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- PDB-4gzn: Mouse ZFP57 zinc fingers in complex with methylated DNA -

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Basic information

Entry
Database: PDB / ID: 4gzn
TitleMouse ZFP57 zinc fingers in complex with methylated DNA
Components
  • DNA (5'-D(*AP*CP*TP*GP*(5CM)P*GP*GP*CP*AP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')
  • Zinc finger protein 57
KeywordsTRANSCRIPTION/DNA / Zinc Finger / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


epigenetic programing of female pronucleus / double-stranded methylated DNA binding / genomic imprinting / autosome genomic imprinting / epigenetic programming in the zygotic pronuclei / negative regulation of gene expression via chromosomal CpG island methylation / heterochromatin / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding ...epigenetic programing of female pronucleus / double-stranded methylated DNA binding / genomic imprinting / autosome genomic imprinting / epigenetic programming in the zygotic pronuclei / negative regulation of gene expression via chromosomal CpG island methylation / heterochromatin / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
Similarity search - Function
: / Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger ...: / Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / Zinc finger protein 57
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.99 Å
AuthorsLiu, Y. / Zhang, X. / Cheng, X.
CitationJournal: Genes Dev. / Year: 2012
Title: An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence.
Authors: Liu, Y. / Toh, H. / Sasaki, H. / Zhang, X. / Cheng, X.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')
B: DNA (5'-D(*AP*CP*TP*GP*(5CM)P*GP*GP*CP*AP*AP*T)-3')
C: Zinc finger protein 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2559
Polymers13,7883
Non-polymers4666
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-35 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.218, 60.641, 96.119
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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DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')


Mass: 3363.224 Da / Num. of mol.: 1 / Fragment: zinc finger domain, UNP residues 137-195 / Source method: obtained synthetically / Details: The DNA sequence occurs naturally in mouse.
#2: DNA chain DNA (5'-D(*AP*CP*TP*GP*(5CM)P*GP*GP*CP*AP*AP*T)-3')


Mass: 3372.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The DNA sequence occurs naturally in mouse.

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Protein , 1 types, 1 molecules C

#3: Protein Zinc finger protein 57 / Zfp-57


Mass: 7053.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zfp57 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C6P8

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Non-polymers , 5 types, 263 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% MPD, 15% PEG8000, 100mM CaCl2 and 100 mM acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 12, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.99→48.6 Å / Num. all: 802194 / Num. obs: 802194 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
0.99-1.033.90.4042.83816158.9
1.03-1.077.60.3295691185.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 0.99→19.683 Å / SU ML: 0.07 / σ(F): 1.02 / Phase error: 10.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1396 5979 5.07 %RANDOM
Rwork0.1314 ---
obs0.1319 117899 93.21 %-
all-126488 --
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.152 Å2 / ksol: 0.471 e/Å3
Displacement parametersBiso mean: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.4432 Å2-0 Å20 Å2
2---0.595 Å2-0 Å2
3---0.1519 Å2
Refinement stepCycle: LAST / Resolution: 0.99→19.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms473 447 23 257 1200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091203
X-RAY DIFFRACTIONf_angle_d1.7991776
X-RAY DIFFRACTIONf_dihedral_angle_d25.061601
X-RAY DIFFRACTIONf_chiral_restr0.075200
X-RAY DIFFRACTIONf_plane_restr0.01137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9902-1.02560.31753950.32516246X-RAY DIFFRACTION52
1.0256-1.06660.19635650.19710204X-RAY DIFFRACTION85
1.0666-1.11520.14035880.127911707X-RAY DIFFRACTION97
1.1152-1.1740.12076070.104511909X-RAY DIFFRACTION99
1.174-1.24750.11516550.103111877X-RAY DIFFRACTION99
1.2475-1.34380.11276720.104711958X-RAY DIFFRACTION100
1.3438-1.4790.11556520.103211948X-RAY DIFFRACTION100
1.479-1.69290.12286640.10711983X-RAY DIFFRACTION100
1.6929-2.13250.13825740.12712091X-RAY DIFFRACTION100
2.1325-19.68670.15276070.152111997X-RAY DIFFRACTION100

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