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- PDB-1g2d: STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (CLONE #2) -

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Basic information

Entry
Database: PDB / ID: 1g2d
TitleSTRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (CLONE #2)
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


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 / response to glucose / BMP signaling pathway / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Griesman, 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, R.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. / Griesman, 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)41,41012
Polymers41,0176
Non-polymers3926
Water4,035224
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)20,7056
Polymers20,5093
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)20,7056
Polymers20,5093
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.100, 105.100, 104.600
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-1001-

HOH

21F-1304-

HOH

31F-1406-

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: 10713.330 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


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, NaCl, Bis-Tris Propane, CoCl2, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2NaCl11
3Bis-Tris Propane11
4CoCl211
Crystal grow
*PLUS
pH: 8
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: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 27, 2000 / Details: Yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 32875 / Num. obs: 358651 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.91 % / Biso Wilson estimate: 31 Å2 / Rsym value: 6.6 / Net I/σ(I): 30.04
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 9 % / Mean I/σ(I) obs: 9.35 / Num. unique all: 3182 / Rsym value: 44.8 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 32875 / Num. measured all: 358651 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.448

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TATA structure of clone #6 solved by MIRAS

Resolution: 2.2→20 Å / Rfactor Rfree error: 0.005 / 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
Rfree0.262 3081 9.8 %RANDOM
Rwork0.225 ---
all-32465 --
obs-31492 94.6 %-
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 1300 6 224 2997
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_d20.1
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_mcbond_it2.461.5
X-RAY DIFFRACTIONx_mcangle_it3.852
X-RAY DIFFRACTIONx_scbond_it3.922
X-RAY DIFFRACTIONx_scangle_it5.952.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 442 9.7 %
Rwork0.362 4110 -
obs--82.2 %
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: 9.8 % / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.6 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_deg20.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
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: 0.397 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.362

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