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- PDB-4v0v: The crystal structure of mouse PP1G in complex with truncated hum... -

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Basic information

Entry
Database: PDB / ID: 4v0v
TitleThe crystal structure of mouse PP1G in complex with truncated human PPP1R15B (631-660)
Components
  • PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
  • SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
KeywordsHYDROLASE/HYDROLASE REGULATOR / HYDROLASE-HYDROLASE REGULATOR COMPLEX
Function / homology
Function and homology information


Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 1 complex / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 1 complex / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids / protein phosphatase 1 binding / lamin binding / protein phosphatase regulator activity / protein serine/threonine phosphatase activity / ER overload response / glycogen metabolic process / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / negative regulation of PERK-mediated unfolded protein response / phosphatase activity / microtubule organizing center / cleavage furrow / negative regulation of protein phosphorylation / blastocyst development / protein dephosphorylation / positive regulation of glial cell proliferation / response to endoplasmic reticulum stress / circadian regulation of gene expression / regulation of circadian rhythm / response to hydrogen peroxide / kinetochore / neuron differentiation / regulation of translation / presynapse / midbody / spermatogenesis / dendritic spine / mitochondrial outer membrane / chromosome, telomeric region / nuclear speck / protein domain specific binding / cell division / protein-containing complex binding / protein kinase binding / nucleolus / glutamatergic synapse / endoplasmic reticulum / mitochondrion / metal ion binding
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. ...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: 1.61 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.pdbx_dist_value / _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_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: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
C: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
D: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1178
Polymers75,9614
Non-polymers1564
Water7,602422
1
A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0363
Polymers37,9812
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-16.8 kcal/mol
Surface area13800 Å2
MethodPISA
2
C: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
D: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0815
Polymers37,9812
Non-polymers1013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-34.3 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.800, 67.890, 156.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G / PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PROTEIN PHOSPHATASE 1C CATALYTIC SUBUNIT


Mass: 33921.035 Da / Num. of mol.: 2 / 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/peptide PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B


Mass: 4059.541 Da / Num. of mol.: 2 / Fragment: RESIDUES 631-660
Source method: isolated from a genetically manipulated source
Details: TRUNCATED HUMAN PPP1R15B INCLUDING RESIDUES OF 631-660
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.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.63 Å3/Da / Density % sol: 53.27 % / Description: NONE
Crystal growpH: 7 / Details: 2.4M SODIUM MALONATE, PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.61→51.26 Å / Num. obs: 92584 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Biso Wilson estimate: 17.56 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FJM

