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- PDB-7q4n: transcription factor CDX2 bound to hydroxymethylated DNA -

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Basic information

Entry
Database: PDB / ID: 7q4n
Titletranscription factor CDX2 bound to hydroxymethylated DNA
Components
  • (DNA (18-MER)) x 2
  • Homeobox protein CDX-2
KeywordsTRANSCRIPTION / transcription factor / homeobox / complex / hydroxymethylated 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 / Homeobox-like domain superfamily
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: 3.2 Å
AuthorsMorgunova, E. / Yin, Y. / Popov, A. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: transcription factor CDX2 bound to hydroxymethylated DNA
Authors: Morgunova, E. / Yin, Y. / Popov, A. / Taipale, J.
History
DepositionNov 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (18-MER)
D: DNA (18-MER)
K: Homeobox protein CDX-2
B: DNA (18-MER)
E: DNA (18-MER)
C: Homeobox protein CDX-2


Theoretical massNumber of molelcules
Total (without water)38,8866
Polymers38,8866
Non-polymers00
Water25214
1
A: DNA (18-MER)
D: DNA (18-MER)
K: Homeobox protein CDX-2


Theoretical massNumber of molelcules
Total (without water)19,4433
Polymers19,4433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-16 kcal/mol
Surface area10400 Å2
MethodPISA
2
B: DNA (18-MER)
E: DNA (18-MER)
C: Homeobox protein CDX-2


Theoretical massNumber of molelcules
Total (without water)19,4433
Polymers19,4433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-21 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.897, 46.634, 120.048
Angle α, β, γ (deg.)90.000, 98.250, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12K
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 39
2010B1 - 39
1020K189 - 250
2020C189 - 250

NCS ensembles :
ID
1
2

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Components

#1: DNA chain DNA (18-MER)


Mass: 5503.560 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (18-MER)


Mass: 5556.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Homeobox protein CDX-2 / / CDX-3 / Caudal-type homeobox protein 2


Mass: 8382.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDX2, CDX3 / Plasmid: pET20A / Details (production host): SBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q99626
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 1500, potassium chloride, magnesium chloride, PEG 200, Bis-tris propane, 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 3.03→43.45 Å / Num. obs: 7406 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.975 / Rmerge(I) obs: 0.272 / Rpim(I) all: 0.155 / Rrim(I) all: 0.315 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.03-3.213.71.409405410920.7450.7881.6231.389.3
9.09-43.413.50.0810362980.9950.0480.09410.396.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTY

5lty


Resolution: 3.2→43.45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.886 / SU B: 82.225 / SU ML: 0.599 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.605 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 341 5.3 %RANDOM
Rwork0.2378 ---
obs0.24 6054 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.54 Å2 / Biso mean: 70.605 Å2 / Biso min: 31 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å2-1.71 Å2
2---6.2 Å20 Å2
3---2.71 Å2
Refinement stepCycle: final / Resolution: 3.2→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 1484 0 14 2636
Biso mean---49.98 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122816
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161987
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.7114096
X-RAY DIFFRACTIONr_angle_other_deg1.0621.5684613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7385127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49919.28684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg29.33915249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8551518
X-RAY DIFFRACTIONr_chiral_restr0.1380.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022123
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02561
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A36120.07
12B36120.07
21K18500.22
22C18500.22
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 34 -
Rwork0.271 423 -
all-457 -
obs--97.03 %
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)
16.6561-0.85380.92544.08480.79672.83140.42370.7153-0.4312-0.545-0.69990.26730.1660.19570.27620.40590.24690.29080.22910.06630.5732-19.0163-7.1777-20.0309
26.43962.38370.99245.30910.8514.86940.3633-0.4622-0.0601-0.0988-0.4806-0.1985-0.0810.030.11740.13660.04460.2080.09490.12120.5115-20.2711-1.8675-9.1209
37.47673.3932-1.15216.27221.00163.09980.1666-0.53160.49350.1505-0.39610.025-0.16920.4640.22960.321-0.1896-0.02220.1890.03810.554-17.6084-5.003819.0437
45.9408-2.9750.7094.4111-1.00234.57470.20290.48840.1623-0.1957-0.3288-0.2220.05870.00930.12580.1523-0.07960.06080.12640.06930.5782-19.8465-10.48297.5757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION1D22 - 39
3X-RAY DIFFRACTION2K187 - 252
4X-RAY DIFFRACTION3B1 - 18
5X-RAY DIFFRACTION3E22 - 39
6X-RAY DIFFRACTION4C189 - 251

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