[English] 日本語
Yorodumi
- PDB-4r30: Structure of human laforin dual specificity phosphatase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r30
TitleStructure of human laforin dual specificity phosphatase domain
ComponentsLaforin
KeywordsHYDROLASE / Dual specificity phosphatase / Glucan phosphatase / Malin / glycogen
Function / homology
Function and homology information


negative regulation of phosphatase activity / carbohydrate phosphatase activity / negative regulation of dephosphorylation / glycogen binding / carbohydrate phosphorylation / regulation of protein import into nucleus / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / L-glutamate transmembrane transport / starch binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases ...negative regulation of phosphatase activity / carbohydrate phosphatase activity / negative regulation of dephosphorylation / glycogen binding / carbohydrate phosphorylation / regulation of protein import into nucleus / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / L-glutamate transmembrane transport / starch binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / habituation / glycogen biosynthetic process / histone H2AXS139 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 / myosin phosphatase activity / calmodulin-dependent protein phosphatase activity / dephosphorylation / cytoplasmic side of rough endoplasmic reticulum membrane / glycogen metabolic process / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / negative regulation of cell cycle / peptidyl-tyrosine dephosphorylation / positive regulation of macroautophagy / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / autophagosome assembly / regulation of protein ubiquitination / glial cell proliferation / regulation of protein localization to plasma membrane / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / regulation of proteasomal protein catabolic process / Myoclonic epilepsy of Lafora / Glycogen synthesis / 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
BETA-MERCAPTOETHANOL / Laforin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSankhala, R.S. / Koksal, A.C. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Dimeric quaternary structure of human laforin.
Authors: Sankhala, R.S. / Koksal, A.C. / Ho, L. / Nitschke, F. / Minassian, B.A. / Cingolani, G.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Sep 20, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Laforin
B: Laforin
C: Laforin
D: Laforin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,31120
Polymers83,9894
Non-polymers1,32216
Water4,378243
1
A: Laforin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3285
Polymers20,9971
Non-polymers3304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Laforin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3285
Polymers20,9971
Non-polymers3304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Laforin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3285
Polymers20,9971
Non-polymers3304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Laforin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3285
Polymers20,9971
Non-polymers3304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.974, 123.974, 160.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

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


Mass: 20997.342 Da / Num. of mol.: 4
Fragment: dual specificity phosphatase domain (UNP residues 148-331)
Mutation: C266S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPM2A / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)
References: UniProt: O95278, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.68 Å3/Da / Density % sol: 66.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.10 M lithium sulfate, 0.05 M sodium cacodylate trihydrate, 0.1 M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 52012 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4738 / Rsym value: 0.8 / % possible all: 88.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RGO

