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- PDB-3qmc: Structural Basis of Selective Binding of Nonmethylated CpG Island... -

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Basic information

Entry
Database: PDB / ID: 3qmc
TitleStructural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of CFP1
Components
  • 5'-D(*GP*CP*CP*AP*CP*CP*GP*CP*TP*GP*GP*C)-3'
  • 5'-D(*GP*CP*CP*AP*GP*CP*GP*GP*TP*GP*GP*C)-3'
  • CpG-binding protein
KeywordsDNA BINDING PROTEIN/DNA / Structural Genomics Consortium / SGC / CXXC-type Zn finger / DNA binding / unmethylated CpG motifs / nucleus speckle / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


unmethylated CpG binding / XBP1(S) activates chaperone genes / Set1C/COMPASS complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / cis-regulatory region sequence-specific DNA binding / methylated histone binding / nuclear matrix / nuclear speck / regulation of DNA-templated transcription ...unmethylated CpG binding / XBP1(S) activates chaperone genes / Set1C/COMPASS complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / cis-regulatory region sequence-specific DNA binding / methylated histone 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
DNA / DNA (> 10) / CXXC-type zinc finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLam, R. / Xu, C. / Bian, C.B. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / 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 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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*CP*CP*GP*CP*TP*GP*GP*C)-3'
C: 5'-D(*GP*CP*CP*AP*GP*CP*GP*GP*TP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9885
Polymers16,8573
Non-polymers1312
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-13 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.545, 75.016, 126.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#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: CXXC1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q9P0U4
#2: DNA chain 5'-D(*GP*CP*CP*AP*CP*CP*GP*CP*TP*GP*GP*C)-3'


Mass: 3624.356 Da / Num. of mol.: 1 / Fragment: DNA (Nonmethylated CpG Island) / Source method: obtained synthetically
Details: DNA was purchased from Integrated DNA Technologies, Inc.
#3: DNA chain 5'-D(*GP*CP*CP*AP*GP*CP*GP*GP*TP*GP*GP*C)-3'


Mass: 3704.404 Da / Num. of mol.: 1 / Fragment: DNA (Nonmethylated CpG Island) / Source method: obtained synthetically
Details: DNA was purchased from Integrated DNA Technologies, Inc.
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M CaCl2, 28% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Jul 21, 2010
Details: Rosenbaum-Rock high-resolution double-crystal monochromator
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 8874 / % possible obs: 100 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.067 / Χ2: 1.089 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.188.50.4938670.944100
2.18-2.268.90.4238630.949100
2.26-2.378.90.318820.962100
2.37-2.498.90.228500.968100
2.49-2.658.90.1448791.013100
2.65-2.858.90.1098701.064100
2.85-3.148.80.0739071.102100
3.14-3.598.80.0458701.039100
3.59-4.528.60.059171.088100
4.52-5080.049691.76499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å28.29 Å
Translation3.5 Å28.29 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3QMB

3qmb


Resolution: 2.1→37.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.738 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 418 4.7 %RANDOM
Rwork0.2142 ---
obs0.2159 8842 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 125.73 Å2 / Biso mean: 53.3165 Å2 / Biso min: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms412 486 2 22 922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021969
X-RAY DIFFRACTIONr_angle_refined_deg1.6052.5771398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.341554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12319.56523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.461583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2181510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02582
X-RAY DIFFRACTIONr_mcbond_it0.5481.5264
X-RAY DIFFRACTIONr_mcangle_it0.9812413
X-RAY DIFFRACTIONr_scbond_it1.6443705
X-RAY DIFFRACTIONr_scangle_it2.614.5984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1540.275250.24257863594.961
2.154-2.2130.292460.231581627100
2.213-2.2770.267260.23587613100
2.277-2.3460.28320.236560592100
2.346-2.4230.342250.22853456099.821
2.423-2.5080.293220.254554576100
2.508-2.6020.265200.244500520100
2.602-2.7080.327190.245517536100
2.708-2.8270.282200.273473493100
2.827-2.9650.386200.288448468100
2.965-3.1240.203200.244457477100
3.124-3.3120.273210.189406427100
3.312-3.5390.203250.198374399100
3.539-3.8190.18170.183374391100
3.819-4.1790.189260.172325351100
4.179-4.6660.22590.166315324100
4.666-5.3730.333180.181282300100
5.373-6.5480.121130.196236249100
6.548-9.1220.32880.222192200100
9.122-37.5080.24960.242131137100
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)
14.13150.18261.16191.641.41556.24650.0664-0.0727-0.06770.06350.1555-0.02320.2242-0.0727-0.22190.0843-0.042-0.02480.2360.03010.0621-4.294-11.05221.881
26.47157.0417-0.128723.53953.3867.60450.7173-0.4545-0.318-0.0375-1.0693-0.20210.4846-0.26680.3520.4755-0.158-0.08670.30440.05390.1713-4.777-11.9188.643
33.79453.8902-0.664310.8017-1.7294.22950.0106-0.3801-0.3964-0.929-0.2203-0.50040.0408-0.23540.20970.2735-0.1088-0.01490.18910.03720.1754-3.767-12.6467.784
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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