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- PDB-5v3j: mouseZFP568-ZnF1-10 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5v3j
TitlemouseZFP568-ZnF1-10 in complex with DNA
Components
  • (DNA (26-MER)) x 2
  • Zinc finger protein 568
Keywordstransferase/dna / C2H2 type Zinc fingers / DNA binding / transferase-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 / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
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
DNA / DNA (> 10) / Zinc finger protein 568
Similarity search - Component
Biological speciesMus musculus (house mouse)
Mus (mice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.064 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 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
DepositionMar 7, 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 1.3Mar 6, 2024Group: 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 / refine / struct_conn
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_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_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_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 / _refine.pdbx_starting_model / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (26-MER)
B: DNA (26-MER)
C: DNA (26-MER)
D: DNA (26-MER)
E: Zinc finger protein 568
F: Zinc finger protein 568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,57830
Polymers96,9776
Non-polymers1,60124
Water6,449358
1
A: DNA (26-MER)
B: DNA (26-MER)
E: Zinc finger protein 568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,28915
Polymers48,4893
Non-polymers80112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-70 kcal/mol
Surface area21990 Å2
MethodPISA
2
C: DNA (26-MER)
D: DNA (26-MER)
F: Zinc finger protein 568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,28915
Polymers48,4893
Non-polymers80112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-69 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.787, 65.706, 73.022
Angle α, β, γ (deg.)100.52, 104.25, 97.25
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 2 types, 4 molecules ACBD

#1: DNA chain DNA (26-MER)


Mass: 8167.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus (mice)
#2: DNA chain DNA (26-MER)


Mass: 7811.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus (mice)

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Protein , 1 types, 2 molecules EF

#3: Protein Zinc finger protein 568


Mass: 32510.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Znf568, chato, Zfp568 / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9PYI1

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Non-polymers , 4 types, 382 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 8% Tacsimate(pH 5.0) and 20% (W/V) PEG3350

