
CitationJournal: Science / Year: 2017
Title: Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / ...Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / Domcke, S. / Yan, J. / Schubeler, D. / Vinson, C. / Taipale, J.
History
DepositionSep 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*C)-3')
K: Homeobox protein CDX-1
B: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3')
L: Homeobox protein CDX-1
F: DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
E: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)37,2746
Polymers37,2746
Non-polymers00
Water18010
1
A: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*C)-3')
K: Homeobox protein CDX-1
F: DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,3283
Polymers18,3283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-15 kcal/mol
Surface area9110 Å2
MethodPISA
2
B: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3')
L: Homeobox protein CDX-1
E: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,9463
Polymers18,9463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-15 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.650, 45.555, 116.499
Angle α, β, γ (deg.)90.000, 93.790, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12K
22L
13F
23E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11DTDTDTDTAA1 - 161 - 16
21DTDTDTDTBC1 - 161 - 16
12THRTHRASNASNKB153 - 2131 - 61
22THRTHRASNASNLD153 - 2131 - 61
13DGDGDADAFE20 - 351 - 16
23DGDGDADAEF20 - 352 - 17

NCS ensembles :
ID
1
2
3

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Components

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DNA chain , 4 types, 4 molecules ABFE

#1: DNA chain DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*C)-3')


Mass: 5173.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3')


Mass: 5462.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Mass: 5267.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Mass: 5596.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / Non-polymers , 2 types, 12 molecules KL

#2: Protein Homeobox protein CDX-1 / Caudal-type homeobox protein 1


Mass: 7887.118 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDX1 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P47902
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG MME (5000),KCl, MgCl2, 2-Methyl propanol, Tris buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 3.23→58.12 Å / Num. obs: 5425 / % possible obs: 97.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 57 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.174 / Net I/σ(I): 5.3
Reflection shellResolution: 3.23→3.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.91 / CC1/2: 0.891 / % possible all: 88.9

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTX

5ltx


Resolution: 3.23→58.12 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.864 / SU B: 100.709 / SU ML: 0.697 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.729
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2995 515 9.5 %RANDOM
Rwork0.2411 ---
obs0.2467 4909 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 237.96 Å2 / Biso mean: 90.603 Å2 / Biso min: 35.87 Å2
Baniso -1Baniso -2Baniso -3
1-4.69 Å20 Å20.38 Å2
2---2.68 Å20 Å2
3----2.04 Å2
Refinement stepCycle: final / Resolution: 3.23→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 1439 0 10 2552
Biso mean---92.56 -
Num. residues----195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0152731
X-RAY DIFFRACTIONr_bond_other_d0.0040.021929
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.5213970
X-RAY DIFFRACTIONr_angle_other_deg1.68934473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1825123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05921.56264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.34815238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5381518
X-RAY DIFFRACTIONr_chiral_restr0.1240.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022042
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02615
X-RAY DIFFRACTIONr_mcbond_it3.5484.388498
X-RAY DIFFRACTIONr_mcbond_other3.5294.371497
X-RAY DIFFRACTIONr_mcangle_it6.0516.54619
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A51980.01
12B51980.01
21K155160.08
22L155160.08
31F53880.01
32E53880.01
LS refinement shellResolution: 3.233→3.317 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 27 -
Rwork0.338 262 -
all-289 -
obs--73.35 %
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)
13.7738-5.34551.11378.5789-0.76861.05030.08830.0943-0.0935-0.2177-0.10550.328-0.0066-0.01230.01720.0627-0.0169-0.13820.07280.09221.2139-16.9594-28.0758-18.8237
23.0003-0.4198-0.77614.9472-0.83688.2518-0.0088-0.19380.40350.15090.37140.1172-0.1827-0.3809-0.36260.08840.0463-0.11020.06830.01971.071-16.3559-19.2056-8.3546
32.46814.1588-0.01377.22390.26360.5077-0.0367-0.08320.4386-0.0412-0.05670.620.08480.08680.09340.1097-0.0271-0.17520.0468-0.01491.4353-17.2022-26.119919.0727
43.86122.7022-0.81182.9736-0.62127.9813-0.35730.6044-0.11850.00090.2294-0.17860.4174-0.45840.12790.114-0.1174-0.10120.14390.0211.1686-15.897-34.02898.425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION1F20 - 36
3X-RAY DIFFRACTION2K153 - 215
4X-RAY DIFFRACTION3B1 - 18
5X-RAY DIFFRACTION3E19 - 36
6X-RAY DIFFRACTION4L153 - 214

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