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- PDB-6es2: Structure of CDX2-DNA(CAA) -

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Basic information

Entry
Database: PDB / ID: 6es2
TitleStructure of CDX2-DNA(CAA)
Components
  • DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*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*TP*TP*GP*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 / methyl-CpG binding / anterior/posterior axis specification / endosome to lysosome transport / blood vessel development / somatic stem cell population maintenance ...regulation of somitogenesis / intestinal epithelial cell differentiation / 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 / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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: 2.95 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 1.2Jan 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
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: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
K: Homeobox protein CDX-2
B: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
L: Homeobox protein CDX-2
D: DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
E: DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)39,8536
Polymers39,8536
Non-polymers00
Water18010
1
A: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
K: Homeobox protein CDX-2
D: DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)19,9263
Polymers19,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-25 kcal/mol
Surface area11260 Å2
MethodPISA
2
B: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP*CP*C)-3')
L: Homeobox protein CDX-2
E: DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)19,9263
Polymers19,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-24 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.248, 46.695, 128.634
Angle α, β, γ (deg.)90.000, 101.400, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12K
22L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 36
2010B1 - 36
1020K187 - 254
2020L187 - 254

NCS ensembles :
ID
1
2

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Components

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


Mass: 5454.521 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: 8896.251 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 (E. coli) / References: UniProt: Q99626
#3: DNA chain DNA (5'-D(P*GP*GP*AP*GP*GP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Mass: 5575.672 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.: 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 27 % PME 5000, 0.15M potassium chloride, 0.1M magnesium chloride, 8% PEG 400, 0.05M TRIS buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.95→66.19 Å / Num. obs: 8494 / % possible obs: 96.6 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.051 / Rrim(I) all: 0.093 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.95-3.133.20.8312640.6110.5390.99390.5
8.86-55.962.80.0383410.9980.0270.04797.4

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTY

5lty


Resolution: 2.95→66.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 53.863 / SU ML: 0.427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.431
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 418 4.9 %RANDOM
Rwork0.2085 ---
obs0.2103 8076 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 204.74 Å2 / Biso mean: 98.684 Å2 / Biso min: 57.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-3.27 Å2
2--0.01 Å20 Å2
3---0.63 Å2
Refinement stepCycle: final / Resolution: 2.95→66.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 1476 0 10 2722
Biso mean---69.9 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0142915
X-RAY DIFFRACTIONr_bond_other_d0.0030.022045
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.4844220
X-RAY DIFFRACTIONr_angle_other_deg1.48834781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21722.63276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.91515277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0841519
X-RAY DIFFRACTIONr_chiral_restr0.1180.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02631
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A7114
12B7114
21K4658
22L4658
LS refinement shellResolution: 2.953→3.029 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.594 30 -
Rwork0.447 469 -
all-499 -
obs--80.23 %
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)
15.0269-3.3912-1.1452.74910.36451.72330.16710.83080.3599-0.3666-0.3174-0.2572-0.1052-0.40620.15030.70570.1852-0.08520.4404-0.03150.771-16.5746-20.3249-20.5073
21.921.0674-1.04223.75-0.22634.55020.2044-0.1166-0.0796-0.1674-0.3160.06410.3293-0.05780.11160.26670.1741-0.09340.3015-0.07080.6783-14.4199-24.5005-8.6993
35.3952.56130.00261.3731-0.18541.60780.0893-0.7146-0.28240.303-0.2761-0.08870.1248-0.41390.18680.7414-0.20420.08770.4143-0.0170.7842-17.1787-21.894419.9231
42.2356-1.7871-0.32881.70230.58081.48350.02910.2182-0.11530.1497-0.28160.1651-0.19560.06190.25260.2421-0.15360.01050.1316-0.09220.5415-15.1249-17.37838.3954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION1D19 - 36
3X-RAY DIFFRACTION2K187 - 256
4X-RAY DIFFRACTION3B1 - 18
5X-RAY DIFFRACTION3E19 - 36
6X-RAY DIFFRACTION4L186 - 255

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