[English] 日本語
Yorodumi
- PDB-2r5z: Structure of Scr/Exd complex bound to a DNA sequence derived from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r5z
TitleStructure of Scr/Exd complex bound to a DNA sequence derived from the fkh gene
Components
  • DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DAP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DGP*DGP*DCP*DTP*DG)-3')
  • DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DTP*DTP*DAP*DGP*DAP*DG)-3')
  • Homeobox protein extradenticle
  • Homeotic protein Sex combs reducedHomeosis
KeywordsTRANSCRIPTION/DNA / Homeodomain / homeotic proteins / specificity / Developmental protein / DNA-binding / Homeobox / Nucleus / Transcription / Transcription regulation / Transcription-DNA COMPLEX
Function / homology
Function and homology information


sex comb development / salivary gland boundary specification / oenocyte development / somatic muscle development / eye development / regulation of cell fate specification / peripheral nervous system development / anterior/posterior pattern specification / midgut development / transcription factor binding ...sex comb development / salivary gland boundary specification / oenocyte development / somatic muscle development / eye development / regulation of cell fate specification / peripheral nervous system development / anterior/posterior pattern specification / midgut development / transcription factor binding / neuron development / embryonic organ development / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / brain development / RNA polymerase II transcription regulator complex / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox KN domain / Homeobox KN domain / Homeobox domain, metazoa / Homeobox, conserved site ...PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox KN domain / Homeobox KN domain / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeotic protein Sex combs reduced / Homeobox protein extradenticle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAggarwal, A.K. / Passner, J.M. / Jain, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Functional specificity of a Hox protein mediated by the recognition of minor groove structure
Authors: Joshi, R. / Passner, J.M. / Rohs, R. / Jain, R. / Sosinsky, A. / Crickmore, M.A. / Jacob, V. / Aggarwal, A.K. / Honig, B. / Mann, R.S.
History
DepositionSep 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 20, 2021Group: Database references / Polymer sequence / Source and taxonomy
Category: database_2 / entity_poly ...database_2 / entity_poly / pdbx_entity_src_syn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_target_identifier / _struct_ref_seq_dif.details
Revision 2.1Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DAP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DGP*DGP*DCP*DTP*DG)-3')
D: DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DTP*DTP*DAP*DGP*DAP*DG)-3')
A: Homeotic protein Sex combs reduced
B: Homeobox protein extradenticle


Theoretical massNumber of molelcules
Total (without water)30,7874
Polymers30,7874
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.840, 92.600, 78.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: DNA chain DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DAP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DGP*DGP*DCP*DTP*DG)-3')


Mass: 6132.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: PDB-2R5Y
#2: DNA chain DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DTP*DTP*DAP*DGP*DAP*DG)-3')


Mass: 6132.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: PDB-2R5Y
#3: Protein Homeotic protein Sex combs reduced / Homeosis


Mass: 10967.711 Da / Num. of mol.: 1 / Fragment: Homeobox DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Scr / Plasmid: pET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P09077
#4: Protein Homeobox protein extradenticle / / Dpbx


Mass: 7553.561 Da / Num. of mol.: 1 / Fragment: Homeobox TALE-type DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: exd / Plasmid: pET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P40427
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growpH: 8.7
Details: 10-14 % PEG 4K, 20 % MPD, 0.1 M Tris, pH 8.7-8.9, 0.2 M Sodium Acetate, 0.2 M Potassium Chloride

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2004
Details: Rosenbaum-Rock high-resolution double-crystal monochromator.
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 10408 / Num. obs: 10189 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Redundancy: 33.6 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 36
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 9.7 / Num. unique all: 1008 / Rsym value: 0.32 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1B8I

1b8i


Resolution: 2.6→11.98 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1949550.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 539 5.5 %RANDOM
Rwork0.233 ---
obs0.233 9733 95.4 %-
all-10272 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4238 Å2 / ksol: 0.325294 e/Å3
Displacement parametersBiso mean: 57.3 Å2
Baniso -1Baniso -2Baniso -3
1--17.29 Å20 Å20 Å2
2---5.57 Å20 Å2
3---22.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 814 0 112 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 85 5.6 %
Rwork0.349 1432 -
obs-1517 90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

+
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://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