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- PDB-8zlx: Crystal Structure of mPPEF2 IQ motif/apo-CaM Complex -

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Basic information

Entry
Database: PDB / ID: 8zlx
TitleCrystal Structure of mPPEF2 IQ motif/apo-CaM Complex
Components
  • Calmodulin (CaM)
  • Serine/threonine-protein phosphatase with EF-hands 2
KeywordsPROTEIN BINDING / complex phosphatase
Function / homology
Function and homology information


histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / detection of stimulus involved in sensory perception / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / calmodulin-dependent protein phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity ...histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / detection of stimulus involved in sensory perception / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / calmodulin-dependent protein phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / myosin II complex / mitogen-activated protein kinase kinase kinase binding / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / negative regulation of MAPK cascade / Hsp70 protein binding / visual perception / Hsp90 protein binding / manganese ion binding / iron ion binding / calcium ion binding
Similarity search - Function
Serine/threonine-protein phosphatase with EF-hands / PPP domain / PPP5 TPR repeat region / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / IQ motif profile. ...Serine/threonine-protein phosphatase with EF-hands / PPP domain / PPP5 TPR repeat region / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / IQ motif profile. / Metallo-dependent phosphatase-like / : / EF-hand domain pair / 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
Calmodulin 3 / Serine/threonine-protein phosphatase with EF-hands 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.0Mar 5, 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
B: Calmodulin (CaM)
D: Calmodulin (CaM)
d: Serine/threonine-protein phosphatase with EF-hands 2
a: Serine/threonine-protein phosphatase with EF-hands 2
C: Calmodulin (CaM)
b: Serine/threonine-protein phosphatase with EF-hands 2
c: Serine/threonine-protein phosphatase with EF-hands 2
A: Calmodulin (CaM)


Theoretical massNumber of molelcules
Total (without water)81,2188
Polymers81,2188
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.451, 134.451, 35.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Calmodulin (CaM) / EF-hand domain-containing protein


Mass: 17427.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CALM3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A7N4P457
#2: Protein/peptide
Serine/threonine-protein phosphatase with EF-hands 2 / PPEF-2


Mass: 2877.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppef2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O35385, protein-serine/threonine phosphatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 1.4 M Sodium citrate tribasic dihydrate pH 6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.5→19.83 Å / Num. obs: 22846 / % possible obs: 99.94 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 17.82
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.959 / Num. unique obs: 22846

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.83 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.886 / SU B: 14.013 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.987 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29083 1161 5.1 %RANDOM
Rwork0.20818 ---
obs0.2124 21696 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.599 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--0.05 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.5→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 0 15 5045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135109
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164587
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.656883
X-RAY DIFFRACTIONr_angle_other_deg1.281.58910525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86723.875289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79415849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2741529
X-RAY DIFFRACTIONr_chiral_restr0.0690.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021148
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1595.2642641
X-RAY DIFFRACTIONr_mcbond_other4.1585.2622640
X-RAY DIFFRACTIONr_mcangle_it6.3167.8623279
X-RAY DIFFRACTIONr_mcangle_other6.3167.8643280
X-RAY DIFFRACTIONr_scbond_it4.5225.4942468
X-RAY DIFFRACTIONr_scbond_other4.5215.4952469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.898.1083604
X-RAY DIFFRACTIONr_long_range_B_refined9.61562.4085719
X-RAY DIFFRACTIONr_long_range_B_other9.61562.4065719
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 99 -
Rwork0.295 1605 -
obs--100 %

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