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- PDB-5lty: Homeobox transcription factor CDX2 bound to methylated DNA -

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Basic information

Entry
Database: PDB / ID: 5lty
TitleHomeobox transcription factor CDX2 bound to methylated DNA
Components
  • 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*CP*C)-3')
  • Homeobox protein CDX-2
KeywordsTRANSCRIPTION / transcription factor / methylated DNA
Function / homology
Function and homology information


intestinal epithelial cell differentiation / regulation of somitogenesis / trophectodermal cell differentiation / labyrinthine layer development / establishment or maintenance of epithelial cell apical/basal polarity / methyl-CpG binding / anterior/posterior axis specification / endosome to lysosome transport / blood vessel development / somatic stem cell population maintenance ...intestinal epithelial cell differentiation / regulation of somitogenesis / trophectodermal cell differentiation / labyrinthine layer development / establishment or maintenance of epithelial cell apical/basal polarity / methyl-CpG binding / anterior/posterior axis specification / endosome to lysosome transport / blood vessel development / somatic stem cell population maintenance / transcription repressor complex / condensed nuclear chromosome / stem cell differentiation / positive regulation of cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 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*CP*C)-3')
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')
K: Homeobox protein CDX-2
M: Homeobox protein CDX-2
F: DNA (5'-D(P*GP*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)39,8576
Polymers39,8576
Non-polymers00
Water61334
1
A: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3')
K: Homeobox protein CDX-2
F: 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)19,9283
Polymers19,9283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-13 kcal/mol
Surface area10570 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')
M: Homeobox protein CDX-2
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)19,9283
Polymers19,9283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-11 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.882, 46.613, 120.428
Angle α, β, γ (deg.)90.000, 98.460, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12K
22M
13F
23E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11DTDTDCDCAA1 - 181 - 18
21DTDTDCDCBB1 - 181 - 18
12LYSLYSGLNGLNKC186 - 2542 - 70
22LYSLYSGLNGLNMD186 - 2542 - 70
13DGDGDADAFE19 - 361 - 18
23DGDGDADAEF19 - 361 - 18

NCS ensembles :
ID
1
2
3

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Components

#1: 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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Homeobox protein CDX-2 / / CDX-3 / Caudal-type homeobox protein 2


Mass: 8869.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDX2, CDX3 / Plasmid: pETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q99626
#3: 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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 5000, potassium chloride, magnesium chloride, PEG 400,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: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.66→63.29 Å / Num. obs: 10979 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 73.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15
Reflection shellResolution: 2.66→2.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.647 / % possible all: 96.7

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Processing

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

5eea


Resolution: 2.66→63.29 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 31.14 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.337
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 519 4.7 %RANDOM
Rwork0.202 ---
obs0.2039 10459 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 201.37 Å2 / Biso mean: 77.843 Å2 / Biso min: 36.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20.76 Å2
2---4.67 Å20 Å2
3---2.6 Å2
Refinement stepCycle: final / Resolution: 2.66→63.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 1480 0 34 2757
Biso mean---64.44 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0152989
X-RAY DIFFRACTIONr_bond_other_d0.0050.022104
X-RAY DIFFRACTIONr_angle_refined_deg2.1611.5334224
X-RAY DIFFRACTIONr_angle_other_deg1.6934876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.3059.68544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01122.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36815262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0371517
X-RAY DIFFRACTIONr_chiral_restr0.1760.24448
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022247
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02671
X-RAY DIFFRACTIONr_mcbond_it1.9883.005562
X-RAY DIFFRACTIONr_mcbond_other1.982.999561
X-RAY DIFFRACTIONr_mcangle_it3.2294.48699
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A56740.04
12B56740.04
21K172760.08
22M172760.08
31F57160.04
32E57160.04
LS refinement shellResolution: 2.656→2.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 38 -
Rwork0.411 727 -
all-765 -
obs--94.21 %
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)
12.5321-1.60110.4683.4671-0.69051.50430.270.2889-0.3026-0.5196-0.25940.1430.10320.0939-0.01060.5150.05730.06450.4157-0.03360.3717-19.4945-7.4969-21.1436
24.54712.3783-0.93534.3190.41451.54220.2038-0.670.4740.2017-0.11760.0966-0.00380.4585-0.08620.441-0.1521-0.11680.48640.02090.3341-17.2056-5.066920.1021
31.9116-0.18130.25523.5473-0.24561.31710.1706-0.14590.159-0.02-0.16-0.0285-0.02710.0931-0.01050.38860.07330.00720.4920.03940.2854-20.3093-2.2104-9.3639
43.2252-0.4367-0.26681.7868-0.87551.02870.0179-0.0133-0.13190.2361-0.1587-0.0570.03560.17380.14080.3379-0.076-0.07210.43510.08460.2701-19.5343-9.82137.9789
52.4813-1.99270.0423.65770.58970.84580.05290.2147-0.0789-0.2131-0.1407-0.00490.0505-0.01250.08770.52010.04980.07940.39180.01240.3573-18.8468-6.6472-19.2811
61.19090.3419-0.71092.13110.49072.04390.0665-0.18490.24180.3026-0.11080.1914-0.25860.1830.04440.3018-0.0953-0.12170.24280.03540.1672-16.8206-5.774618.0904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2B1 - 18
3X-RAY DIFFRACTION3K185 - 255
4X-RAY DIFFRACTION4M186 - 255
5X-RAY DIFFRACTION5F19 - 36
6X-RAY DIFFRACTION6E19 - 36

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