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- PDB-8zlw: Crystal Structure of RDGC IQ motif/dCaM Complex -

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Basic information

Entry
Database: PDB / ID: 8zlw
TitleCrystal Structure of RDGC IQ motif/dCaM Complex
Components
  • Calmodulin
  • Maltodextrin-binding protein
  • Serine/threonine-protein phosphatase rdgC
KeywordsPROTEIN BINDING / complex serine-threonine phosphatase
Function / homology
Function and homology information


detection of stimulus involved in sensory perception / negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / detection of chemical stimulus involved in sensory perception of smell / rhabdomere ...detection of stimulus involved in sensory perception / negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / detection of chemical stimulus involved in sensory perception of smell / rhabdomere / calcium-dependent protein serine/threonine phosphatase activity / myosin V complex / kinetochore organization / autophagic cell death / G protein-coupled opsin signaling pathway / actin filament-based movement / thermotaxis / myosin V binding / channel regulator activity / cell envelope / myosin heavy chain binding / muscle cell cellular homeostasis / protein-serine/threonine phosphatase / mitotic spindle pole / protein serine/threonine phosphatase activity / centriole replication / cellular response to ethanol / carbohydrate transmembrane transporter activity / phototransduction / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / enzyme regulator activity / visual perception / centriole / calcium-mediated signaling / sensory perception of sound / microtubule cytoskeleton organization / spindle / mitotic spindle / sensory perception of smell / manganese ion binding / midbody / cell cortex / periplasmic space / calmodulin binding / iron ion binding / calcium ion binding / centrosome / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein phosphatase with EF-hands / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / IQ motif profile. ...Serine/threonine-protein phosphatase with EF-hands / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / IQ motif profile. / Metallo-dependent phosphatase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / : / Bacterial extracellular solute-binding protein / ACP-like superfamily / EF-hand domain pair / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Maltodextrin-binding protein / Serine/threonine-protein phosphatase rdgC / Calmodulin
Similarity search - Component
Biological speciesEscherichia coli #1/H766 (bacteria)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, J. / Ding, Y.Z. / Li, J.C. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870746 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the dual Ca 2+ -sensor-mediated activation of the PPEF phosphatase family.
Authors: Liu, J. / Wu, C. / Liu, Y. / Chen, Q. / Ding, Y. / Lin, Z. / Pan, L. / Xiao, K. / Li, J. / Liu, Z. / Liu, W.
History
DepositionMay 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein
N: Calmodulin
R: Serine/threonine-protein phosphatase rdgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3607
Polymers62,2003
Non-polymers1604
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.664, 61.590, 88.002
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltodextrin-binding protein


Mass: 40807.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli #1/H766 (bacteria) / Gene: malE, JW3994
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A4P1LXE0
#2: Protein Calmodulin / CaM


Mass: 17123.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cam, CG8472
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P62152
#3: Protein/peptide Serine/threonine-protein phosphatase rdgC / Retinal degeneration C protein


Mass: 4268.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rdgC, CG44746
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P40421, protein-serine/threonine phosphatase
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 2 % v/v Tacsimate pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→29.26 Å / Num. obs: 28328 / % possible obs: 98.68 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.554 / Num. unique obs: 28328

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.26 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2536 1389 4.9 %
Rwork0.2162 --
obs0.218 28328 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4157 0 4 58 4219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084243
X-RAY DIFFRACTIONf_angle_d0.9495752
X-RAY DIFFRACTIONf_dihedral_angle_d6.088565
X-RAY DIFFRACTIONf_chiral_restr0.056630
X-RAY DIFFRACTIONf_plane_restr0.007758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.34291400.33212652X-RAY DIFFRACTION99
2.28-2.370.37271340.29772683X-RAY DIFFRACTION99
2.37-2.480.29261340.26162721X-RAY DIFFRACTION100
2.48-2.610.31971520.2482686X-RAY DIFFRACTION99
2.61-2.770.29341430.242677X-RAY DIFFRACTION98
2.77-2.990.30121350.24852650X-RAY DIFFRACTION98
2.99-3.290.27281440.23892715X-RAY DIFFRACTION99
3.29-3.760.25611290.21552723X-RAY DIFFRACTION99
3.76-4.730.17951400.1752684X-RAY DIFFRACTION97
4.73-29.260.22251380.17412748X-RAY DIFFRACTION98

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