[English] 日本語
Yorodumi
- PDB-7ytj: Cryo-EM structure of VTC complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ytj
TitleCryo-EM structure of VTC complex
Components(Vacuolar transporter chaperone ...) x 3
KeywordsTRANSPORT PROTEIN / VTC complex / Poly P.
Function / homology
Function and homology information


vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / vacuole fusion, non-autophagic / microautophagy / polyphosphate metabolic process / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding ...vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / vacuole fusion, non-autophagic / microautophagy / polyphosphate metabolic process / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / vacuolar transport / fungal-type vacuole membrane / vacuolar membrane / autophagosome membrane / cell periphery / cell cortex / cytoplasmic vesicle / nuclear membrane / calmodulin binding / mRNA binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
VTC domain superfamily / Domain of unknown function DUF202 / VTC domain / Domain of unknown function (DUF202) / VTC domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PHOSPHATE ION / Vacuolar transporter chaperone complex subunit 1 / Vacuolar transporter chaperone complex subunit 4 / Vacuolar transporter chaperone 3 complex subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsGuan, Z.Y. / Chen, J. / Liu, R.W. / Chen, Y.K. / Xing, Q. / Du, Z.M. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: The cytoplasmic synthesis and coupled membrane translocation of eukaryotic polyphosphate by signal-activated VTC complex.
Authors: Zeyuan Guan / Juan Chen / Ruiwen Liu / Yanke Chen / Qiong Xing / Zhangmeng Du / Meng Cheng / Jianjian Hu / Wenhui Zhang / Wencong Mei / Beijing Wan / Qiang Wang / Jie Zhang / Peng Cheng / ...Authors: Zeyuan Guan / Juan Chen / Ruiwen Liu / Yanke Chen / Qiong Xing / Zhangmeng Du / Meng Cheng / Jianjian Hu / Wenhui Zhang / Wencong Mei / Beijing Wan / Qiang Wang / Jie Zhang / Peng Cheng / Huanyu Cai / Jianbo Cao / Delin Zhang / Junjie Yan / Ping Yin / Michael Hothorn / Zhu Liu /
Abstract: Inorganic polyphosphate (polyP) is an ancient energy metabolite and phosphate store that occurs ubiquitously in all organisms. The vacuolar transporter chaperone (VTC) complex integrates cytosolic ...Inorganic polyphosphate (polyP) is an ancient energy metabolite and phosphate store that occurs ubiquitously in all organisms. The vacuolar transporter chaperone (VTC) complex integrates cytosolic polyP synthesis from ATP and polyP membrane translocation into the vacuolar lumen. In yeast and in other eukaryotes, polyP synthesis is regulated by inositol pyrophosphate (PP-InsP) nutrient messengers, directly sensed by the VTC complex. Here, we report the cryo-electron microscopy structure of signal-activated VTC complex at 3.0 Å resolution. Baker's yeast VTC subunits Vtc1, Vtc3, and Vtc4 assemble into a 3:1:1 complex. Fifteen trans-membrane helices form a novel membrane channel enabling the transport of newly synthesized polyP into the vacuolar lumen. PP-InsP binding orients the catalytic polymerase domain at the entrance of the trans-membrane channel, both activating the enzyme and coupling polyP synthesis and membrane translocation. Together with biochemical and cellular studies, our work provides mechanistic insights into the biogenesis of an ancient energy metabolite.
History
DepositionAug 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Vacuolar transporter chaperone 4
A: Vacuolar transporter chaperone 1
B: Vacuolar transporter chaperone 1
C: Vacuolar transporter chaperone 1
E: Vacuolar transporter chaperone 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,12812
Polymers234,3785
Non-polymers3,7507
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Vacuolar transporter chaperone ... , 3 types, 5 molecules DABCE

#1: Protein Vacuolar transporter chaperone 4 / Phosphate metabolism protein 3


Mass: 86425.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VTC4, PHM3, YJL012C, J1345 / Production host: Homo sapiens (human) / References: UniProt: P47075
#2: Protein Vacuolar transporter chaperone 1 / Negative regulator of CDC42 protein 1 / Phosphate metabolism protein 4


Mass: 15943.701 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VTC1, NRF1, PHM4, YER072W / Production host: Homo sapiens (human) / References: UniProt: P40046
#3: Protein Vacuolar transporter chaperone 3 / Phosphate metabolism protein 2


Mass: 100120.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VTC3, PHM2, YPL019C / Production host: Homo sapiens (human) / References: UniProt: Q02725

-
Non-polymers , 3 types, 7 molecules

#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: VTC complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 8
SpecimenConc.: 6.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: cryoSPARC / Category: classification
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 734934 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313433
ELECTRON MICROSCOPYf_angle_d0.61518185
ELECTRON MICROSCOPYf_dihedral_angle_d8.6121888
ELECTRON MICROSCOPYf_chiral_restr0.0432001
ELECTRON MICROSCOPYf_plane_restr0.0062268

+
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