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- PDB-6b67: Human PP2Calpha (PPM1A) complexed with cyclic peptide c(MpSIpYVA) -

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Basic information

Entry
Database: PDB / ID: 6b67
TitleHuman PP2Calpha (PPM1A) complexed with cyclic peptide c(MpSIpYVA)
Components
  • Protein phosphatase 1A
  • cyclic peptide c(MpSIpYVA)
KeywordsHYDROLASE / Phosphatase
Function / homology
Function and homology information


N-terminal protein myristoylation / calmodulin-dependent protein phosphatase activity / peptidyl-threonine dephosphorylation / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of non-canonical NF-kappaB signal transduction / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / R-SMAD binding / negative regulation of BMP signaling pathway ...N-terminal protein myristoylation / calmodulin-dependent protein phosphatase activity / peptidyl-threonine dephosphorylation / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of non-canonical NF-kappaB signal transduction / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / R-SMAD binding / negative regulation of BMP signaling pathway / negative regulation of canonical NF-kappaB signal transduction / dephosphorylation / cellular response to transforming growth factor beta stimulus / protein export from nucleus / protein dephosphorylation / positive regulation of protein export from nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of canonical Wnt signaling pathway / manganese ion binding / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein serine/threonine phosphatase 2C, C-terminal / Phosphatase 2C, C-terminal domain superfamily / Protein serine/threonine phosphatase 2C, C-terminal domain / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain ...Protein serine/threonine phosphatase 2C, C-terminal / Phosphatase 2C, C-terminal domain superfamily / Protein serine/threonine phosphatase 2C, C-terminal domain / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein phosphatase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDyda, F. / Kosek, D.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity.
Authors: Debnath, S. / Kosek, D. / Tagad, H.D. / Durell, S.R. / Appella, D.H. / Acevedo, R. / Grishaev, A. / Dyda, F. / Appella, E. / Mazur, S.J.
History
DepositionOct 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase 1A
B: Protein phosphatase 1A
C: Protein phosphatase 1A
D: cyclic peptide c(MpSIpYVA)
E: cyclic peptide c(MpSIpYVA)
F: cyclic peptide c(MpSIpYVA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,94716
Polymers101,5476
Non-polymers40110
Water11,403633
1
A: Protein phosphatase 1A
D: cyclic peptide c(MpSIpYVA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0096
Polymers33,8492
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-47 kcal/mol
Surface area13250 Å2
MethodPISA
2
B: Protein phosphatase 1A
E: cyclic peptide c(MpSIpYVA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9695
Polymers33,8492
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-48 kcal/mol
Surface area12950 Å2
MethodPISA
3
C: Protein phosphatase 1A
F: cyclic peptide c(MpSIpYVA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9695
Polymers33,8492
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-46 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.030, 89.570, 70.050
Angle α, β, γ (deg.)90.00, 113.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein phosphatase 1A / Protein phosphatase 2C isoform alpha / PP2C-alpha / Protein phosphatase IA


Mass: 32845.914 Da / Num. of mol.: 3 / Mutation: D146E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1A, PPPM1A / Production host: Escherichia coli (E. coli)
References: UniProt: P35813, protein-serine/threonine phosphatase
#2: Protein/peptide cyclic peptide c(MpSIpYVA)


Mass: 1002.981 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The cyclic peptide is a synthetic construct whose structure is represented in the attached files. We can also provide th is information in other formats, if this is more convenient. A ...Details: The cyclic peptide is a synthetic construct whose structure is represented in the attached files. We can also provide th is information in other formats, if this is more convenient. A general method for preparation of thioether cyclic peptid es is given by Long et al. (2003). The specific cyclic peptide, c(M-pS-I-pY-V-A) was first reported to be a substrate of PPM1A by Yamaguchi et al. 2006.
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Protein conc: 20 mg/ml Protein buffer: 10 mM MES, pH 7.0, 150 mM NaCl, 2 mM TCEP and 2 mM MgCl2 Protein and cyclic peptide was dialyzed against above buffer and mixed at the 1:2 molar ratio ...Details: Protein conc: 20 mg/ml Protein buffer: 10 mM MES, pH 7.0, 150 mM NaCl, 2 mM TCEP and 2 mM MgCl2 Protein and cyclic peptide was dialyzed against above buffer and mixed at the 1:2 molar ratio Precipitant: 0.1M HEPES (pH 7.3), 0.1M calcium acetate and 40% PEG400

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 6, 2016
RadiationMonochromator: Multilayer KB pair / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 43867 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.87 % / Rsym value: 0.03 / Net I/σ(I): 25.09
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 4.63 / Rsym value: 0.093

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A6Q

1a6q


Resolution: 2.2→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: CARTESIAN SIMULATED ANNEALING, RESTRAINED APD REFINEMENT, ENERGY MIMIZATION
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1096 2.4 %RANDOM
Rwork0.169 ---
obs0.169 42734 95.9 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7083 0 10 633 7726
LS refinement shellResolution: 2.2→2.24 Å / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.2177

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