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- PDB-4v0x: The crystal structure of mouse PP1G in complex with truncated hum... -

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Basic information

Entry
Database: PDB / ID: 4v0x
TitleThe crystal structure of mouse PP1G in complex with truncated human PPP1R15B (631-684)
Components
  • PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
  • PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
KeywordsHYDROLASE/HYDROLASE REGULATOR / HYDROLASE-HYDROLASE REGULATOR COMPLEX
Function / homology
Function and homology information


positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / RAF activation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins ...positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / RAF activation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids / protein phosphatase regulator activity / protein phosphatase 1 binding / lamin binding / microtubule organizing center / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / negative regulation of PERK-mediated unfolded protein response / protein-serine/threonine phosphatase / ER overload response / entrainment of circadian clock by photoperiod / phosphatase activity / cleavage furrow / blastocyst development / positive regulation of glial cell proliferation / response to endoplasmic reticulum stress / protein dephosphorylation / negative regulation of protein phosphorylation / circadian regulation of gene expression / response to hydrogen peroxide / neuron differentiation / regulation of circadian rhythm / kinetochore / presynapse / regulation of translation / midbody / postsynapse / spermatogenesis / protein phosphatase binding / mitochondrial outer membrane / dendritic spine / chromosome, telomeric region / nuclear speck / cell cycle / protein domain specific binding / cell division / glutamatergic synapse / protein-containing complex binding / nucleolus / protein kinase binding / endoplasmic reticulum / mitochondrion / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Protein phosphatase 1, regulatory subunit 15B, N-terminal / eIF2-alpha phosphatase phosphorylation constitutive repressor / Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / Phosphatase-1 catalytic subunit binding region / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases ...Protein phosphatase 1, regulatory subunit 15B, N-terminal / eIF2-alpha phosphatase phosphorylation constitutive repressor / Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / Phosphatase-1 catalytic subunit binding region / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Protein phosphatase 1 regulatory subunit 15B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChen, R. / Yan, Y. / Casado, A.C. / Ron, D. / Read, R.J.
CitationJournal: Elife / Year: 2015
Title: G-actin provides substrate-specificity to eukaryotic initiation factor 2 alpha holophosphatases.
Authors: Chen, R. / Rato, C. / Yan, Y. / Crespillo-Casado, A. / Clarke, H.J. / Harding, H.P. / Marciniak, S.J. / Read, R.J. / Ron, D.
History
DepositionSep 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / pdbx_database_proc / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1May 1, 2024Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9043
Polymers40,8492
Non-polymers551
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-21.4 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.540, 67.540, 158.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G / PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PROT


Mass: 33921.035 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-300
Source method: isolated from a genetically manipulated source
Details: TRUNCATED MOUSE PP1G INCLUDING RESIDUES OF 7-300 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21 (bacteria)
References: UniProt: P63087, protein-serine/threonine phosphatase
#2: Protein PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B


Mass: 6927.684 Da / Num. of mol.: 1 / Fragment: RESIDUES 631-684
Source method: isolated from a genetically manipulated source
Details: TRUNCATED HUMAN PPP1R15B INCLUDING RESIDUES OF 631-684
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5SWA1
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.67 Å3/Da / Density % sol: 54.02 % / Description: NONE
Crystal growpH: 6 / Details: 2.0 M SODIUM MALONATE, PH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→51.34 Å / Num. obs: 32078 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 7.8 % / Biso Wilson estimate: 28.03 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE CRYSTAL STRUCTURE OF MOUSE PP1G IN COMPLEX WITH TRUNCATED HUMAN PPP1R15B INCLUDING 631-660