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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: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→34.5 Å / Num. obs: 58341 / % possible obs: 97.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.425 / Χ2: 1.012 / Net I/σ(I): 12.9
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5723 / CC1/2: 0.941 / Rpim(I) all: 0.425 / Χ2: 1.002 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.064→34.503 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 1996 3.43 %
Rwork0.192 --
obs0.1936 58177 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.064→34.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4199 2123 38 358 6718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086712
X-RAY DIFFRACTIONf_angle_d1.0499486
X-RAY DIFFRACTIONf_dihedral_angle_d22.2773623
X-RAY DIFFRACTIONf_chiral_restr0.0491002
X-RAY DIFFRACTIONf_plane_restr0.007877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0637-2.11530.40611340.32373794X-RAY DIFFRACTION93
2.1153-2.17250.37041410.29364001X-RAY DIFFRACTION97
2.1725-2.23640.35491430.28634013X-RAY DIFFRACTION97
2.2364-2.30860.3731420.30143992X-RAY DIFFRACTION97
2.3086-2.39110.31391410.26213980X-RAY DIFFRACTION98
2.3911-2.48680.32271440.25274046X-RAY DIFFRACTION98
2.4868-2.59990.27381430.23474057X-RAY DIFFRACTION98
2.5999-2.7370.26951440.22514019X-RAY DIFFRACTION98
2.737-2.90840.28791430.23324058X-RAY DIFFRACTION98
2.9084-3.13280.26811440.22524046X-RAY DIFFRACTION98
3.1328-3.44780.22631430.1873973X-RAY DIFFRACTION96
3.4478-3.94610.21911440.15934050X-RAY DIFFRACTION98
3.9461-4.96930.20941460.14884103X-RAY DIFFRACTION99
4.9693-34.50750.13581440.13564049X-RAY DIFFRACTION98
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)
11.6961-1.41341.36921.4808-0.52072.4832-0.104-0.8893-0.74880.7369-0.3754-0.3730.31030.57680.35250.82360.0112-0.1450.66850.35010.7611-25.2998-2.44146.0292
25.4409-1.28250.68385.5335-4.76377.31440.3751-0.0786-0.2653-0.2092-0.1418-0.16020.0836-0.1683-0.23690.3162-0.0517-0.00170.2321-0.03550.2269-34.775115.4819-19.1021
30.2828-0.33111.06983.4665-4.34017.28120.12640.5565-0.0488-0.103-0.04010.2101-0.1084-0.0935-0.03970.51810.13530.15580.62080.07820.3619-38.721427.578-41.8916
49.27025.8459-6.733.8113-4.14064.9730.80.2610.9313-0.0245-0.2806-0.3038-0.94531.0692-0.56870.76680.09240.19330.86510.240.486-37.133535.4916-41.1239
56.0337-2.54313.92972.9499-1.91518.21880.2405-0.2209-0.0644-0.09360.07880.00590.2899-0.344-0.2780.2356-0.02060.05820.22330.00380.2515-34.991118.3571-21.846
65.62630.30830.7084.8951-3.30328.21320.2584-0.7228-0.46380.59580.38380.15710.4473-0.2942-0.57360.7107-0.0265-0.14130.47990.25020.7285-25.8955-1.84574.9908
76.31525.0153-0.65544.9304-2.07856.2688-0.3838-0.11971.1855-0.7377-0.7493-1.2099-0.70940.30471.11440.77430.16470.01930.74640.05861.1996-11.57578.3019-31.3302
82.1818-0.64580.24531.7873-0.60412.07570.30110.2511-0.0031-0.1813-0.2188-0.23950.0380.1785-0.08180.2831-0.0090.02830.2940.00560.3488-32.425118.2794-25.3936
91.2233-0.55221.48757.9393-2.082.03110.1583-0.0175-0.07690.4566-0.20810.8862-0.0114-0.07250.06160.4645-0.04540.08440.54270.10040.5811-35.9392-6.45544.2358
100.08640.1259-0.45141.1919-1.0953.0037-0.53870.98950.9572-0.50820.13580.0717-0.5662-0.2083-0.00110.7951-0.1316-0.35560.88230.53880.825-9.418152.999-30.649
113.71150.0666-1.0215.8202-2.3717.5106-0.0195-0.321-0.31790.30990.05250.16660.10030.11390.00620.10030.00170.00480.2935-0.00160.2215-1.663428.05011.8803
123.7208-0.2731-0.83856.8637-4.37926.33670.1289-0.2147-0.0659-0.1268-0.04250.143-0.16160.3483-0.0140.1896-0.03340.02850.2309-0.09320.1777-1.178832.0354-2.2881
130.64580.1132-1.36833.3663-3.32325.702-0.34990.92931.0685-0.3931-0.0418-0.1318-0.12790.2143-0.16060.9115-0.151-0.34581.05990.6630.9892-8.993557.8937-35.7675
144.64744.97125.01015.46155.43575.4324-0.3376-0.65761.39090.19360.3861-0.9839-1.28320.3673-0.16150.95040.0604-0.11580.8714-0.26861.4021-17.642253.54313.9214
157.9705-1.65292.12923.2672-0.26757.1768-0.0704-0.5245-0.44960.2006-0.13420.73910.0932-0.43990.18070.2220.03060.08410.4570.02170.4694-19.680231.50336.729
162.1408-0.04350.59741.5657-0.15182.4306-0.0529-0.09030.0836-0.10170.04990.0466-0.1998-0.065-0.01410.2113-0.00870.03050.25110.00450.2508-2.569435.7605-4.7125
173.0855-0.90810.91651.99370.89213.2617-0.37631.50810.5959-0.30030.2830.07550.27240.1790.11940.7989-0.2368-0.1781.10590.38890.6459-4.686448.963-35.011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 26 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 26 )
7X-RAY DIFFRACTION7chain 'E' and (resid 362 through 388 )
8X-RAY DIFFRACTION8chain 'E' and (resid 389 through 598 )
9X-RAY DIFFRACTION9chain 'E' and (resid 599 through 638 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 15 )
11X-RAY DIFFRACTION11chain 'C' and (resid 16 through 26 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 15 )
13X-RAY DIFFRACTION13chain 'D' and (resid 16 through 26 )
14X-RAY DIFFRACTION14chain 'F' and (resid 362 through 387 )
15X-RAY DIFFRACTION15chain 'F' and (resid 388 through 430 )
16X-RAY DIFFRACTION16chain 'F' and (resid 431 through 570 )
17X-RAY DIFFRACTION17chain 'F' and (resid 571 through 638 )

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