[English] 日本語
Yorodumi
- PDB-4rkk: Structure of a product bound phosphatase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rkk
TitleStructure of a product bound phosphatase
ComponentsLaforin
KeywordsHYDROLASE / Dual Specificity Phosphatase / Carbohydrate Binding Module / Phosphatase
Function / homology
Function and homology information


negative regulation of phosphatase activity / carbohydrate phosphatase activity / negative regulation of dephosphorylation / glycogen binding / regulation of protein import into nucleus / carbohydrate phosphorylation / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / L-glutamate transmembrane transport / starch binding / habituation ...negative regulation of phosphatase activity / carbohydrate phosphatase activity / negative regulation of dephosphorylation / glycogen binding / regulation of protein import into nucleus / carbohydrate phosphorylation / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / L-glutamate transmembrane transport / starch binding / habituation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / glycogen biosynthetic process / dephosphorylation / cytoplasmic side of rough endoplasmic reticulum membrane / glycogen metabolic process / protein-serine/threonine phosphatase / phosphatase activity / protein serine/threonine phosphatase activity / negative regulation of cell cycle / peptidyl-tyrosine dephosphorylation / positive regulation of macroautophagy / autophagosome assembly / regulation of protein ubiquitination / regulation of proteasomal protein catabolic process / Myoclonic epilepsy of Lafora / Glycogen synthesis / glial cell proliferation / regulation of protein localization to plasma membrane / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitochondrion organization / regulation of cell growth / Wnt signaling pathway / calcium ion transport / carbohydrate binding / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / protein dimerization activity / negative regulation of gene expression / dendrite / protein homodimerization activity / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Laforin, CBM20 domain / Laforin / Laforin-like, dual specificity phosphatase domain / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Dual specificity phosphatase, catalytic domain / Carbohydrate-binding-like fold / Dual specificity phosphatase, catalytic domain ...Laforin, CBM20 domain / Laforin / Laforin-like, dual specificity phosphatase domain / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Dual specificity phosphatase, catalytic domain / Carbohydrate-binding-like fold / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / alpha-maltotetraose / alpha-maltohexaose / alpha-D-glucopyranose / PHOSPHATE ION / Laforin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsVander Kooi, C.W.
CitationJournal: Mol.Cell / Year: 2015
Title: Structural mechanism of laforin function in glycogen dephosphorylation and lafora disease.
Authors: Raththagala, M. / Brewer, M.K. / Parker, M.W. / Sherwood, A.R. / Wong, B.K. / Hsu, S. / Bridges, T.M. / Paasch, B.C. / Hellman, L.M. / Husodo, S. / Meekins, D.A. / Taylor, A.O. / Turner, B.D. ...Authors: Raththagala, M. / Brewer, M.K. / Parker, M.W. / Sherwood, A.R. / Wong, B.K. / Hsu, S. / Bridges, T.M. / Paasch, B.C. / Hellman, L.M. / Husodo, S. / Meekins, D.A. / Taylor, A.O. / Turner, B.D. / Auger, K.D. / Dukhande, V.V. / Chakravarthy, S. / Sanz, P. / Woods, V.L. / Li, S. / Vander Kooi, C.W. / Gentry, M.S.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Laforin
C: Laforin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,73312
Polymers74,5352
Non-polymers5,19810
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint44 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.706, 78.706, 321.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 2 molecules AC

#1: Protein Laforin / Glucan phosphatase / Lafora PTPase / LAFPTPase


Mass: 37267.480 Da / Num. of mol.: 2 / Mutation: C266S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPM2A / Production host: Escherichia coli (E. coli)
References: UniProt: O95278, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase

-
Sugars , 4 types, 8 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltohexaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 990.860 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltohexaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 146 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.3463.13
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, hanging drop5250 mM maltohexaose, 0.19 M Sodium Acetate, 0.1 M Sodium Citrate, 25.5% PEG3350, 15% Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2772vapor diffusion, hanging drop5250 mM maltohexaose, 0.17 M Sodium Acetate, 0.08 M Sodium Citrate, 25.5% PEG4000, 15% Glycerol, 30 mM Sodium Tungstate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11.0000, 1.2148
2
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDJun 7, 2013
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)SINGLE WAVELENGTHMx-ray1
2Si (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.21481
ReflectionResolution: 2.4→20 Å / Num. obs: 37585 / % possible obs: 92.3 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.49 Å / % possible all: 92

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.8.2model building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.026 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21053 3582 9.6 %RANDOM
Rwork0.16634 ---
obs0.17055 33896 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.542 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 345 144 5511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195542
X-RAY DIFFRACTIONr_bond_other_d0.0010.025060
X-RAY DIFFRACTIONr_angle_refined_deg1.5432.0127571
X-RAY DIFFRACTIONr_angle_other_deg0.952311566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4322.846246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38815825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5891542
X-RAY DIFFRACTIONr_chiral_restr0.1450.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021281
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_it3.3856.3722526
X-RAY DIFFRACTIONr_mcbond_other3.3876.3692525
X-RAY DIFFRACTIONr_mcangle_it5.00111.9113151
X-RAY DIFFRACTIONr_mcangle_other511.9163152
X-RAY DIFFRACTIONr_scbond_it5.2358.1453016
X-RAY DIFFRACTIONr_scbond_other5.2348.1483017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.65514.8084420
X-RAY DIFFRACTIONr_long_range_B_refined9.31138.396040
X-RAY DIFFRACTIONr_long_range_B_other9.31638.2535992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 253 -
Rwork0.244 2408 -
obs--90.63 %
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)
12.1409-0.9442-0.55651.6434-0.0191.4378-0.0811-0.05090.12220.16540.16130.0178-0.3132-0.2079-0.08020.19930.1038-0.01110.0683-0.0080.031247.45775.316137.657
21.7888-1.02060.68961.8298-0.34431.4029-0.1493-0.0683-0.13840.12340.18730.02580.12080.1131-0.03790.12890.0730.05470.05630.02060.04866.84433.966139.893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 325
2X-RAY DIFFRACTION2C-2 - 323

+
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://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