[English] 日本語
Yorodumi
- PDB-3lny: Second PDZ domain from human PTP1E in complex with RA-GEF2 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lny
TitleSecond PDZ domain from human PTP1E in complex with RA-GEF2 peptide
Components
  • Rap guanine nucleotide exchange factor 6
  • Tyrosine-protein phosphatase non-receptor type 13
Keywordssignaling protein/signaling protein / PDZ2 / Structural Genomics / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG / Cytoskeleton / Cell membrane / Guanine-nucleotide releasing factor / signaling protein-signaling protein complex
Function / homology
Function and homology information


negative regulation of excitatory synapse assembly / microvillus assembly / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTP-dependent protein binding / phosphatidic acid binding / phosphatidylinositol 3-kinase regulatory subunit binding / cellular response to toxic substance / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle ...negative regulation of excitatory synapse assembly / microvillus assembly / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTP-dependent protein binding / phosphatidic acid binding / phosphatidylinositol 3-kinase regulatory subunit binding / cellular response to toxic substance / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of GTPase activity / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation / negative regulation of protein phosphorylation / endocytic vesicle / protein dephosphorylation / protein tyrosine phosphatase activity / positive regulation of GTPase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / guanyl-nucleotide exchange factor activity / protein localization to plasma membrane / small GTPase binding / lamellipodium / cell body / Ras protein signal transduction / cytoskeleton / apical plasma membrane / centrosome / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / PDZ domain / Pdz3 Domain / Cyclic nucleotide-monophosphate binding domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / RmlC-like jelly roll fold / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Tyrosine-protein phosphatase non-receptor type 13 / Rap guanine nucleotide exchange factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhang, J. / Chang, A. / Ke, H. / Phillips Jr., G.N. / Lee, A.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Biochemistry / Year: 2010
Title: Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E.
Authors: Zhang, J. / Sapienza, P.J. / Ke, H. / Chang, A. / Hengel, S.R. / Wang, H. / Phillips, G.N. / Lee, A.L.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Tyrosine-protein phosphatase non-receptor type 13
B: Rap guanine nucleotide exchange factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9025
Polymers10,6522
Non-polymers2503
Water4,288238
1
A: Tyrosine-protein phosphatase non-receptor type 13
B: Rap guanine nucleotide exchange factor 6
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)65,41330
Polymers63,91212
Non-polymers1,50118
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area11900 Å2
ΔGint-258 kcal/mol
Surface area24080 Å2
Unit cell
Length a, b, c (Å)73.965, 73.965, 134.056
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-99-

SO4

21A-209-

HOH

31A-255-

HOH

41A-263-

HOH

DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: -x+y,-x,z:-y,x-y,z:Y+2/3,x+1/3,-z+1/3:X-Y+2/3,-Y+1/3,-Z+1/3,-X+2/3,-X+Y+1/3, -Z+1/3

-
Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 13 / Protein-tyrosine phosphatase 1E / PTP-E1 / hPTPE1 / PTP-BAS / Protein-tyrosine phosphatase PTPL1 / ...Protein-tyrosine phosphatase 1E / PTP-E1 / hPTPE1 / PTP-BAS / Protein-tyrosine phosphatase PTPL1 / Fas-associated protein-tyrosine phosphatase 1 / FAP-1


Mass: 10020.252 Da / Num. of mol.: 1 / Fragment: PDZ2 domain
Source method: isolated from a genetically manipulated source
Details: NdeI BamHI restriction sites / Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN13, PNP1, PTP1E, PTPL1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12923
#2: Protein/peptide Rap guanine nucleotide exchange factor 6 / PDZ domain-containing guanine nucleotide exchange factor 2 / PDZ-GEF2 / RA-GEF-2


Mass: 631.675 Da / Num. of mol.: 1 / Fragment: C-terminal residues 1596-1601
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAPGEF6, PDZGEF2 / References: UniProt: Q8TEU7
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 3350, 0.8 M (NH4)2SO4, 0.2 M NaSCN, 0.1 M Na citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0809
SYNCHROTRONNSLS X29A21.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHx-ray1
2Si(111)SINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 34689 / % possible obs: 99.1 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.056 / Χ2: 1.237 / Net I/σ(I): 21.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.3210.70.1817111.3591,297.7
1.32-1.3510.80.14916831.3471,297.9
1.35-1.3710.80.1316951.3661,298
1.37-1.410.80.11716861.4021,298.3
1.4-1.4310.80.10217101.3981,298.3
1.43-1.4610.80.09516961.3851,298.5
1.46-1.510.80.0817191.3561,298.7
1.5-1.5410.80.0717191.2531,298.7
1.54-1.5910.80.06417071.1261,299.1
1.59-1.6410.80.06317361.0691,299.1
1.64-1.710.80.05917111.0681,299.2
1.7-1.7610.80.06217531.161,299.4
1.76-1.8410.80.06117281.1141,299.6
1.84-1.9410.80.05917410.7061,299.7
1.94-2.0615.90.10217620.8481,299.7
2.06-2.2221.30.09317371.3661,299.9
2.22-2.4520.60.07917551.5131,299.8
2.45-2.821.60.06517731.1621,2100
2.8-3.5319.70.05117951.0761,2100
3.53-5014.60.03418721.5651,299.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→29.695 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.15 / σ(F): 0.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 1974 5.77 %
Rwork0.163 --
obs0.164 34191 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.695 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 374.25 Å2 / Biso mean: 33.131 Å2 / Biso min: 8.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.917 Å20 Å20 Å2
2---2.917 Å2-0 Å2
3---5.027 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 0 12 238 984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016821
X-RAY DIFFRACTIONf_angle_d1.6051102
X-RAY DIFFRACTIONf_chiral_restr0.091131
X-RAY DIFFRACTIONf_plane_restr0.007148
X-RAY DIFFRACTIONf_dihedral_angle_d15.696299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.3320.2111320.162195232794
1.332-1.3680.1851390.1462225236495
1.368-1.4090.1991360.1462232236896
1.409-1.4540.1951380.1462256239497
1.454-1.5060.211410.1432292243397
1.506-1.5660.1871380.1462262240098
1.566-1.6380.1921420.1472312245498
1.638-1.7240.181400.1392294243498
1.724-1.8320.1671430.1412308245199
1.832-1.9740.1511420.1352318246099
1.974-2.1720.1771430.1412344248799
2.172-2.4860.1991440.1512344248899
2.486-3.1320.1941440.1592367251199
3.132-29.7030.1871520.1922468262099

+
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