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- PDB-1f2i: COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1f2i
TitleCOCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA
Components
  • 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
  • FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
KeywordsTRANSCRIPTION/DNA / zinc finger / dimer / protein-DNA complex / cooperativity / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of protein sumoylation / glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...regulation of protein sumoylation / glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / locomotor rhythm / skeletal muscle cell differentiation / T cell differentiation / BMP signaling pathway / response to glucose / estrous cycle / positive regulation of chemokine production / regulation of neuron apoptotic process / response to ischemia / positive regulation of interleukin-1 beta production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / circadian regulation of gene expression / cellular response to gamma radiation / negative regulation of canonical Wnt signaling pathway / response to insulin / positive regulation of miRNA transcription / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / 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) / Early growth response protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsWang, B.S. / Grant, R.A. / Pabo, C.O.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Selected peptide extension contacts hydrophobic patch on neighboring zinc finger and mediates dimerization on DNA.
Authors: Wang, B.S. / Grant, R.A. / Pabo, C.O.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences
Authors: Wang, B.S. / Pabo, C.O.
History
DepositionMay 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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

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Assembly

Deposited unit
A: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
B: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
C: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
D: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
E: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
F: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
G: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
H: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
I: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
J: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
K: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
L: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,17524
Polymers78,39012
Non-polymers78512
Water5,747319
1
A: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
B: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
G: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
H: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3928
Polymers26,1304
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
D: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
I: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
J: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3928
Polymers26,1304
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
F: 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
K: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
L: FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3928
Polymers26,1304
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.300, 86.300, 133.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Cell settingtrigonal
Space group name H-MP31
DetailsThe biological assembly is a dimer constructed from chains A, B, G, and H / The biological assembly is a dimer constructed from chains C, D, I, and J / The biological assembly is a dimer constructed from chains E, F, K, and L

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Components

#1: DNA chain
5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'


Mass: 4281.780 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Protein
FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12 / EARLY GROWTH RESPONSE 1 / EGR-1 / KROX-24 PROTEIN / ZIF268


Mass: 8783.174 Da / Num. of mol.: 6 / Fragment: ZIF12 CONTAINS ZINC FINGERS 1 AND 2 OF ZIF268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GENE FOR ZIF12 / Plasmid: PET-21D / Production host: Escherichia coli (E. coli) / References: UniProt: P08046
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, NaCl, MgCl2, MES, pH 6.2, VAPOR DIFFUSION, HANGING DROP at 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCl11
2MgCl211
3MES11
4PEG 400011
5PEG 400012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.1 mMprotein1drop
21.5 mMDNA1dropduplex
30.4 M1dropNaCl
413-20 %(w/v)PEG40001reservoir
550-150 mM1reservoir
610 mM1reservoirMgCl2
750 mMMES1reservoirpH6.2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11251
21251
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X4A21.0093
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEMay 23, 1999
ADSC QUANTUM 42CCDMar 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.00931
ReflectionResolution: 2.35→20 Å / Num. all: 45864 / Num. obs: 45805 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4 % / Rmerge(I) obs: 0.345 / Num. unique all: 4571 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 191628
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
DMmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementResolution: 2.35→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3849 10.1 %RANDOM
Rwork0.21 ---
all0.25 46014 --
obs0.215 38060 82.6 %-
Displacement parametersBiso mean: 41.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 1704 12 319 5329
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_deg1.16
X-RAY DIFFRACTIONx_mcbond_it2.810.75
X-RAY DIFFRACTIONx_mcangle_it4.51
X-RAY DIFFRACTIONx_scbond_it4.631
X-RAY DIFFRACTIONx_scangle_it7.031.25
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 528 11 %
Rwork0.331 4274 -
obs--62.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_mcbond_it0.75
X-RAY DIFFRACTIONx_scbond_it1
X-RAY DIFFRACTIONx_mcangle_it1
X-RAY DIFFRACTIONx_scangle_it1.25
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / % reflection Rfree: 11 % / Rfactor Rwork: 0.331

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