[English] 日本語
Yorodumi
- PDB-2n73: Solution structure of the ACBD3:PI4KB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n73
TitleSolution structure of the ACBD3:PI4KB complex
Components
  • Golgi resident protein GCP60
  • Phosphatidylinositol 4-kinase beta
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / kinase / TRANSFERASE-TRANSFERASE REGULATOR complex
Function / homology
Function and homology information


1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / fatty-acyl-CoA binding / Synthesis of PIPs at the Golgi membrane / steroid biosynthetic process / phosphatidylinositol biosynthetic process / Golgi Associated Vesicle Biogenesis / lysosome organization / protein kinase A regulatory subunit binding ...1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / fatty-acyl-CoA binding / Synthesis of PIPs at the Golgi membrane / steroid biosynthetic process / phosphatidylinositol biosynthetic process / Golgi Associated Vesicle Biogenesis / lysosome organization / protein kinase A regulatory subunit binding / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / inner ear development / 14-3-3 protein binding / receptor-mediated endocytosis / mitochondrial outer membrane / endosome / phosphorylation / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / mitochondrion / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
Golgi-dynamics membrane-trafficking / : / PI4KB/PIK1, accessory (PIK) domain / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily ...Golgi-dynamics membrane-trafficking / : / PI4KB/PIK1, accessory (PIK) domain / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / FERM/acyl-CoA-binding protein superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 4-kinase beta / Golgi resident protein GCP60 / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsVeverka, V. / Hexnerova, R.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights and in vitro reconstitution of membrane targeting and activation of human PI4KB by the ACBD3 protein.
Authors: Klima, M. / Toth, D.J. / Hexnerova, R. / Baumlova, A. / Chalupska, D. / Tykvart, J. / Rezabkova, L. / Sengupta, N. / Man, P. / Dubankova, A. / Humpolickova, J. / Nencka, R. / Veverka, V. / Balla, T. / Boura, E.
History
DepositionSep 2, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Golgi resident protein GCP60
B: Phosphatidylinositol 4-kinase beta


Theoretical massNumber of molelcules
Total (without water)16,3032
Polymers16,3032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-13 kcal/mol
Surface area13140 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)45 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Golgi resident protein GCP60 / Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi ...Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi phosphoprotein 1 / GOLPH1 / PBR- and PKA-associated protein 7 / Peripheral benzodiazepine receptor-associated protein PAP7


Mass: 8293.208 Da / Num. of mol.: 1 / Fragment: UNP residues 241-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACBD3, GCP60, GOCAP1, GOLPH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3P7
#2: Protein Phosphatidylinositol 4-kinase beta


Mass: 8010.131 Da / Num. of mol.: 1 / Fragment: UNP residues 5-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J1S8, UniProt: Q9UBF8*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CO)CA
1512D 1H-15N HSQC
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY

-
Sample preparation

DetailsContents: 0.47 mM [U-13C; U-15N] protein_1, 0.47 mM [U-13C; U-15N] protein_2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.47 mMprotein_1-1[U-13C; U-15N]1
0.47 mMprotein_2-2[U-13C; U-15N]1
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8502

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 45

+
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://pdbjlvh1.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