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- PDB-2drp: THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXT... -

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Basic information

Entry
Database: PDB / ID: 2drp
TitleTHE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXTENSION TO THE RULES FOR ZINC-FINGER/DNA RECOGNITION
Components
  • DNA (5'-D(*CP*TP*AP*AP*TP*AP*AP*GP*GP*AP*TP*AP*AP*CP*GP*TP*C P*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*GP*AP*CP*GP*TP*TP*AP*TP*CP*CP*TP*TP*AP*T P*TP*A)-3')
  • PROTEIN (TRAMTRACK DNA-BINDING DOMAIN)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


dorsal trunk growth, open tracheal system / regulation of compound eye cone cell fate specification / R1/R6 development / compound eye corneal lens morphogenesis / branch fusion, open tracheal system / regulation of tube size, open tracheal system / chitin-based cuticle development / compound eye cone cell differentiation / R7 cell development / branching involved in open tracheal system development ...dorsal trunk growth, open tracheal system / regulation of compound eye cone cell fate specification / R1/R6 development / compound eye corneal lens morphogenesis / branch fusion, open tracheal system / regulation of tube size, open tracheal system / chitin-based cuticle development / compound eye cone cell differentiation / R7 cell development / branching involved in open tracheal system development / regulation of embryonic cell shape / tracheal outgrowth, open tracheal system / myoblast fate specification / dorsal appendage formation / follicle cell of egg chamber development / positive regulation of border follicle cell migration / polytene chromosome / peripheral nervous system development / transcription repressor complex / promoter-specific chromatin binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of cell shape / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
: / Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. ...: / Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein tramtrack, beta isoform
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsFairall, L. / Schwabe, J.W.R. / Chapman, L. / Finch, J.T. / Rhodes, D.
Citation
Journal: Nature / Year: 1993
Title: The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition.
Authors: Fairall, L. / Schwabe, J.W. / Chapman, L. / Finch, J.T. / Rhodes, D.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Sequence-Specific Binding by a Two Zinc-Finger Peptide from the Drosophila Melanogaster Tramtrack Protein
Authors: Fairall, L. / Harrison, S.D. / Travers, A.A. / Rhodes, D.
#2: Journal: Embo J. / Year: 1990
Title: The Tramtrack Gene Encodes a Drosophila Finger Protein that Interacts with the ftz Transcriptional Regulatory Region and Shows a Novel Embryonic Expression Pattern
Authors: Harrison, S.D. / Travers, A.A.
#3: Journal: Nucleic Acids Res. / Year: 1988
Title: Identification of the Binding Sites for Potential Regulatory Proteins in the Upstream Enhancer Element of the Drosophila Fushi Tarazu Gene
Authors: Harrison, S.D. / Travers, A.A.
History
DepositionJun 6, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*TP*AP*AP*TP*AP*AP*GP*GP*AP*TP*AP*AP*CP*GP*TP*C P*CP*G)-3')
C: DNA (5'-D(*TP*CP*GP*GP*AP*CP*GP*TP*TP*AP*TP*CP*CP*TP*TP*AP*T P*TP*A)-3')
E: DNA (5'-D(*CP*TP*AP*AP*TP*AP*AP*GP*GP*AP*TP*AP*AP*CP*GP*TP*C P*CP*G)-3')
F: DNA (5'-D(*TP*CP*GP*GP*AP*CP*GP*TP*TP*AP*TP*CP*CP*TP*TP*AP*T P*TP*A)-3')
A: PROTEIN (TRAMTRACK DNA-BINDING DOMAIN)
D: PROTEIN (TRAMTRACK DNA-BINDING DOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,59810
Polymers39,3366
Non-polymers2624
Water1,02757
1
B: DNA (5'-D(*CP*TP*AP*AP*TP*AP*AP*GP*GP*AP*TP*AP*AP*CP*GP*TP*C P*CP*G)-3')
C: DNA (5'-D(*TP*CP*GP*GP*AP*CP*GP*TP*TP*AP*TP*CP*CP*TP*TP*AP*T P*TP*A)-3')
A: PROTEIN (TRAMTRACK DNA-BINDING DOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7995
Polymers19,6683
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*CP*TP*AP*AP*TP*AP*AP*GP*GP*AP*TP*AP*AP*CP*GP*TP*C P*CP*G)-3')
F: DNA (5'-D(*TP*CP*GP*GP*AP*CP*GP*TP*TP*AP*TP*CP*CP*TP*TP*AP*T P*TP*A)-3')
D: PROTEIN (TRAMTRACK DNA-BINDING DOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7995
Polymers19,6683
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.700, 64.600, 117.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 5837.812 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*CP*GP*GP*AP*CP*GP*TP*TP*AP*TP*CP*CP*TP*TP*AP*T P*TP*A)-3')


Mass: 5785.757 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein PROTEIN (TRAMTRACK DNA-BINDING DOMAIN)


Mass: 8044.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P17789
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXPRESSED CONSTRUCT IS NUMBERED 104 - 166 CORRESPONDING TO AMINO ACIDS 499 - 561 IN THE INTACT ...THE EXPRESSED CONSTRUCT IS NUMBERED 104 - 166 CORRESPONDING TO AMINO ACIDS 499 - 561 IN THE INTACT PROTEIN. RESIDUES 101 - 103 ARE FROM THE EXPRESSION VECTOR. THE DNA DUPLEX IS NUMBERED 1 - 19 AND 21 - 39.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growMethod: small tubes / pH: 6 / Details: pH 6.00, SMALL TUBES / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MES11
4NACL11
5SPERMINE11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMMES1reservoir
25-20 mM1reservoirNaCl
31.75-3.5 mMspermine1reservoir
41
51

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. all: 43552 / % possible obs: 99.2 %
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 11994 / % possible obs: 99.2 % / Rmerge(I) obs: 0.056

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.193 --
obs0.193 11994 99.2 %
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 1542 4 57 2670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 6 Å / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.76

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