Resolution: 1.85→51.337 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 1626 5.1 %
Rwork0.1766 --
obs0.1789 32078 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→51.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 1 88 2657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112625
X-RAY DIFFRACTIONf_angle_d1.2213542
X-RAY DIFFRACTIONf_dihedral_angle_d14.737982
X-RAY DIFFRACTIONf_chiral_restr0.054378
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90440.3681440.30022484X-RAY DIFFRACTION99
1.9044-1.96590.31441300.25672458X-RAY DIFFRACTION100
1.9659-2.03620.28191300.22432498X-RAY DIFFRACTION100
2.0362-2.11770.26681220.22822517X-RAY DIFFRACTION100
2.1177-2.21410.24411220.19892499X-RAY DIFFRACTION100
2.2141-2.33080.23351420.192507X-RAY DIFFRACTION100
2.3308-2.47690.22391410.18922494X-RAY DIFFRACTION100
2.4769-2.66810.21691330.1792532X-RAY DIFFRACTION100
2.6681-2.93660.22321490.18332523X-RAY DIFFRACTION100
2.9366-3.36140.20531410.1692561X-RAY DIFFRACTION100
3.3614-4.23470.18311340.14632598X-RAY DIFFRACTION100
4.2347-51.35720.21391380.1572781X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.50242.9413-0.2188.0689-1.3090.83580.27390.48150.7297-0.37260.35880.1215-0.95450.8092-0.45450.6075-0.21870.24410.7301-0.01420.4373-23.470421.6744-25.8765
28.44634.7294-4.14162.9322-2.25614.95470.01571.01480.3776-0.70730.57210.6508-0.1017-1.0263-0.60930.2735-0.0344-0.01110.55440.07690.2708-37.273414.8031-21.1595
32.5550.3667-0.46692.18580.53331.9775-0.0255-0.10180.3347-0.12460.4415-0.35290.00340.7664-0.22880.2128-0.04680.05440.5348-0.10860.3068-22.537613.4724-11.0586
41.9728-1.1596-1.37712.26521.16184.0105-0.00650.03080.2045-0.07130.32370.0219-0.0923-0.1156-0.31280.1245-0.05830.01660.32050.03240.2453-33.169216.0312-9.7302
55.9506-0.4551.66124.92150.96538.1055-0.13030.18060.05760.17210.1880.75720.5231-0.8757-0.0480.2168-0.07950.04690.46820.13220.3637-43.13098.1825-2.0082
64.068-0.02121.72715.0171-0.794.2419-0.1287-0.57110.12230.5420.2358-0.13130.56680.5752-0.06470.27730.13460.03590.53780.02750.1996-31.846810.674111.0413
71.4419-0.6781-0.29171.20610.75521.1572-0.2258-0.66840.15850.32910.5928-0.66230.36551.10550.1770.09960.2739-0.00261.0904-0.26160.3781-20.280511.4014.2629
84.08611.2483-0.68510.4358-0.55241.92050.1586-0.51270.38360.0707-0.0732-0.22140.01341.0557-0.06850.22410.144-0.0151.1098-0.29890.504-14.402114.7876-2.9752
93.39823.74282.40195.07932.21896.83060.1184-0.1297-0.62750.1395-0.1671-0.06180.25570.004-0.00150.66850.4316-0.17330.8171-0.13390.5591-16.0143-3.12051.8209
105.58334.8427-3.31664.7096-2.30054.465-0.1921-0.6246-0.08060.3722-0.2378-1.0148-0.05260.97320.45310.63230.058-0.11760.8452-0.19110.9705-6.357914.5423-3.8158
110.69490.4526-2.18390.6375-0.668.5640.46641.10872.6206-0.1057-0.0092-0.3458-2.01870.3995-0.44370.9593-0.0410.09780.77840.05721.3479-14.539931.2868-9.851
120.95551.52021.2693.10962.49392.24320.0133-0.0897-0.6830.4220.24111.17060.1045-0.9021-0.171.11670.1082-0.08930.70140.13651.8106-27.634934.1112-5.7916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 31 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 32 THROUGH 48 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 49 THROUGH 99 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 100 THROUGH 183 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 184 THROUGH 199 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 200 THROUGH 239 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 240 THROUGH 271 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 272 THROUGH 300 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 639 THROUGH 643 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 644 THROUGH 653 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 654 THROUGH 658 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 659 THROUGH 662 )

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