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- PDB-7q3o: Structure of CDX1 bound to hydroxymethylated DNA -

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Basic information

Entry
Database: PDB / ID: 7q3o
TitleStructure of CDX1 bound to hydroxymethylated DNA
Components
  • (hydroxymethylated DNA (18-MER)) x 2
  • Homeobox protein CDX-1
KeywordsTRANSCRIPTION / transcription factor / DNA-binding protein / hydroxymethylated DNA
Function / homology
Function and homology information


regulation of somitogenesis / methyl-CpG binding / bone morphogenesis / anterior/posterior axis specification / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding ...regulation of somitogenesis / methyl-CpG binding / bone morphogenesis / anterior/posterior axis specification / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / 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 / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein CDX-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsMorgunova, E. / Yin, Y. / Popov, A. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of CDX1 bound to hydroxymethylated DNA
Authors: Morgunova, E. / Yin, Y. / Popov, A. / Taipale, J.
History
DepositionOct 28, 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: hydroxymethylated DNA (18-MER)
H: hydroxymethylated DNA (18-MER)
B: hydroxymethylated DNA (18-MER)
I: hydroxymethylated DNA (18-MER)
D: hydroxymethylated DNA (18-MER)
J: hydroxymethylated DNA (18-MER)
F: hydroxymethylated DNA (18-MER)
L: hydroxymethylated DNA (18-MER)
K: Homeobox protein CDX-1
C: Homeobox protein CDX-1
E: Homeobox protein CDX-1
G: Homeobox protein CDX-1


Theoretical massNumber of molelcules
Total (without water)76,82312
Polymers76,82312
Non-polymers00
Water1,26170
1
A: hydroxymethylated DNA (18-MER)
H: hydroxymethylated DNA (18-MER)
K: Homeobox protein CDX-1


Theoretical massNumber of molelcules
Total (without water)19,2063
Polymers19,2063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-16 kcal/mol
Surface area9700 Å2
MethodPISA
2
B: hydroxymethylated DNA (18-MER)
I: hydroxymethylated DNA (18-MER)
C: Homeobox protein CDX-1


Theoretical massNumber of molelcules
Total (without water)19,2063
Polymers19,2063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-19 kcal/mol
Surface area9790 Å2
MethodPISA
3
D: hydroxymethylated DNA (18-MER)
J: hydroxymethylated DNA (18-MER)
E: Homeobox protein CDX-1


Theoretical massNumber of molelcules
Total (without water)19,2063
Polymers19,2063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-18 kcal/mol
Surface area9610 Å2
MethodPISA
4
F: hydroxymethylated DNA (18-MER)
L: hydroxymethylated DNA (18-MER)
G: Homeobox protein CDX-1


Theoretical massNumber of molelcules
Total (without water)19,2063
Polymers19,2063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-20 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.373, 64.669, 67.028
Angle α, β, γ (deg.)112.370, 108.110, 93.930
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23F
14B
24D
15B
25F
16D
26F
17K
27C
18K
28E
19K
29G
110C
210E
111C
211G
112E
212G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 39
2010B1 - 39
1020A1 - 39
2020D1 - 39
1030A1 - 39
2030F1 - 39
1040B1 - 39
2040D1 - 39
1050B1 - 39
2050F1 - 39
1060D1 - 39
2060F1 - 39
1070K183 - 242
2070C183 - 242
1080K185 - 242
2080E185 - 242
1090K183 - 243
2090G183 - 243
10100C185 - 243
20100E185 - 243
10110C183 - 242
20110G183 - 242
10120E185 - 242
20120G185 - 242

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: DNA chain
hydroxymethylated DNA (18-MER)


Mass: 5503.560 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain
hydroxymethylated DNA (18-MER)


Mass: 5556.660 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
Homeobox protein CDX-1 / / Caudal-type homeobox protein 1


Mass: 8145.416 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDX1 / Plasmid: pETG20A / Details (production host): pETG20A-SBP / Production host: Escherichia coli (E. coli) / References: UniProt: P47902
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 3350, potassium chloride, magnesium chloride, PEG 200, Tris

