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- PDB-6es3: Structure of CDX2-DNA(TCG) -

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Basic information

Entry
Database: PDB / ID: 6es3
TitleStructure of CDX2-DNA(TCG)
Components
  • DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*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*CP*GP*AP*CP*CP*TP*CP*C)-3')
  • Homeobox protein CDX-2
KeywordsTRANSCRIPTION / homeodomain transcription factor / CDX2-DNA complex
Function / homology
Function and homology information


regulation of somitogenesis / intestinal epithelial cell differentiation / trophectodermal cell differentiation / labyrinthine layer development / establishment or maintenance of epithelial cell apical/basal polarity / embryonic pattern specification / methyl-CpG binding / digestive tract development / anterior/posterior axis specification / endosome to lysosome transport ...regulation of somitogenesis / intestinal epithelial cell differentiation / trophectodermal cell differentiation / labyrinthine layer development / establishment or maintenance of epithelial cell apical/basal polarity / embryonic pattern specification / methyl-CpG binding / digestive tract development / anterior/posterior axis specification / endosome to lysosome transport / blood vessel development / somatic stem cell population maintenance / transcription repressor complex / condensed nuclear chromosome / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of cell differentiation / stem cell differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / 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 / regulation of transcription by RNA polymerase II / chromatin / 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: 2.57 Å
AuthorsMorgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, J.
CitationJournal: Elife / Year: 2018
Title: Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.
Authors: Morgunova, E. / Yin, Y. / Das, P.K. / Jolma, A. / Zhu, F. / Popov, A. / Xu, Y. / Nilsson, L. / Taipale, J.
History
DepositionOct 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Jan 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*CP*GP*AP*CP*CP*TP*CP*C)-3')
B: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*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*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
E: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)40,1156
Polymers40,1156
Non-polymers00
Water1,67593
1
A: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*CP*CP*TP*CP*C)-3')
K: Homeobox protein CDX-2
F: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)20,0583
Polymers20,0583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-22 kcal/mol
Surface area11030 Å2
MethodPISA
2
B: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*CP*CP*TP*CP*C)-3')
M: Homeobox protein CDX-2
E: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)20,0583
Polymers20,0583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-25 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.950, 46.490, 68.890
Angle α, β, γ (deg.)90.000, 113.270, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12K
22M
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
11DTDTDCDCAA1 - 181 - 18
21DTDTDCDCBB1 - 181 - 18
12ARGARGGLNGLNKC184 - 2551 - 72
22ARGARGGLNGLNMD184 - 2551 - 72
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*CP*GP*AP*CP*CP*TP*CP*C)-3')


Mass: 5448.524 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: 9026.421 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDX2, CDX3 / Plasmid: pETG20A-SBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q99626
#3: DNA chain DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Mass: 5582.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 19% PME 5000, 0.15 M potassium chloride, 0.1 M magnesium chloride, 8% PEG 400, 0.05M TRIS-buffer pH 8.0

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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: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.18→43.23 Å / Num. obs: 19575 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 16.093 % / Biso Wilson estimate: 65.834 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.185 / Rrim(I) all: 0.191 / Χ2: 1.191 / Net I/σ(I): 8.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.18-2.246.0192.9910.4313880.1073.27397.8
2.24-2.36.8962.2020.6914150.3712.38399.6
2.3-2.377.2491.9660.7913640.5082.118100
2.37-2.4412.0512.3171.1113250.6012.41799.8
2.44-2.5215.3012.5441.4812870.6622.6399.6
2.52-2.6118.2121.9492.0612370.8082.005100
2.61-2.7120.4431.5552.7712040.8461.59599.6
2.71-2.8220.1031.2073.5211390.8891.23899.9
2.82-2.9420.5110.84.9911290.9570.821100
2.94-3.0919.9660.4976.9910600.9830.5199.3
3.09-3.2519.8810.2211.1310100.9980.226100
3.25-3.4519.6110.17414.319560.9970.17999.5
3.45-3.6920.0550.17916.778950.9960.18499.9
3.69-3.9919.5680.16719.248520.9950.172100
3.99-4.3719.2030.14321.427780.9970.14799.6
4.37-4.8819.7810.13124.17110.9970.13599.6
4.88-5.6419.5620.12624.476260.9960.1399.4
5.64-6.918.3350.11924.425400.9970.12399.8
6.9-9.7619.6230.08727.244160.9990.0999
9.76-43.2317.4240.08428.252430.9980.08798.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTY

5lty


Resolution: 2.57→43.23 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 31.815 / SU ML: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.378
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 1210 10 %RANDOM
Rwork0.2161 ---
obs0.2221 10891 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 183.04 Å2 / Biso mean: 67.057 Å2 / Biso min: 37.37 Å2
Baniso -1Baniso -2Baniso -3
1-7.15 Å20 Å22.1 Å2
2---8.04 Å20 Å2
3----0.66 Å2
Refinement stepCycle: final / Resolution: 2.57→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 1476 0 93 2841
Biso mean---67.4 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0143030
X-RAY DIFFRACTIONr_bond_other_d0.0030.022076
X-RAY DIFFRACTIONr_angle_refined_deg2.0531.4874254
X-RAY DIFFRACTIONr_angle_other_deg1.55834848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.4386.323532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43222.43274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.44815273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9581519
X-RAY DIFFRACTIONr_chiral_restr0.1830.247464
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022242
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02646
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A31300.06
12B31300.06
21K48120.09
22M48120.09
31F32500.04
32E32500.04
LS refinement shellResolution: 2.57→2.637 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 90 -
Rwork0.439 808 -
all-898 -
obs--100 %
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)
13.0779-0.8501-1.37156.25951.85193.6449-0.11910.323-0.3158-0.1371-0.27090.41940.446-0.28520.390.225-0.0025-0.18290.4123-0.05580.375773.7954-4.781672.8029
21.52161.4213-0.53395.5696-2.16846.52440.24030.17450.11130.3719-0.2159-0.1383-0.71870.8957-0.02440.1121-0.0321-0.03590.55120.09630.5289112.0127-1.896787.1855
32.0391-0.2953-0.59594.3039-0.56372.89510.03070.0550.02330.0549-0.1685-0.0816-0.1680.16150.13780.09720.0445-0.19580.5962-0.04140.418584.12280.780877.7448
41.4844-1.23680.31333.7177-0.11892.1440.11530.1191-0.0274-0.0573-0.275-0.24310.14130.09620.15970.05030.0197-0.11570.61630.09560.4763100.853-7.214484.2767
50.9475-0.68-1.14196.50823.26933.4680.17890.1122-0.02450.0194-0.1933-0.02390.0097-0.43640.01440.15630.0253-0.19490.3775-0.05390.385975.7866-3.844272.9801
61.98912.1669-1.05046.7929-4.83415.96690.17880.03320.40420.1307-0.1170.2082-0.2980.3026-0.06180.1948-0.0138-0.07020.46260.04130.5676110.3897-2.788386.0577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2B1 - 18
3X-RAY DIFFRACTION3K184 - 255
4X-RAY DIFFRACTION4M184 - 255
5X-RAY DIFFRACTION5F19 - 36
6X-RAY DIFFRACTION6E19 - 36

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