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- PDB-3qmi: Structural Basis of Selective Binding of Non-Methylated CpG islan... -

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Basic information

Entry
Database: PDB / ID: 3qmi
TitleStructural Basis of Selective Binding of Non-Methylated CpG islands (DNA-ACGT) by the CXXC Domain of CFP1
Components
  • 5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3'
  • CpG-binding protein
KeywordsDNA BINDING PROTEIN/DNA / Structural Genomics Consortium / SGC / DNA BINDING / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


unmethylated CpG binding / XBP1(S) activates chaperone genes / Set1C/COMPASS complex / histone H3K4me3 reader activity / Formation of WDR5-containing histone-modifying complexes / : / histone methyltransferase complex / cis-regulatory region sequence-specific DNA binding / nuclear matrix / nuclear speck ...unmethylated CpG binding / XBP1(S) activates chaperone genes / Set1C/COMPASS complex / histone H3K4me3 reader activity / Formation of WDR5-containing histone-modifying complexes / : / histone methyltransferase complex / cis-regulatory region sequence-specific DNA binding / nuclear matrix / nuclear speck / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
CpG binding protein, C-terminal / CpG binding protein C-terminal domain / Spp1/CFP1 / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...CpG binding protein, C-terminal / CpG binding protein C-terminal domain / Spp1/CFP1 / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / DNA / DNA (> 10) / CXXC-type zinc finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXu, C. / Bian, C. / MacKenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2011
Title: The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain.
Authors: Xu, C. / Bian, C. / Lam, R. / Dong, A. / Min, J.
History
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CpG-binding protein
B: 5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3'
C: 5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2938
Polymers16,8553
Non-polymers4385
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-26 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.624, 75.009, 125.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein CpG-binding protein / CXXC-type zinc finger protein 1 / PHD finger and CXXC domain-containing protein 1


Mass: 9527.962 Da / Num. of mol.: 1 / Fragment: CXXC-type Zn finger, residues 161-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP1, CGBP, CXXC1, PCCX1, PHF18 / Plasmid: BL21-V2R-pRARE2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9P0U4
#2: DNA chain 5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3'


Mass: 3663.392 Da / Num. of mol.: 2 / Fragment: DNA (nonmethylated CpG island) / Source method: obtained synthetically

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Non-polymers , 4 types, 38 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.14 Å3/Da / Density % sol: 42.65 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 8362

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Processing

SoftwareName: REFMAC / Version: 5.5.0110 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QMB

3qmb


Resolution: 2.1→37.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.463 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 420 4.8 %RANDOM
Rwork0.207 ---
obs0.209 8362 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms402 486 21 33 942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3612.5961394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.157551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59520.47621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1931578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.281158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5641.5256
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2312399
X-RAY DIFFRACTIONr_scbond_it3.5593714
X-RAY DIFFRACTIONr_scangle_it4.6794.5995
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 25 -
Rwork0.278 558 -
obs--91.67 %
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)
13.31280.2027-0.40251.50180.7676.2860.0267-0.1913-0.04380.04940.12710.02740.2696-0.0638-0.15380.0237-0.0341-0.01620.21330.03320.0568-4.1023-11.013521.8801
22.91022.4324-0.55775.7273-1.83781.62080.1374-0.1652-0.1359-0.5314-0.2705-0.1659-0.0224-0.11120.13310.2457-0.0432-0.00720.20840.00170.1255-3.1161-12.62017.6954
31.50391.5769-0.48839.0857-0.31381.01010.20620.0148-0.00480.0364-0.27030.07670.0911-0.08650.06410.1487-0.1012-0.0210.1585-0.00370.0441-4.1469-11.8698.4577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999

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