[English] 日本語
Yorodumi
- PDB-2drp: THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXT... -

+
Open data


ID or keywords:

Loading...

-
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 / tracheal outgrowth, open tracheal system / regulation of embryonic cell shape / myoblast fate specification / follicle cell of egg chamber development / dorsal appendage formation / positive regulation of border follicle cell migration / polytene chromosome / peripheral nervous system development / positive regulation of DNA binding / 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 / nucleus / metal ion binding
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. / Zinc finger C2H2 superfamily ...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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more