[English] 日本語
Yorodumi
- PDB-4xpn: Crystal Structure of Protein Phosphate 1 complexed with PP1 bindi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xpn
TitleCrystal Structure of Protein Phosphate 1 complexed with PP1 binding domain of GADD34
Components
  • Protein phosphatase 1 regulatory subunit 15A
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / eIF2alpha phosphatase / PP1 regulator
Function / homology
Function and homology information


positive regulation of translational initiation in response to stress / positive regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation / regulation of translational initiation by eIF2 alpha dephosphorylation / positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / regulation of glycogen catabolic process / Response of EIF2AK1 (HRI) to heme deficiency / PTW/PP1 phosphatase complex / negative regulation of protein dephosphorylation / glycogen granule ...positive regulation of translational initiation in response to stress / positive regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation / regulation of translational initiation by eIF2 alpha dephosphorylation / positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / regulation of glycogen catabolic process / Response of EIF2AK1 (HRI) to heme deficiency / PTW/PP1 phosphatase complex / negative regulation of protein dephosphorylation / glycogen granule / regulation of glycogen biosynthetic process / protein localization to endoplasmic reticulum / protein phosphatase regulator activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / negative regulation of phosphoprotein phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / negative regulation of PERK-mediated unfolded protein response / protein-serine/threonine phosphatase / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / protein phosphatase activator activity / phosphatase activity / positive regulation of phosphoprotein phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / ribonucleoprotein complex binding / dephosphorylation / response to endoplasmic reticulum stress / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / mitochondrial outer membrane / dendritic spine / regulation of cell cycle / cell cycle / cell division / glutamatergic synapse / apoptotic process / DNA damage response / endoplasmic reticulum membrane / nucleolus / protein kinase binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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
: / PHOSPHATE ION / Protein phosphatase 1 regulatory subunit 15A / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.285 Å
AuthorsChoy, M.S. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
CitationJournal: Cell Rep / Year: 2015
Title: Structural and Functional Analysis of the GADD34:PP1 eIF2 alpha Phosphatase.
Authors: Choy, M.S. / Yusoff, P. / Lee, I.C. / Newton, J.C. / Goh, C.W. / Page, R. / Shenolikar, S. / Peti, W.
History
DepositionJan 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Protein phosphatase 1 regulatory subunit 15A
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Protein phosphatase 1 regulatory subunit 15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,80212
Polymers78,2084
Non-polymers5948
Water4,017223
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Protein phosphatase 1 regulatory subunit 15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4016
Polymers39,1042
Non-polymers2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-32 kcal/mol
Surface area12840 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Protein phosphatase 1 regulatory subunit 15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4016
Polymers39,1042
Non-polymers2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-34 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.311, 112.853, 125.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALAchain AAA4 - 2993 - 298
21SERSERALAALAchain CCC6 - 2995 - 298
12ALAALAALAALAchain BBB553 - 5685 - 20
22ARGARGLEULEUchain DDD554 - 5676 - 19

NCS ensembles :
ID
1
2

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: UNP residues 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein/peptide Protein phosphatase 1 regulatory subunit 15A / Growth arrest and DNA damage-inducible protein GADD34 / Myeloid differentiation primary response ...Growth arrest and DNA damage-inducible protein GADD34 / Myeloid differentiation primary response protein MyD116 homolog


Mass: 4941.704 Da / Num. of mol.: 2 / Fragment: UNP residues 552-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R15A, GADD34 / Production host: Escherichia coli (E. coli) / References: UniProt: O75807

-
Non-polymers , 4 types, 231 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 49300 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.32 Å2 / Rmerge(I) obs: 0.108 / Χ2: 1.09 / Net I/av σ(I): 19.577 / Net I/σ(I): 4.8 / Num. measured all: 307472
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.17-2.214.823920.47499.3
2.21-2.255.624051.83199.80.965
2.25-2.29624430.52699.9
2.29-2.346.124210.4831000.725
2.34-2.396.224560.4971000.652
2.39-2.446.424210.52799.90.548
2.44-2.516.524480.53799.90.512
2.51-2.576.524350.53799.90.465
2.57-2.656.524400.6161000.404
2.65-2.736.324530.7511000.339
2.73-2.835.724680.68899.90.275
2.83-2.956.524450.7751000.216
2.95-3.086.824710.8511000.172
3.08-3.246.724640.99899.90.144
3.24-3.446.624661.36799.80.123
3.44-3.716.624671.62499.60.105
3.71-4.08624801.94199.30.088
4.08-4.676.425121.88899.80.068
4.67-5.896.625471.7199.90.065
5.89-505.826662.99699.60.073

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHASER2.5.3phasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E7A

3e7a


Resolution: 2.285→31.428 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 2053 5.03 %
Rwork0.159 38736 -
obs0.1613 40789 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.58 Å2 / Biso mean: 58.9756 Å2 / Biso min: 31.23 Å2
Refinement stepCycle: final / Resolution: 2.285→31.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4917 0 26 223 5166
Biso mean--68.77 58.17 -
Num. residues----620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115078
X-RAY DIFFRACTIONf_angle_d1.0076836
X-RAY DIFFRACTIONf_chiral_restr0.041742
X-RAY DIFFRACTIONf_plane_restr0.004885
X-RAY DIFFRACTIONf_dihedral_angle_d13.6381852
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2734X-RAY DIFFRACTION3.804TORSIONAL
12C2734X-RAY DIFFRACTION3.804TORSIONAL
21B128X-RAY DIFFRACTION3.804TORSIONAL
22D128X-RAY DIFFRACTION3.804TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.285-2.33820.30621120.22222049216179
2.3382-2.39660.28511350.20362407254292
2.3966-2.46140.27141380.19152474261294
2.4614-2.53380.2441310.19122549268098
2.5338-2.61550.22061390.18732593273299
2.6155-2.7090.28241350.199926272762100
2.709-2.81740.25091470.192226342781100
2.8174-2.94550.2151410.184326212762100
2.9455-3.10070.23511510.179526252776100
3.1007-3.29470.21781310.183426402771100
3.2947-3.54880.21891350.16662661279699
3.5488-3.90530.20931160.15592680279699
3.9053-4.46910.15851420.12592640278299
4.4691-5.62530.16461390.124727292868100
5.6253-31.43080.18081610.14732807296899
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)
11.4661-0.61660.37463.56290.35011.63540.05740.0616-0.0987-0.1535-0.01570.15130.2558-0.0319-0.0330.4587-0.0477-0.00770.3044-0.01450.2823-16.889316.4702-12.8947
23.53422.4605-2.14365.4629-2.4971.56980.05030.37860.1117-1.5460.12910.22770.4631-0.251-0.01010.9344-0.0599-0.17880.463-0.11240.5012-24.01165.4067-28.4403
31.48350.5962-0.57623.5368-0.79322.1505-0.175-0.0932-0.3206-0.1842-0.0169-0.39040.80720.0390.0790.7210.05530.07990.33320.02050.41547.6285-9.79629.1649
46.6323-6.8502-2.65577.44382.34761.4885-0.5995-0.3669-1.1950.90330.23871.13680.69740.29620.31931.2272-0.00420.10480.55140.08880.5801-2.0729-20.975323.0865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 4:299A4 - 299
2X-RAY DIFFRACTION2chain B and resid 553:568B553 - 568
3X-RAY DIFFRACTION3chain C and resid 6:299C6 - 299
4X-RAY DIFFRACTION4chain D and resid 554:568D554 - 568

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more