3rgo


Resolution: 2.3→14.875 Å / SU ML: 0.28 / σ(F): 1 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1969 3.79 %RANDOM
Rwork0.1883 ---
obs0.1894 51890 96.91 %-
all-52012 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→14.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 68 243 6051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085952
X-RAY DIFFRACTIONf_angle_d1.1598056
X-RAY DIFFRACTIONf_dihedral_angle_d13.6062184
X-RAY DIFFRACTIONf_chiral_restr0.075864
X-RAY DIFFRACTIONf_plane_restr0.0061012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.33981480.31273162X-RAY DIFFRACTION87
2.3575-2.4210.38281140.31033480X-RAY DIFFRACTION95
2.421-2.49190.29271400.29643636X-RAY DIFFRACTION99
2.4919-2.57190.32271460.27583645X-RAY DIFFRACTION99
2.5719-2.66330.2861590.24233575X-RAY DIFFRACTION99
2.6633-2.76930.28511270.24243667X-RAY DIFFRACTION99
2.7693-2.89450.28011460.22033649X-RAY DIFFRACTION99
2.8945-3.04590.24251550.21143618X-RAY DIFFRACTION99
3.0459-3.23490.2161310.20183613X-RAY DIFFRACTION98
3.2349-3.48170.20621280.18613647X-RAY DIFFRACTION99
3.4817-3.82660.17781550.16993575X-RAY DIFFRACTION98
3.8266-4.3680.17711400.143596X-RAY DIFFRACTION98
4.368-5.45770.16321340.1373557X-RAY DIFFRACTION96
5.4577-14.87520.18991460.14943501X-RAY DIFFRACTION94
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)
12.6474-0.43240.42332.9739-0.26023.8379-0.0350.14470.049-0.1698-0.2667-0.5670.03581.02360.28980.4960.03730.02880.77510.13840.3766-3.3671-24.751622.6967
23.8233-0.88694.84599.2333-4.1727.2024-0.1908-0.7392-0.27790.6612-0.0320.1582-0.2587-0.21340.31450.35250.02970.03520.65270.01020.2815-18.6731-24.174937.3232
30.01790.2774-0.31373.18-3.69064.2639-0.3495-0.34470.25592.0043-0.8906-1.9764-1.38450.57351.33391.053-0.2226-0.25341.0201-0.09930.9569-8.7828-15.357237.0878
44.95294.55564.80274.30944.34114.762-0.4538-0.9591.06270.0039-0.5760.5592-1.5854-1.50251.19180.65320.0988-0.09380.7407-0.09470.473-22.0902-11.967326.2217
51.4152-2.7528-3.15315.34886.12867.0161-1.2422-0.9512-0.62461.68521.3414-0.18131.50490.3645-0.080.68170.05890.02650.66710.08450.4769-25.3514-28.22125.6095
63.4711.575-1.02264.0264-0.97693.2893-0.4645-0.36381.02590.69320.2265-0.1694-1.1985-0.01260.17960.61190.0536-0.24120.3597-0.08870.5044-31.5391-0.784855.5543
73.804-1.9671-0.51155.108-1.40453.9243-0.2391-0.26740.73520.074-0.0074-0.0552-0.8451-0.29950.28180.56830.0613-0.230.3562-0.06550.4854-35.6321.409249.1487
87.1904-3.0379-3.32779.66420.58711.6373-0.28571.20691.1434-0.3686-0.3493-0.4073-1.71750.1610.56880.9768-0.1121-0.29770.51870.10760.5162-34.09746.479839.9997
93.18531.17220.48841.9296-0.14662.5256-0.1596-0.36060.31770.2177-0.17140.1997-0.4437-0.50430.28660.29370.0842-0.09330.3714-0.10740.305-41.7306-10.543650.3562
105.20664.08564.33024.06414.20484.42350.1533-1.1652-0.30380.8479-0.3577-0.23680.0661-0.65640.02220.4660.0145-0.0360.53640.00550.2736-37.977-18.465364.2478
117.7498-1.04735.40780.1257-0.71483.753-0.9358-1.09870.43740.33240.6195-0.5395-0.8523-0.78110.08860.80260.29890.04431.134-0.31970.7016-46.7245-8.644463.6938
129.0533-4.8888-4.58858.85144.56653.1977-0.0623-0.56190.12220.963-0.1970.30390.5039-1.25030.31060.3671-0.12740.00070.709-0.00350.329-50.2493-22.141552.9724
134.01053.36733.04027.8840.52543.33550.6363-1.8788-0.11851.97-0.47770.58980.8807-0.5298-0.19620.6201-0.02060.15280.64890.03050.4984-33.877-25.352352.6899
145.07360.1430.85733.9488-0.63516.62750.30830.8332-0.206-0.4222-0.5875-0.58820.62321.39880.32450.61530.1410.13270.78790.11830.4111-2.8473-41.786842.2067
152.3029-0.32472.66886.6263-0.03763.2672-0.11490.56810.1275-0.289-0.1546-0.55570.0110.40450.23010.54790.06740.0680.68290.1380.4538-4.1168-40.562347.7183
