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- PDB-5vc9: Zinc finger of human CXXC4 in complex with CpG DNA -

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Basic information

Entry
Database: PDB / ID: 5vc9
TitleZinc finger of human CXXC4 in complex with CpG DNA
Components
  • CXXC-type zinc finger protein 4
  • CpG DNA
KeywordsDNA BINDING PROTEIN / CXXC / DNA / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


zygotic specification of dorsal/ventral axis / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / methyl-CpG binding / negative regulation of Wnt signaling pathway / PDZ domain binding / Wnt signaling pathway / cytoplasmic vesicle / zinc ion binding / cytoplasm
Similarity search - Function
CXXC-type zinc finger protein CXXC4/CXXC5 / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / CXXC-type zinc finger protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, K. / Xu, C. / Tempel, W. / Walker, J.R. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2018
Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CpG DNA
B: CpG DNA
C: CXXC-type zinc finger protein 4
D: CpG DNA
E: CpG DNA
F: CXXC-type zinc finger protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,13917
Polymers25,8776
Non-polymers26211
Water54030
1
A: CpG DNA
B: CpG DNA
C: CXXC-type zinc finger protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0707
Polymers12,9393
Non-polymers1314
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-14 kcal/mol
Surface area7190 Å2
MethodPISA
2
D: CpG DNA
E: CpG DNA
F: CXXC-type zinc finger protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,07010
Polymers12,9393
Non-polymers1317
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-13 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.983, 40.290, 57.760
Angle α, β, γ (deg.)70.980, 86.430, 67.830
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
CpG DNA


Mass: 3663.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide CXXC-type zinc finger protein 4 / Inhibition of the Dvl and axin complex protein


Mass: 5611.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXXC4, IDAX / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9H2H0
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 49.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 30% PEG-1500, 5% MPD, 0.2 M sodium chloride, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→27.24 Å / Num. obs: 13389 / % possible obs: 97.2 % / Redundancy: 2.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.054 / Rrim(I) all: 0.081 / Net I/σ(I): 10.1 / Num. measured all: 28017 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.161.80.597187410570.6530.5590.821.392.6
8.91-27.242.10.053461640.9920.0420.0663288.2

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished model of related protein-DNA complex

Resolution: 2.1→27.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.841 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.196
Details: coot was used for interactive model building. Model geometry was assessed with phenix.molprobity.
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 750 5.6 %thin resolution shells (sftools)
Rwork0.211 ---
obs0.2132 12637 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.52 Å2 / Biso mean: 45.818 Å2 / Biso min: 14.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20.7 Å2-0.78 Å2
2---1.17 Å20.4 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2.1→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms668 972 11 30 1681
Biso mean--39.77 32.8 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0141790
X-RAY DIFFRACTIONr_bond_other_d0.0050.021206
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.4562602
X-RAY DIFFRACTIONr_angle_other_deg1.4743.0112790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.769592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97219.625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36715134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.251511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021333
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02394
X-RAY DIFFRACTIONr_mcbond_it1.7813.003367
X-RAY DIFFRACTIONr_mcbond_other1.7833.001365
X-RAY DIFFRACTIONr_mcangle_it2.4894.488455
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 36 -
Rwork0.301 903 -
all-939 -
obs--92.06 %
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)
13.9792.4752-1.3274.52820.29361.79080.3049-0.3141-0.13590.8907-0.42210.1779-0.0913-0.15640.11720.2808-0.04880.0080.10160.02020.1448-0.6601-0.47166.9319
22.04421.384-0.43717.24350.37482.53770.0707-0.1488-0.15260.0904-0.1255-0.04630.1473-0.07580.05480.1163-0.06490.0030.15130.0390.11210.3908-0.8385.8869
34.0198-0.5037-0.22043.54950.75817.54130.24320.3657-0.2139-0.0952-0.1483-0.08040.32720.0167-0.09490.03710.0235-0.00480.06650.00810.08011.20480.138-6.9295
43.8986-3.0752.00276.1102-0.88311.23930.13370.2436-0.0952-0.4505-0.16220.28830.04390.06550.02860.19060.04660.06990.1127-0.00180.1053-3.99819.6941-29.8204
52.2442-2.69040.56486.8196-0.10552.01910.09450.17850.0805-0.15-0.05590.041-0.1827-0.0559-0.03860.12780.0350.03440.14270.03240.1051-2.856619.9392-28.8634
63.5640.86360.1113.32050.70367.19390.2631-0.24890.39410.0611-0.0846-0.0029-0.41110.0089-0.17840.06440.01160.06370.06650.01390.1031-2.243919.0941-15.8201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C134 - 1002
4X-RAY DIFFRACTION4D1 - 12
5X-RAY DIFFRACTION5E1 - 12
6X-RAY DIFFRACTION6F134 - 1002

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