[English] 日本語
Yorodumi
- PDB-4cyc: CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cyc
TitleCRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPTIDE AND UBDA MOTIFS
Components
  • 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3'
  • 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3'
  • HOMEOBOX PROTEIN EXTRADENTICLE
  • HOMEOTIC PROTEIN ULTRABITHORAX
KeywordsTRANSCRIPTION / HOX / PBC / DNA PROTEIN COMPLEX
Function / homology
Function and homology information


dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / salivary gland boundary specification / haltere development / oenocyte development / mesodermal cell fate specification / specification of segmental identity, thorax ...dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / salivary gland boundary specification / haltere development / oenocyte development / mesodermal cell fate specification / specification of segmental identity, thorax / imaginal disc-derived leg morphogenesis / somatic muscle development / open tracheal system development / muscle cell fate specification / polytene chromosome band / endoderm formation / midgut development / eye development / regulation of cell fate specification / peripheral nervous system development / cell fate determination / anterior/posterior pattern specification / embryonic organ development / neuron development / cis-regulatory region sequence-specific DNA binding / transcription repressor complex / animal organ morphogenesis / transcription coregulator binding / transcription coregulator activity / protein-DNA complex / brain development / RNA polymerase II transcription regulator complex / heart development / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / protein domain specific binding / negative regulation of DNA-templated transcription / 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 / nucleus / cytoplasm
Similarity search - Function
PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / : / : / Homeobox KN domain / Homeobox KN domain / Homeobox domain, metazoa ...PBX, PBC domain / PBC domain / PBC domain profile. / 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) / Homeobox protein extradenticle / Homeotic protein ultrabithorax
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsFoos, N. / Mate, M.J. / Ortiz-Lombardia, M.
CitationJournal: Structure / Year: 2015
Title: A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/Pbc Interaction Mode.
Authors: Foos, N. / Maurel-Zaffran, C. / Mate, M.J. / Vincentelli, R. / Hainaut, M. / Berenger, H. / Pradel, J. / Saurin, A.J. / Ortiz-Lombardia, M. / Graba, Y.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HOMEOTIC PROTEIN ULTRABITHORAX
B: HOMEOBOX PROTEIN EXTRADENTICLE
C: 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3'
D: 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)29,4954
Polymers29,4954
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-28.5 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.707, 97.707, 73.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein HOMEOTIC PROTEIN ULTRABITHORAX


Mass: 11459.246 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN WITH HX AND UBDA, RESIDUES 233-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: UBXIVA PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P83949
#2: Protein HOMEOBOX PROTEIN EXTRADENTICLE / DPBX / HOMEOTIC PROTEIN EXTRADENTICLE


Mass: 8857.946 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN RESIDUES 238-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: EXD2 PETG20A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P40427
#3: DNA chain 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3'


Mass: 4537.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly)
#4: DNA chain 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3'


Mass: 4640.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST METHIONINE FROM EXPRESSION VECTOR FIRST GLYCINE FROM EXPRESSION VECTOR

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 68.5 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M AMMONIUM PHOSPHATE, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.3853
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3853 Å / Relative weight: 1
ReflectionResolution: 2.36→84.62 Å / Num. obs: 17094 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 10.8 % / Biso Wilson estimate: 83.97 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 41.2
Reflection shellResolution: 2.36→2.37 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BZL

4bzl
PDB Unreleased entry


Resolution: 2.36→25 Å / Cor.coef. Fo:Fc: 0.9425 / Cor.coef. Fo:Fc free: 0.9429 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.218 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 863 5.07 %RANDOM
Rwork0.2121 ---
obs0.2128 17038 99.94 %-
Displacement parametersBiso mean: 87.18 Å2
Baniso -1Baniso -2Baniso -3
1--3.8322 Å20 Å20 Å2
2---3.8322 Å20 Å2
3---7.6643 Å2
Refine analyzeLuzzati coordinate error obs: 0.828 Å
Refinement stepCycle: LAST / Resolution: 2.36→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1079 609 0 68 1756
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091807HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.882556HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d572SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes190HARMONIC5
X-RAY DIFFRACTIONt_it1807HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.02
X-RAY DIFFRACTIONt_other_torsion21.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion230SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1909SEMIHARMONIC4
LS refinement shellResolution: 2.36→2.5 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2745 141 5.18 %
Rwork0.2472 2579 -
all0.2487 2720 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6769-0.6148-1.66765.6381-1.387611.0884-0.1314-0.06290.73130.76990.3419-0.2977-1.48590.399-0.21050.103-0.1121-0.1088-0.4696-0.0142-0.1948-41.301615.95328.9342
23.8978-1.02620.87953.09770.298816.42340.12240.4397-0.0097-0.4562-0.14230.0803-0.67650.05870.01990.2836-0.1484-0.0454-0.24350.0368-0.177-46.64485.818-16.1441
34.08143.3726-1.647713.6297-4.801914.6098-0.43350.06030.4909-0.51410.1258-0.525-1.12380.53960.30770.0777-0.2833-0.1139-0.29720.0059-0.0396-39.299613.20770.0095
4-0.0594-1.2302-0.47574.4397-3.300912.81310.0611-0.0513-0.0593-0.3246-0.2167-0.4859-0.32390.29740.15560.2032-0.2147-0.0137-0.25090.02460.0554-41.96687.5963-2.0011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

+
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