1fjm


Resolution: 1.61→51.263 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 19.09 / Stereochemistry target values: ML / Details: RESIDUE 22-26 IN CHAIN C ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2029 4634 5 %
Rwork0.1763 --
obs0.1776 92584 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.41 Å2
Refinement stepCycle: LAST / Resolution: 1.61→51.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 4 422 5443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065183
X-RAY DIFFRACTIONf_angle_d1.0447005
X-RAY DIFFRACTIONf_dihedral_angle_d13.0391945
X-RAY DIFFRACTIONf_chiral_restr0.043753
X-RAY DIFFRACTIONf_plane_restr0.004913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.62830.29821690.26342895X-RAY DIFFRACTION100
1.6283-1.64750.30651640.25032880X-RAY DIFFRACTION100
1.6475-1.66760.28241460.23992912X-RAY DIFFRACTION100
1.6676-1.68870.25191630.23052868X-RAY DIFFRACTION100
1.6887-1.71090.27341430.22362931X-RAY DIFFRACTION100
1.7109-1.73430.22511450.22442908X-RAY DIFFRACTION100
1.7343-1.75910.2561610.21292924X-RAY DIFFRACTION100
1.7591-1.78540.21361590.20092873X-RAY DIFFRACTION100
1.7854-1.81330.26271480.19452901X-RAY DIFFRACTION100
1.8133-1.8430.22191510.19182916X-RAY DIFFRACTION100
1.843-1.87480.22611840.18642875X-RAY DIFFRACTION100
1.8748-1.90890.20741520.18042941X-RAY DIFFRACTION100
1.9089-1.94560.19551430.18572905X-RAY DIFFRACTION100
1.9456-1.98530.20061500.1752919X-RAY DIFFRACTION100
1.9853-2.02850.18831580.17352927X-RAY DIFFRACTION100
2.0285-2.07560.221450.16942922X-RAY DIFFRACTION100
2.0756-2.12760.19241620.17362895X-RAY DIFFRACTION100
2.1276-2.18510.20431480.16792931X-RAY DIFFRACTION100
2.1851-2.24940.19951610.16332906X-RAY DIFFRACTION100
2.2494-2.3220.19981630.15982931X-RAY DIFFRACTION100
2.322-2.4050.19181650.162920X-RAY DIFFRACTION100
2.405-2.50130.20591530.16942933X-RAY DIFFRACTION100
2.5013-2.61510.2071490.1872938X-RAY DIFFRACTION100
2.6151-2.7530.20151540.17792938X-RAY DIFFRACTION100
2.753-2.92540.19581610.17922935X-RAY DIFFRACTION99
2.9254-3.15130.21851450.17182977X-RAY DIFFRACTION100
3.1513-3.46830.17791360.16082964X-RAY DIFFRACTION99
3.4683-3.970.17841510.15423009X-RAY DIFFRACTION99
3.97-5.00120.14261410.15053010X-RAY DIFFRACTION99
5.0012-51.2890.23461640.19483166X-RAY DIFFRACTION99
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)
17.45172.2131.18065.8441.1043.243-0.20430.36020.3794-0.45780.2209-0.0878-0.21990.3067-0.03220.23910.04440.06540.29520.0310.1709-3.6451-12.6787-4.9424
21.8613-0.00820.22381.9659-0.16031.7430.04760.10340.0436-0.0127-0.0077-0.0433-0.05590.1117-0.0360.07650.00410.03560.1274-0.02790.0985-7.9184-20.7386.797
30.8908-0.3216-0.2321.1737-0.04471.73960.05370.04170.0760.0403-0.01980.0903-0.1981-0.1402-0.03680.0838-0.00040.01770.1383-0.01280.1239-14.1903-16.8088.3093
41.8076-0.00920.27451.7252-0.15423.6094-0.0115-0.1113-0.01470.06270.07670.2020.1233-0.3136-0.05050.13720.01650.02920.15560.02510.1704-19.8543-24.266923.9139
53.1277-2.47140.04295.71860.55232.3879-0.1575-0.2807-0.01160.26180.1627-0.0886-0.0264-0.0491-0.00320.0923-0.01230.02950.13310.02910.0742-14.9588-24.843232.4812
62.60610.3712-0.7094.1964-2.00393.2326-0.1104-0.3013-0.07790.1671-0.0561-0.3111-0.02070.32960.14230.09630.0080.00010.1835-0.01490.128-2.8189-23.284125.1839
72.65911.4445-0.16481.217-0.81091.84370.0125-0.0360.325-0.1111-0.0441-0.3246-0.2150.18520.0380.1581-0.02170.0110.231-0.0160.23653.5714-20.278718.1027
83.7198-0.75070.16363.7102-0.57051.98510.0665-0.61940.23061.00120.0895-0.3971-0.21280.2903-0.15750.5603-0.0144-0.05780.3171-0.0750.2138-29.64529.114546.441
94.06160.94441.54412.74120.71124.15340.3099-0.3903-0.47010.6724-0.0923-0.18150.58790.0154-0.03720.3704-0.0162-0.00130.13370.02560.1445-35.5091-3.670740.1714
102.10330.0143-0.15392.32410.41262.38880.11930.00910.09560.0876-0.0087-0.0928-0.14240.057-0.06770.1501-0.01580.01970.0924-0.00920.0905-35.88311.347730.3011
111.8484-0.1869-0.25371.97510.41682.73540.0048-0.0744-0.06360.1685-0.0037-0.05850.08590.0497-0.03780.1209-0.0108-0.00020.06290.00080.0898-35.47964.478733.6261
123.44110.04990.41512.95180.01387.69810.0536-0.22850.06090.1857-0.0357-0.49370.17190.4731-0.03160.17920.0503-0.03720.1738-0.02210.2223-19.6117-1.597731.6524
134.2865-1.76632.05852.6252-0.87393.72720.0347-0.1412-0.16830.11610.0730.01030.3054-0.0895-0.13530.123-0.01420.02330.0768-0.01930.097-36.9653-0.939928.0182
141.41880.86990.01872.5441-1.06653.2369-0.01790.1434-0.2326-0.20430.04450.05880.6165-0.1497-0.01310.2563-0.0227-0.00180.1714-0.02880.1917-41.0808-6.650617.7848
152.6576-1.04571.29463.4117-0.17683.9515-0.01150.12850.1421-0.4377-0.0199-0.22240.02070.0550.01690.1448-0.01090.0080.1336-0.0220.1404-34.66272.08129.6558
163.5999-1.76630.00823.71460.06353.15830.09910.1544-0.0996-0.3162-0.11510.02060.0449-0.07260.01880.1412-0.0151-0.00350.0952-0.01360.1031-39.52882.44776.905
173.0122-0.35251.54872.33630.20313.4368-0.02720.14020.2869-0.2311-0.0524-0.0703-0.4140.06750.07670.1582-0.00570.02640.09120.00110.1292-37.477913.957414.7409
181.34051.12861.08222.96960.18592.9805-0.03630.0499-0.0372-0.11920.03-0.2861-0.18250.1798-0.03120.213-0.00550.03840.1096-0.01670.1921-34.367719.497822.4041
193.37072.75263.22253.4161.84663.978-0.37780.1660.8752-0.2685-0.04860.3172-0.6398-0.04090.30430.32870.01140.01560.1734-0.00890.2651-40.562324.328820.8844
204.88181.5291-0.84068.1978-1.88486.143-0.0435-0.4843-0.46240.0657-0.1198-1.00360.30470.68390.13010.17950.04720.04540.33120.03860.35556.0353-33.235622.2774
216.0240.50711.03974.4069-0.15016.445-0.3815-0.1280.3779-0.0006-0.06190.0144-1.14470.39090.41540.5205-0.17730.08480.4587-0.04660.50629.0075-10.154314.7416
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 99 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 100 THROUGH 172 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 173 THROUGH 215 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 216 THROUGH 239 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 240 THROUGH 271 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 272 THROUGH 300 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 6 THROUGH 31 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 32 THROUGH 48 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 49 THROUGH 99 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 100 THROUGH 127 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 128 THROUGH 145 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 146 THROUGH 172 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 173 THROUGH 199 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 200 THROUGH 215 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 216 THROUGH 239 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 240 THROUGH 271 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 272 THROUGH 300 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 639 THROUGH 653 )
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 639 THROUGH 648 )
21X-RAY DIFFRACTION21CHAIN 'B' AND (RESID 649 THROUGH 658 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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