[English] 日本語
Yorodumi
- PDB-9f6s: PDZ domain in complex with the peptide from AP2-associated protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f6s
TitlePDZ domain in complex with the peptide from AP2-associated protein kinase 1
Components
  • AP2-associated protein kinase 1
  • PDZ and LIM domain protein 5
KeywordsCYTOSOLIC PROTEIN / PDZ / AP2 / kinase
Function / homology
Function and homology information


muscle structure development / regulation of clathrin-dependent endocytosis / cell growth involved in cardiac muscle cell development / AP-2 adaptor complex binding / muscle alpha-actinin binding / cadherin binding involved in cell-cell adhesion / regulation of dendritic spine morphogenesis / membrane organization / actinin binding / Notch binding ...muscle structure development / regulation of clathrin-dependent endocytosis / cell growth involved in cardiac muscle cell development / AP-2 adaptor complex binding / muscle alpha-actinin binding / cadherin binding involved in cell-cell adhesion / regulation of dendritic spine morphogenesis / membrane organization / actinin binding / Notch binding / clathrin-coated vesicle / Neurexins and neuroligins / regulation of synapse assembly / positive regulation of Notch signaling pathway / presynaptic endocytosis / cell leading edge / filamentous actin / stress fiber / clathrin-coated pit / protein kinase C binding / cell projection / adherens junction / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / Z disc / terminal bouton / Cargo recognition for clathrin-mediated endocytosis / actin cytoskeleton / presynapse / Clathrin-mediated endocytosis / regulation of protein localization / actin binding / heart development / actin cytoskeleton organization / non-specific serine/threonine protein kinase / protein stabilization / postsynaptic density / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / ATP binding / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...: / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
AP2-associated protein kinase 1 / PDZ and LIM domain protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsBenova, V. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: PDZ domain in complex with the peptide from AP2-associated protein kinase 1
Authors: Benova, V. / Boura, E.
History
DepositionMay 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PDZ and LIM domain protein 5
B: AP2-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)10,0712
Polymers10,0712
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-2 kcal/mol
Surface area5110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.930, 37.840, 52.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein PDZ and LIM domain protein 5 / Enigma homolog / Enigma-like PDZ and LIM domains protein


Mass: 9355.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDLIM5, ENH, L9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96HC4
#2: Protein/peptide AP2-associated protein kinase 1 / Adaptor-associated kinase 1


Mass: 715.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAK1, KIAA1048 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2M2I8, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 2.0 M Ammonium sulfate, 0.1 M Sodium cacodylate 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1→30.68 Å / Num. obs: 39979 / % possible obs: 98.88 % / Redundancy: 12 % / CC1/2: 1 / Rmerge(I) obs: 0.03947 / Net I/σ(I): 24.56
Reflection shellResolution: 1→1.036 Å / Rmerge(I) obs: 2.353 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 3611 / CC1/2: 0.466

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→30.68 Å / SU ML: 0.1166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 1106 2.77 %
Rwork0.2 38827 -
obs0.2004 39933 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.58 Å2
Refinement stepCycle: LAST / Resolution: 1→30.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms659 0 0 104 763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084715
X-RAY DIFFRACTIONf_angle_d1.0687972
X-RAY DIFFRACTIONf_chiral_restr0.0802111
X-RAY DIFFRACTIONf_plane_restr0.0093131
X-RAY DIFFRACTIONf_dihedral_angle_d6.4022105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.050.38411260.37284416X-RAY DIFFRACTION91.72
1.05-1.10.31531370.29074807X-RAY DIFFRACTION99.52
1.1-1.170.26551380.23914860X-RAY DIFFRACTION99.98
1.17-1.260.24861400.21954891X-RAY DIFFRACTION99.94
1.26-1.390.22511370.2134838X-RAY DIFFRACTION99.96
1.39-1.590.22211410.19414930X-RAY DIFFRACTION99.96
1.59-20.211400.20484938X-RAY DIFFRACTION99.98
2-30.680.19361470.18125147X-RAY DIFFRACTION99.87

+
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