167.49970.3206-1.70293.12433.01113.44340.3324-0.0161-1.3458-0.2025-0.4069-1.13051.91371.31720.28961.22830.37930.07940.95390.23470.75760.8736-55.246750.2047
175.95650.3015-2.33347.61192.70052.0743-0.0063-0.5278-0.13740.415-0.4223-0.82730.46310.67060.43140.67760.1341-0.00541.00590.20090.54913.1162-46.560757.8137
182.33681.2047-0.27382.62820.24512.8038-0.13630.2765-0.224-0.2165-0.104-0.25920.90090.01290.23030.78260.05370.10410.52380.03330.3357-15.4549-48.054647.4456
198.79661.2821-5.21243.135-3.92556.6255-0.51630.83260.0089-0.6810.46310.03720.2107-1.01370.23890.7012-0.0792-0.02930.74840.04010.3897-21.6726-41.908133.5375
202.1412-2.62682.22213.9763-2.44832.4042-0.00310.7007-0.1868-1.765-0.0595-1.44070.98930.6282-0.26751.3234-0.0110.29291.0769-0.24560.7016-15.5385-53.411633.9244
217.4906-4.1392-4.73524.2064.56789.0564-0.05380.9757-0.8406-0.2316-0.84660.39451.2406-1.75970.96090.8686-0.17620.03440.7627-0.1130.3979-29.2403-52.170944.886
225.2265.2916-2.55075.3558-2.61772.1241-0.69782.20070.3074-1.42451.14740.2560.7006-0.876-0.35160.81760.0145-0.02110.96180.01380.6204-26.7431-35.654545.18
233.466-0.1442-1.7112.70110.57932.3085-0.19990.26630.0481-0.244-0.10440.6918-0.0314-1.00560.24560.24140.0129-0.04950.5807-0.14410.4031-58.6644-20.689330.9596
242.91271.0153-2.8111.8958-2.43057.63220.29940.47371.27060.12140.29630.9692-1.15710.0122-0.47450.53070.3955-0.0340.8807-0.2170.7004-62.7779-6.675936.6422
252.6887-0.77420.49291.88680.68383.0605-0.2721-0.15090.15030.0222-0.06870.1555-0.4143-0.28740.2420.23510.0352-0.0670.2962-0.08080.2748-49.7647-15.297434.2528
260.26130.58640.33144.21512.70371.7354-0.74130.98280.8428-1.3770.00111.1628-1.6075-0.95420.58741.00320.0941-0.18040.95460.23160.7001-46.519-8.781820.5802
277.8367-0.2006-1.36378.9761-6.50018.0358-0.01280.56550.3187-0.6324-0.2465-0.5127-0.05770.51680.21050.274-0.0489-0.010.512-0.04750.2922-33.7142-15.895531.6208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 153 through 283 )
2X-RAY DIFFRACTION2chain 'A' and (resid 284 through 296 )
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 306 )
4X-RAY DIFFRACTION4chain 'A' and (resid 307 through 321 )
5X-RAY DIFFRACTION5chain 'A' and (resid 322 through 331 )
6X-RAY DIFFRACTION6chain 'B' and (resid 153 through 177 )
7X-RAY DIFFRACTION7chain 'B' and (resid 178 through 205 )
8X-RAY DIFFRACTION8chain 'B' and (resid 206 through 224 )
9X-RAY DIFFRACTION9chain 'B' and (resid 225 through 283 )
10X-RAY DIFFRACTION10chain 'B' and (resid 284 through 296 )
11X-RAY DIFFRACTION11chain 'B' and (resid 297 through 306 )
12X-RAY DIFFRACTION12chain 'B' and (resid 307 through 321 )
13X-RAY DIFFRACTION13chain 'B' and (resid 322 through 331 )
14X-RAY DIFFRACTION14chain 'C' and (resid 153 through 177 )
15X-RAY DIFFRACTION15chain 'C' and (resid 178 through 194 )
16X-RAY DIFFRACTION16chain 'C' and (resid 195 through 205 )
17X-RAY DIFFRACTION17chain 'C' and (resid 206 through 224 )
18X-RAY DIFFRACTION18chain 'C' and (resid 225 through 283 )
19X-RAY DIFFRACTION19chain 'C' and (resid 284 through 296 )
20X-RAY DIFFRACTION20chain 'C' and (resid 297 through 306 )
21X-RAY DIFFRACTION21chain 'C' and (resid 307 through 321 )
22X-RAY DIFFRACTION22chain 'C' and (resid 322 through 331 )
23X-RAY DIFFRACTION23chain 'D' and (resid 153 through 194 )
24X-RAY DIFFRACTION24chain 'D' and (resid 195 through 205 )
25X-RAY DIFFRACTION25chain 'D' and (resid 206 through 296 )
26X-RAY DIFFRACTION26chain 'D' and (resid 297 through 306 )
27X-RAY DIFFRACTION27chain 'D' and (resid 307 through 331 )

+
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