[English] 日本語
Yorodumi
- PDB-2ej8: Crystal structure of APPL1 PTB domain at 1.8A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ej8
TitleCrystal structure of APPL1 PTB domain at 1.8A
ComponentsDCC-interacting protein 13 alpha
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / protein kinase B binding / regulation of D-glucose import / maintenance of synapse structure / signaling / positive regulation of melanin biosynthetic process ...negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / protein kinase B binding / regulation of D-glucose import / maintenance of synapse structure / signaling / positive regulation of melanin biosynthetic process / regulation of toll-like receptor 4 signaling pathway / early phagosome / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of cytokine production involved in inflammatory response / vesicle membrane / cellular response to hepatocyte growth factor stimulus / intracellular vesicle / regulation of innate immune response / phosphatidylserine binding / beta-tubulin binding / regulation of G1/S transition of mitotic cell cycle / regulation of protein localization to plasma membrane / ruffle / transforming growth factor beta receptor signaling pathway / phosphatidylinositol binding / positive regulation of D-glucose import / protein import into nucleus / insulin receptor signaling pathway / presynapse / early endosome membrane / cytoplasmic vesicle / postsynapse / early endosome / endosome membrane / endosome / glutamatergic synapse / protein-containing complex binding / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
APPL1, BAR domain / : / : / : / BAR domain of APPL family / BAR domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain ...APPL1, BAR domain / : / : / : / BAR domain of APPL family / BAR domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / AH/BAR domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
DCC-interacting protein 13-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsTanabe, H. / Hosaka, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of APPL1 PTB domain at 1.8A
Authors: Tanabe, H. / Hosaka, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMar 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DCC-interacting protein 13 alpha
B: DCC-interacting protein 13 alpha


Theoretical massNumber of molelcules
Total (without water)36,1092
Polymers36,1092
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-10.8 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.230, 63.566, 52.449
Angle α, β, γ (deg.)90.00, 102.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DCC-interacting protein 13 alpha / Dip13 alpha / Adapter protein containing PH domain / PTB domain and leucine zipper motif 1


Mass: 18054.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: E.coli Cell-free expression system / Gene: APPL1 / References: UniProt: Q9UKG1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100mM Na Citrate, 10% PEG 3350, 15% Isopropanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 24816 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5652 % / Rmerge(I) obs: 0.104 / Rsym value: 0.103 / Net I/σ(I): 9.59801
Reflection shellResolution: 1.84→1.92 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.73783 / Num. unique all: 1784 / Rsym value: 0.331 / % possible all: 91.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.075 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; ANOMALOUS DATA WAS USED IN THE REFINEMENT. THE FRIEDEL PAIRS WERE USED FOR POHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.23014 1280 5.1 %RANDOM
Rwork0.19332 ---
obs0.19526 23949 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.701 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-1.48 Å2
2--0.16 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 0 168 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212123
X-RAY DIFFRACTIONr_bond_other_d0.0050.021923
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9542878
X-RAY DIFFRACTIONr_angle_other_deg0.80534449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6845260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022328
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02426
X-RAY DIFFRACTIONr_nbd_refined0.3640.2449
X-RAY DIFFRACTIONr_nbd_other0.2530.22287
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.21310
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4761.51316
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.79722143
X-RAY DIFFRACTIONr_scbond_it3.7933807
X-RAY DIFFRACTIONr_scangle_it6.4084.5735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 72
Rwork0.258 1784

+
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