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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 / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.78→42.18 Å / Num. obs: 14867 / % possible obs: 90 % / Redundancy: 2.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.052 / Rrim(I) all: 0.078 / Net I/σ(I): 7.6 / Num. measured all: 30774
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.78-2.930.693428221210.640.6380.944187.6
8.78-42.180.0268984510.9970.0240.03618.585.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LUX

5lux


Resolution: 2.78→42.18 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 54.294 / SU ML: 0.476 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2857 709 4.8 %RANDOM
Rwork0.2169 ---
obs0.2203 14157 90.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 290.45 Å2 / Biso mean: 81.18 Å2 / Biso min: 26.74 Å2
Baniso -1Baniso -2Baniso -3
1--3.7 Å23.78 Å2-0.02 Å2
2--3.36 Å20.75 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 2.78→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 2968 0 70 5215
Biso mean---58.02 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125672
X-RAY DIFFRACTIONr_bond_other_d0.0020.0193790
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.3968063
X-RAY DIFFRACTIONr_angle_other_deg1.4922.2158835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg26.666.678992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.06718.75152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.78615428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.441538
X-RAY DIFFRACTIONr_chiral_restr0.2460.243829
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024113
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021252
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35360.04
12B35360.04
21A35350.04
22D35350.04
31A35650.03
32F35650.03
41B35910.03
42D35910.03
51B35400.04
52F35400.04
61D35350.04
62F35350.04
71K20440.1
72C20440.1
81K19720.1
82E19720.1
91K20690.09
92G20690.09
101C20180.09
102E20180.09
111C20640.1
112G20640.1
121E19740.1
122G19740.1
LS refinement shellResolution: 2.78→2.85 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.491 53 -
Rwork0.455 946 -
obs--81.68 %
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)
11.8443-0.28140.01981.5373-0.15350.9395-0.14730.0849-0.1377-0.1481-0.0910.0607-0.04380.14780.23830.0976-0.1450.05960.3477-0.06240.3704-7.156818.7467-20.2358
23.4109-1.7905-1.52522.65670.14391.3482-0.2803-0.0914-0.00810.27530.1223-0.134-0.00240.04260.1580.0670.06370.00450.2894-0.02260.2151-6.159216.990418.2277
33.4705-2.1676-0.05292.7442-0.19460.874-0.3798-0.4127-0.13370.23580.30080.1862-0.00460.07710.0790.06450.12340.03490.36780.02850.1957-10.540846.548219.0251
42.64520.5942-0.31381.88550.11210.9648-0.21720.00870.0033-0.1462-0.0165-0.1417-0.0211-0.17690.23370.0775-0.1053-0.00120.29810.0380.3781-9.375447.0668-19.5527
50.42130.84550.14052.79882.06234.83910.00850.0819-0.02120.26530.0642-0.18290.12480.2316-0.07260.1277-0.04650.03350.2489-0.0110.29960.961517.4148-10.117
60.9838-0.7241-1.08183.5496-1.05313.0113-0.0618-0.05410.0331-0.19720.04460.24650.1847-0.29330.01720.09380.02820.0280.2919-0.00610.2402-13.138317.11747.989
71.59950.32260.63044.9713-0.032.4766-0.0864-0.2603-0.0315-0.19660.2064-0.2362-0.06930.2345-0.120.06170.06480.02020.2964-0.00390.2007-2.852846.82968.4397
80.6520.3399-0.02242.429-1.63183.9268-0.04860.2071-0.01640.37060.07680.2915-0.1704-0.161-0.02820.0949-0.00650.01140.23360.00970.2614-17.45447.8539-9.3116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION1H1 - 18
3X-RAY DIFFRACTION2B1 - 18
4X-RAY DIFFRACTION2I1 - 18
5X-RAY DIFFRACTION3D1 - 18
6X-RAY DIFFRACTION3J1 - 18
7X-RAY DIFFRACTION4F1 - 18
8X-RAY DIFFRACTION4L1 - 18
9X-RAY DIFFRACTION5K183 - 243
10X-RAY DIFFRACTION6C183 - 243
11X-RAY DIFFRACTION7E185 - 243
12X-RAY DIFFRACTION8G183 - 243

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