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- PDB-7mfw: Drosophila melanogaster Canoe PDZ domain in complex with Echinoid... -

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Basic information

Entry
Database: PDB / ID: 7mfw
TitleDrosophila melanogaster Canoe PDZ domain in complex with Echinoid C-terminal region
ComponentsCanoe,Echinoid
KeywordsCELL ADHESION / Afadin / Canoe / PDZ / Echinoid
Function / homology
Function and homology information


branch fusion, open tracheal system / regulation of actin cytoskeleton organization by cell-cell adhesion / negative regulation of fusion cell fate specification / regulation of establishment of planar polarity / second mitotic wave involved in compound eye morphogenesis / ommatidial rotation / dorsal closure / rhabdomere / muscle organ morphogenesis / dorsal appendage formation ...branch fusion, open tracheal system / regulation of actin cytoskeleton organization by cell-cell adhesion / negative regulation of fusion cell fate specification / regulation of establishment of planar polarity / second mitotic wave involved in compound eye morphogenesis / ommatidial rotation / dorsal closure / rhabdomere / muscle organ morphogenesis / dorsal appendage formation / compound eye development / contractile actin filament bundle assembly / imaginal disc-derived wing morphogenesis / epidermis morphogenesis / sensory organ development / embryonic morphogenesis / positive regulation of smoothened signaling pathway / plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules / establishment of mitotic spindle orientation / regulation of JNK cascade / glial cell proliferation / cell adhesion molecule binding / morphogenesis of an epithelium / regulation of actin cytoskeleton organization / adherens junction / wound healing / cytoplasmic side of plasma membrane / small GTPase binding / negative regulation of neurogenesis / cell-cell adhesion / regulation of protein localization / cell-cell junction / cell cortex / regulation of cell shape / cell adhesion / protein domain specific binding / signal transduction / ATP binding / plasma membrane
Similarity search - Function
Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / CD80-like, immunoglobulin C2-set ...Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / Immunoglobulin domain / SMAD/FHA domain superfamily / PDZ domain / Fibronectin type III domain / Fibronectin type 3 domain / PDZ domain profile. / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ubiquitin-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Echinoid / Canoe, isoform E
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.104 Å
AuthorsSlep, K.C. / Peifer, M. / Byrnes, A.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118096 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008570 United States
CitationJournal: J.Cell Biol. / Year: 2021
Title: Multivalent interactions make adherens junction-cytoskeletal linkage robust during morphogenesis.
Authors: Perez-Vale, K.Z. / Yow, K.D. / Johnson, R.I. / Byrnes, A.E. / Finegan, T.M. / Slep, K.C. / Peifer, M.
History
DepositionApr 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Canoe,Echinoid
B: Canoe,Echinoid


Theoretical massNumber of molelcules
Total (without water)21,7612
Polymers21,7612
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, Wei, S.Y. et al., 2005, Dev Cell. 8:493-504
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Canoe,Echinoid

B: Canoe,Echinoid


Theoretical massNumber of molelcules
Total (without water)21,7612
Polymers21,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Unit cell
Length a, b, c (Å)114.563, 114.563, 31.637
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Canoe,Echinoid


Mass: 10880.543 Da / Num. of mol.: 2
Fragment: PDZ domain of Canoe, C-terminal region of Echinoid
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: cno, AF-6, anon-WO0172774.47, Canoe, CG2534, CG31537, Cno, cno-RB, cno?, dlhA, Dmel\CG42312, EC3-10, lip, mis, CG42312, Dmel_CG42312, ed, CG12676
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VN82, UniProt: Q9BN17
#2: Water ChemComp-HOH / water


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

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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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3350, 300 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13954 / % possible obs: 98.6 % / Redundancy: 11 % / Biso Wilson estimate: 28.33 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.022 / Rrim(I) all: 0.074 / Χ2: 1.007 / Net I/σ(I): 10.4 / Num. measured all: 154188
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1811.30.47413600.9660.1470.4970.54199.3
2.18-2.2611.40.36113950.9760.110.3780.52998.9
2.26-2.3711.40.27513890.9830.0850.2880.571100
2.37-2.4910.80.20213940.9890.0640.2120.61299.3
2.49-2.6510.70.13413500.9930.0420.1410.7695.1
2.65-2.8511.70.09914030.9960.030.1030.937100
2.85-3.1411.10.06814060.9980.0210.0721.21399.7
3.14-3.5910.40.05414200.9980.0180.0571.64299.8
3.59-4.5211.10.04313850.9990.0130.0451.6696.1
4.52-5010.70.03814520.9990.0120.041.64697.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å37.5 Å
Translation5.45 Å37.5 Å

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Processing

Software
NameVersionClassification
PHENIX1.8refinement
HKL-2000data scaling
PHENIX1.8phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3axa (Chain A res 1-91)

3axa


Resolution: 2.104→37.5 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 1388 10.02 %
Rwork0.1922 12465 -
obs0.1956 13853 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.48 Å2 / Biso mean: 62.64 Å2 / Biso min: 37 Å2
Refinement stepCycle: final / Resolution: 2.104→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 0 112 1517
Biso mean---65 -
Num. residues----191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031413
X-RAY DIFFRACTIONf_angle_d0.7241901
X-RAY DIFFRACTIONf_chiral_restr0.045229
X-RAY DIFFRACTIONf_plane_restr0.002247
X-RAY DIFFRACTIONf_dihedral_angle_d13.003536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.104-2.1790.26811360.2351120497
2.179-2.26620.30531360.2337122597
2.2662-2.36940.30391390.2391122999
2.3694-2.49420.30061380.2359124298
2.4942-2.65050.28251350.2219121295
2.6505-2.85510.22931420.22471256100
2.8551-3.14220.23891390.20611267100
3.1422-3.59660.20971410.17951275100
3.5966-4.53010.18241390.1575124896
4.5301-37.50.18111430.1646130797
Refinement TLS params.Method: refined / Origin x: -19.1373 Å / Origin y: 74.4773 Å / Origin z: 7.724 Å
111213212223313233
T0.4632 Å2-0.0251 Å2-0.0139 Å2-0.4236 Å20.0048 Å2--0.4129 Å2
L0.6545 °20.1898 °20.2152 °2-1.6094 °20.4345 °2--0.3775 °2
S0.0554 Å °-0.0014 Å °-0.0292 Å °0.0037 Å °-0.0291 Å °0.0629 Å °0.082 Å °-0.068 Å °-0.0331 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1011 - 1105
2X-RAY DIFFRACTION1allB1008 - 1105
3X-RAY DIFFRACTION1allS1 - 112

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