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- PDB-5wjq: mouseZFP568-ZnF2-11 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5wjq
TitlemouseZFP568-ZnF2-11 in complex with DNA
Components
  • (DNA (28-MER)) x 2
  • Zinc finger protein 568
Keywordsgene regulation/DNA / C2H2 type Zinc fingers / DNA binding / transferase-dna complex / GENE REGULATION / gene regulation-DNA complex
Function / homology
Function and homology information


convergent extension involved in axis elongation / convergent extension involved in neural plate elongation / embryonic placenta morphogenesis / regulation of cell communication / transcription corepressor binding / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription ...convergent extension involved in axis elongation / convergent extension involved in neural plate elongation / embryonic placenta morphogenesis / regulation of cell communication / transcription corepressor binding / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger protein 568
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsPatel, A. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Cell / Year: 2018
Title: DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins.
Authors: Patel, A. / Yang, P. / Tinkham, M. / Pradhan, M. / Sun, M.A. / Wang, Y. / Hoang, D. / Wolf, G. / Horton, J.R. / Zhang, X. / Macfarlan, T. / Cheng, X.
History
DepositionJul 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (28-MER)
B: DNA (28-MER)
D: Zinc finger protein 568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,58718
Polymers50,3223
Non-polymers1,26515
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-79 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.641, 35.239, 81.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-101-

TRS

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Components

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DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (28-MER)


Mass: 8784.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: DNA chain DNA (28-MER)


Mass: 8428.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Protein , 1 types, 1 molecules D

#3: Protein Zinc finger protein 568


Mass: 33109.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Znf568, chato, Zfp568
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E9PYI1

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Non-polymers , 3 types, 46 molecules

#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / Details: 0.2 M calcium acetate 16% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→39.9 Å / Num. obs: 13731 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.933 / Rmerge(I) obs: 0.132 / Net I/σ(I): 17.6
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1328 / CC1/2: 0.933 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V3M

5v3m


Resolution: 2.794→33.865 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.14
RfactorNum. reflection% reflection
Rfree0.263 1239 5 %
Rwork0.1928 --
obs0.1963 13562 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.794→33.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 1142 50 31 3350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083497
X-RAY DIFFRACTIONf_angle_d1.0394946
X-RAY DIFFRACTIONf_dihedral_angle_d19.2821873
X-RAY DIFFRACTIONf_chiral_restr0.054519
X-RAY DIFFRACTIONf_plane_restr0.006445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.794-2.90580.36411420.30732641X-RAY DIFFRACTION100
2.9058-3.0380.38241400.28652615X-RAY DIFFRACTION100
3.038-3.1980.3671420.28962652X-RAY DIFFRACTION98
3.198-3.39820.28411340.22542472X-RAY DIFFRACTION96
3.3982-3.66030.33451380.18612574X-RAY DIFFRACTION98
3.6603-4.02810.24981400.18872652X-RAY DIFFRACTION100
4.0281-4.60980.21821330.16342637X-RAY DIFFRACTION100
4.6098-5.80310.23471410.16112668X-RAY DIFFRACTION100
5.8031-33.86730.20391290.15822627X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 42.3439 Å / Origin y: 4.3969 Å / Origin z: 102.2634 Å
111213212223313233
T0.246 Å20.0274 Å2-0.0179 Å2-0.408 Å20.0066 Å2--0.5205 Å2
L4.8429 °20.8244 °21.3831 °2-1.4269 °2-0.074 °2--1.3151 °2
S-0.2701 Å °0.1663 Å °-0.1429 Å °0.0757 Å °0.0426 Å °-0.2334 Å °0.0365 Å °0.1755 Å °0.1516 Å °
Refinement TLS groupSelection details: all

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