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- PDB-4m9v: Zfp57 mutant (E182Q) in complex with 5-carboxylcytosine DNA -

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Basic information

Entry
Database: PDB / ID: 4m9v
TitleZfp57 mutant (E182Q) in complex with 5-carboxylcytosine DNA
Components
  • DNA (5'-D(*AP*CP*TP*GP*(1CC)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 / epigenetics / transcription factor / 5-carboxylcytosine / C2H2 Zinc finger / DNA binding / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


epigenetic programing of female pronucleus / epigenetic programming of gene expression / 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 ...epigenetic programing of female pronucleus / epigenetic programming of gene expression / 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 / Zinc finger C2H2 type domain profile. ...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 / MOLECULAR REPLACEMENT / Resolution: 0.969 Å
AuthorsLiu, Y. / Olanrewaju, Y.O. / Zhang, X. / Cheng, X.
CitationJournal: Biochemistry / Year: 2013
Title: DNA recognition of 5-carboxylcytosine by a zfp57 mutant at an atomic resolution of 0.97 angstrom.
Authors: Liu, Y. / Olanrewaju, Y.O. / Zhang, X. / Cheng, X.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 2.0Jun 24, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_ref_seq_dif.details
Revision 2.1Sep 20, 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_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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _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*(1CC)P*GP*GP*CP*AP*AP*T)-3')
C: Zinc finger protein 57
D: DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')
E: DNA (5'-D(*AP*CP*TP*GP*(1CC)P*GP*GP*CP*AP*AP*T)-3')
F: Zinc finger protein 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,33420
Polymers28,2846
Non-polymers1,05114
Water8,503472
1
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*(1CC)P*GP*GP*CP*AP*AP*T)-3')
C: Zinc finger protein 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,72611
Polymers14,1423
Non-polymers5848
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-39 kcal/mol
Surface area7010 Å2
MethodPISA
2
D: DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')
E: DNA (5'-D(*AP*CP*TP*GP*(1CC)P*GP*GP*CP*AP*AP*T)-3')
F: Zinc finger protein 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6089
Polymers14,1423
Non-polymers4666
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-39 kcal/mol
Surface area7030 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-90 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.388, 96.093, 36.408
Angle α, β, γ (deg.)90.00, 113.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules ADBE

#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.: 2 / Source method: obtained synthetically / Details: DNA synthesis
#2: DNA chain DNA (5'-D(*AP*CP*TP*GP*(1CC)P*GP*GP*CP*AP*AP*T)-3')


Mass: 3402.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA synthesis

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Protein , 1 types, 2 molecules CF

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


Mass: 7376.424 Da / Num. of mol.: 2 / Mutation: E182Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zfp57 / Plasmid: pXC1158 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C6P8

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Non-polymers , 5 types, 486 molecules

#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 35% 2-methyl-2,4-pentanediol, 15% polyethylene glycol 8000, 100 mM CaCl2, and 100 mM acetate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 31, 2012
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.969→33.5 Å / Num. obs: 129957 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 8.63 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 0.969→1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.4 / Num. unique all: 12599 / % possible all: 92.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GZN

4gzn


Resolution: 0.969→33.459 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.11 / Stereochemistry target values: ML / Details: FLAT BULK SOLVENT MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.1426 6543 5.04 %RANDOM
Rwork0.1301 ---
obs0.1307 129906 95.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.7 Å2
Refinement stepCycle: LAST / Resolution: 0.969→33.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 898 54 472 2390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092197
X-RAY DIFFRACTIONf_angle_d1.8153190
X-RAY DIFFRACTIONf_dihedral_angle_d26.406919
X-RAY DIFFRACTIONf_chiral_restr0.085338
X-RAY DIFFRACTIONf_plane_restr0.01252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
0.9685-0.97960.28212090.28513681368184
0.9796-0.99110.28622070.2613945394593
0.9911-1.00320.27032040.2554125412595
1.0032-1.01590.25182200.24084025402595
1.0159-1.02920.23052260.21194071407195
1.0292-1.04330.22242090.19094035403595
1.0433-1.05820.20381850.17454122412295
1.0582-1.0740.1672050.164086408695
1.074-1.09080.15962210.14824064406495
1.0908-1.10870.15272070.14164145414595
1.1087-1.12780.14442130.13274104410496
1.1278-1.14830.14932110.12974144414496
1.1483-1.17040.15022150.12844128412896
1.1704-1.19430.13992000.1234124412497
1.1943-1.22030.13612110.11814153415395
1.2203-1.24870.14532480.11874122412297
1.2487-1.27990.12532350.11074127412797
1.2799-1.31450.12882160.11014169416997
1.3145-1.35320.12532580.10864182418297
1.3532-1.39690.12652200.10514208420898
1.3969-1.44680.14332030.1024222422298
1.4468-1.50470.1152560.10274168416897
1.5047-1.57320.12011980.10674213421398
1.5732-1.65610.12392260.0994186418697
1.6561-1.75990.11612440.10444121412197
1.7599-1.89580.12842090.1124187418797
1.8958-2.08650.13332490.12284125412597
2.0865-2.38840.15071990.13064203420397
2.3884-3.00880.13452150.1454182418296
3.0088-33.47920.14512240.13663996399692

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