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- PDB-6m3d: X-ray crystal structure of tandemly connected engrailed homeodoma... -

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Basic information

Entry
Database: PDB / ID: 6m3d
TitleX-ray crystal structure of tandemly connected engrailed homeodomains (EHD) with R53A mutations and DNA complex
Components
  • DNA (5'-D(*GP*GP*AP*TP*TP*AP*GP*GP*AP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*AP*TP*CP*CP*TP*AP*AP*TP*CP*C)-3')
  • Segmentation polarity homeobox protein engrailed,Segmentation polarity homeobox protein engrailed
KeywordsDNA BINDING PROTEIN/DNA / HOMEODOMAIN FOLD / PROTEIN-DNA COMPLEX / GENOME EDITING / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation ...posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / wing disc morphogenesis / neuroblast fate determination / imaginal disc-derived wing vein specification / segment polarity determination / ventral midline development / compartment pattern specification / gonad development / axon guidance / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / sequence-specific DNA binding / negative regulation of neuron apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / : / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. ...Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / : / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Segmentation polarity homeobox protein engrailed
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSunami, T. / Hirano, Y. / Tamada, T. / Kono, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)26840054 Japan
Japan Society for the Promotion of Science (JSPS)26330339 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structural basis for designing an array of engrailed homeodomains.
Authors: Sunami, T. / Hirano, Y. / Tamada, T. / Kono, H.
History
DepositionMar 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*AP*AP*TP*CP*CP*TP*AP*AP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*TP*TP*AP*GP*GP*AP*TP*TP*A)-3')
C: Segmentation polarity homeobox protein engrailed,Segmentation polarity homeobox protein engrailed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6904
Polymers24,6673
Non-polymers231
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-29 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.798, 61.437, 39.976
Angle α, β, γ (deg.)90.000, 106.447, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 3581.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*GP*AP*TP*TP*AP*GP*GP*AP*TP*TP*A)-3')


Mass: 3741.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Segmentation polarity homeobox protein engrailed,Segmentation polarity homeobox protein engrailed


Mass: 17344.592 Da / Num. of mol.: 1 / Mutation: Q503K,R506A
Source method: isolated from a genetically manipulated source
Details: the fusion protein of EHD (UNP RESIDUES 453-512), linkers GGGGG, EHD (UNP RESIDUES 453-512)
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: en, CG9015 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02836
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 8% (w/v) PEG 4000, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→38.17 Å / Num. obs: 24423 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.1623401697 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.025 / Rrim(I) all: 0.034 / Net I/σ(I): 15.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1183 / CC1/2: 0.921 / Rrim(I) all: 0.338 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HDD

2hdd


Resolution: 1.6→38.17 Å / SU ML: 0.174027637387 / Cross valid method: FREE R-VALUE / σ(F): 1.40888796396 / Phase error: 23.6012510998
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235863688164 1204 4.94618355106 %
Rwork0.18834877636 23138 -
obs0.190614050402 24342 99.6805896806 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.5017300563 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 486 1 207 1607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007081855559112150
X-RAY DIFFRACTIONf_angle_d1.004560253753100
X-RAY DIFFRACTIONf_chiral_restr0.0473394368983335
X-RAY DIFFRACTIONf_plane_restr0.00633961639965237
X-RAY DIFFRACTIONf_dihedral_angle_d26.91049348551167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.66410.2609177900661380.2147460488942537X-RAY DIFFRACTION98.7449243263
1.6641-1.73980.2955913229711290.2056942038992548X-RAY DIFFRACTION99.4797473058
1.7398-1.83150.2286567961191600.2075469428912533X-RAY DIFFRACTION99.8146775389
1.8315-1.94630.3390891902291260.2174026952212561X-RAY DIFFRACTION99.962797619
1.9463-2.09650.2441871180121470.2105464019232567X-RAY DIFFRACTION99.8895841001
2.0965-2.30750.2158898487911240.1980255722652576X-RAY DIFFRACTION99.9629766753
2.3075-2.64130.2654700511221160.2091496705172601X-RAY DIFFRACTION99.8897058824
2.6413-3.32750.2818112573751160.1966109751212598X-RAY DIFFRACTION99.3775173929
3.3275-38.170.1931459766131480.1612908881922617X-RAY DIFFRACTION100

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