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- PDB-1g2f: STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (TATAZF;CLONE #6) -

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Basic information

Entry
Database: PDB / ID: 1g2f
TitleSTRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (TATAZF;CLONE #6)
Components
  • 5'-D(*GP*AP*CP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*AP*G)-3'
  • 5'-D(*TP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*GP*TP*CP*C)-3'
  • TATA BOX ZINC FINGER PROTEIN
KeywordsTRANSCRIPTION/DNA / phage display / zinc finger-DNA complex / TATA box / Cys2His2 / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to mycophenolic acid / cellular response to heparin / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to mycophenolic acid / cellular response to heparin / 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 / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / cellular response to organic substance / positive regulation of smooth muscle cell migration / skeletal muscle cell differentiation / locomotor rhythm / estrous cycle / T cell differentiation / long-term memory / RNA polymerase II core promoter sequence-specific DNA binding / BMP signaling pathway / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / regulation of long-term neuronal synaptic plasticity / positive regulation of smooth muscle cell proliferation / negative regulation of canonical Wnt signaling pathway / circadian regulation of gene expression / response to insulin / cellular response to gamma radiation / positive regulation of miRNA transcription / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / response to hypoxia / learning or memory / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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 / MIR / Resolution: 2 Å
AuthorsWolfe, S.A. / Grant, R.A. / Elrod-Erickson, M. / Pabo, C.O.
Citation
Journal: Structure / Year: 2001
Title: Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes.
Authors: Wolfe, S.A. / Grant, R.A. / Elrod-Erickson, M. / Pabo, C.O.
#1: Journal: Science / Year: 1997
Title: A General Strategy for Selecting High-Affinity Zinc Finger Proteins for Diverse DNA Target Sites
Authors: Greisman, H.A. / Pabo, C.O.
#2: Journal: Structure / Year: 1996
Title: Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions
Authors: Elrod-Erickson, M. / Rould, M.A. / Nekludova, L. / Pabo, C.O.
#3: Journal: J.Mol.Biol. / Year: 1999
Title: Analysis of Zinc Fingers Optimized via Phage Display: Evaluating the Utility of a Recognition Code
Authors: Wolfe, S.A. / Greisman, H.A. / Ramm, E.I. / Pabo, C.O.
History
DepositionOct 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*AP*CP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*AP*G)-3'
B: 5'-D(*TP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*GP*TP*CP*C)-3'
D: 5'-D(*GP*AP*CP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*AP*G)-3'
E: 5'-D(*TP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*GP*TP*CP*C)-3'
C: TATA BOX ZINC FINGER PROTEIN
F: TATA BOX ZINC FINGER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,24812
Polymers40,8556
Non-polymers3926
Water4,089227
1
A: 5'-D(*GP*AP*CP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*AP*G)-3'
B: 5'-D(*TP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*GP*TP*CP*C)-3'
C: TATA BOX ZINC FINGER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6246
Polymers20,4283
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-D(*GP*AP*CP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*AP*G)-3'
E: 5'-D(*TP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*GP*TP*CP*C)-3'
F: TATA BOX ZINC FINGER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6246
Polymers20,4283
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.800, 104.800, 104.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11F-1101-

HOH

21F-1185-

HOH

31F-1301-

HOH

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Components

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


Mass: 4980.269 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*GP*TP*CP*C)-3'


Mass: 4815.126 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein TATA BOX ZINC FINGER PROTEIN


Mass: 10632.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: PROTEIN SELECTED BY PHAGE DISPLAY; / Plasmid: PET21D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P08046
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.97 Å3/Da / Density % sol: 69.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400; NaCl; Bis-Tris Propane; CoCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2NaClSodium chloride11
3Bis-Tris Propane11
4CoCl211
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
21.1 mMDNA1drop
3100 mMBis-Tris-propane1drop
430-35 %PEG4001reservoir
5100-200 mM1reservoirNaCl
610-50 mMBis-Tris propane1reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2000 / Details: KOHZU double crystal monochromator
RadiationMonochromator: KOHZU double crystal monochormator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 43331 / Num. obs: 43331 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.46 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 7.4 / Net I/σ(I): 28.52
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.14 % / Mean I/σ(I) obs: 6.58 / Num. unique all: 3595 / Rsym value: 56.7 / % possible all: 96.2
Reflection
*PLUS
Num. measured all: 496779 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.567

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: Zif268

Resolution: 2→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 / σ(I): 0
Stereochemistry target values: Xplor parameter set: param19.sol;parhcsdx.pro;dna-rna.param
RfactorNum. reflection% reflectionSelection details
Rfree0.263 4029 10 %RANDOM
Rwork0.233 ---
all-43331 --
obs-40380 92.2 %-
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 1300 6 227 2980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d20.5
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_mcbond_it2.081.5
X-RAY DIFFRACTIONx_mcangle_it3.472
X-RAY DIFFRACTIONx_scbond_it3.572
X-RAY DIFFRACTIONx_scangle_it5.722.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 585 10.3 %
Rwork0.365 5087 -
obs--78.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.376 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.365

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