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- EMDB-34090: Cryo-EM structure of VTC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-34090
TitleCryo-EM structure of VTC complex
Map data
Sample
  • Complex: VTC complex
    • Protein or peptide: Vacuolar transporter chaperone 4
    • Protein or peptide: Vacuolar transporter chaperone 1
    • Protein or peptide: Vacuolar transporter chaperone 3
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PHOSPHATE ION
KeywordsVTC complex / Poly P. / TRANSPORT PROTEIN
Function / homology
Function and homology information


vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / vacuole fusion, non-autophagic / 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 / microautophagy / vacuole fusion, non-autophagic / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGuan ZY / Chen J / Liu RW / Chen YK / Xing Q / Du ZM / Liu Z
Funding support China, 1 items
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, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34090.png

Downloads & links

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Map

FileDownload / File: emd_34090.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-3.0776942 - 4.564936
Average (Standard dev.)0.0021790557 (±0.08858412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34090_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34090_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VTC complex

EntireName: VTC complex
Components
  • Complex: VTC complex
    • Protein or peptide: Vacuolar transporter chaperone 4
    • Protein or peptide: Vacuolar transporter chaperone 1
    • Protein or peptide: Vacuolar transporter chaperone 3
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PHOSPHATE ION

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Supramolecule #1: VTC complex

SupramoleculeName: VTC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Vacuolar transporter chaperone 4

MacromoleculeName: Vacuolar transporter chaperone 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 86.425984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAKFGEHLSK SLIRQYSYYY ISYDDLKTEL EDNLSKNNGQ WTQELETDFL ESLEIELDKV YTFCKVKHSE VFRRVKEVQE QVQHTVRLL DSNNPPTQLD FEILEEELSD IIADVHDLAK FSRLNYTGFQ KIIKKHDKKT GFILKPVFQV RLDSKPFFKE N YDELVVKI ...String:
MAKFGEHLSK SLIRQYSYYY ISYDDLKTEL EDNLSKNNGQ WTQELETDFL ESLEIELDKV YTFCKVKHSE VFRRVKEVQE QVQHTVRLL DSNNPPTQLD FEILEEELSD IIADVHDLAK FSRLNYTGFQ KIIKKHDKKT GFILKPVFQV RLDSKPFFKE N YDELVVKI SQLYDIARTS GRPIKGDSSA GGKQQNFVRQ TTKYWVHPDN ITELKLIILK HLPVLVFNTN KEFEREDSAI TS IYFDNEN LDLYYGRLRK DEGAEAHALA WYGGMSTDTI FVERKTHRED WTGEKSVKAR FALKERHVND FLKGKYTVDQ VFA KMRKEG KKPMNEIENL EALASEIQYV MLKKKLRPVV RSFYNRTAFQ LPGDARVRIS LDTELTMVRE DNFDGVDRTH KNWR RTDIG VDWPFKQLDD KDICRFPYAV LNVKLQTQLG QEPPEWVREL VGSHLVEPVP KFSKFIHGVA TLLNDKVDSI PFWLP QMDV DIRKPPLPTN IEITRPGRSD NEDNDFDEDD EDDAALVAAM TNAPGNSLDI EESVGYGATS APTSNTNHVV ESANAA YYQ RKIRNAENPI SKKYYEIVAF FDHYFNGDQI SKIPKGTTFD TQIRAPPGKT ICVPVRVEPK VYFATERTYL SWLSISI LL GGVSTTLLTY GSPTAMIGSI GFFITSLAVL IRTVMVYAKR VVNIRLKRAV DYEDKIGPGM VSVFLILSIL FSFFCNLV A KLESAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

UniProtKB: Vacuolar transporter chaperone complex subunit 4

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Macromolecule #2: Vacuolar transporter chaperone 1

MacromoleculeName: Vacuolar transporter chaperone 1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.943701 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASSAPLLQR TPGKKIALPT RVEPKVFFAN ERTFLSWLNF TVMLGGLGVG LLNFGDKIGR VSAGLFTFVA MGTMIYALVT YHWRAAAIR RRGSGPYDDR LGPTLLCFFL LVAVIINFIL RLKYNDANTK LLESAYPYDV PDYA

UniProtKB: Vacuolar transporter chaperone complex subunit 1

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Macromolecule #3: Vacuolar transporter chaperone 3

MacromoleculeName: Vacuolar transporter chaperone 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 100.120773 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG DYKDDDDKID YKDDDDKGSM LFGIKLANDV YPPWKDSYID YERLKKLLKE SVIHDGRSSV DSWSERNESD FVEALDKEL EKVYTFQISK YNAVLRKLDD LEENTKSAEK IQKINSEQFK NTLEECLDEA QRLDNFDRLN FTGFIKIVKK H DKLHPNYP ...String:
MDYKDDDDKG DYKDDDDKID YKDDDDKGSM LFGIKLANDV YPPWKDSYID YERLKKLLKE SVIHDGRSSV DSWSERNESD FVEALDKEL EKVYTFQISK YNAVLRKLDD LEENTKSAEK IQKINSEQFK NTLEECLDEA QRLDNFDRLN FTGFIKIVKK H DKLHPNYP SVKSLLQVRL KELPFNNSEE YSPLLYRISY LYEFLRSNYD HPNTVSKSLA STSKLSHFSN LEDASFKSYK FW VHDDNIM EVKARILRHL PALVYASVPN ENDDFVDNLE SDVRVQPEAR LNIGSKSNSL SSDGNSNQDV EIGKSKSVIF PQS YDPTIT TLYFDNDFFD LYNNRLLKIS GAPTLRLRWI GKLLDKPDIF LEKRTFTENT ETGNSSFEEI RLQMKAKFIN NFIF KNDPS YKNYLINQLR ERGTQKEELE KLSRDFDNIQ NFIVEEKLQP VLRATYNRTA FQIPGDQSIR VTIDSNIMYI REDSL DKNR PIRNPENWHR DDIDSNIPNP LRFLRAGEYS KFPYSVMEIK VINQDNSQMP NYEWIKDLTN SHLVNEVPKF SLYLQG VAS LFGEDDKYVN ILPFWLPDLE TDIRKNPQEA YEEEKKTLQK QKSIHDKLDN MRRLSKISVP DGKTTERQGQ KDQNTRH VI ADLEDHESSD EEGTALPKKS AVKKGKKFKT NAAFLKILAG KNISENGNDP YSDDTDSASS FQLPPGVKKP VHLLKNAG P VKVEAKVWLA NERTFNRWLS VTTLLSVLTF SIYNSVQKAE FPQLADLLAY VYFFLTLFCG VWAYRTYLKR LTLIKGRSG KHLDAPVGPI LVAVVLIVTL VVNFSVAFKE AARRERGLVN VSSQPSLPRT LKPIQDFIFN LVGE

UniProtKB: Vacuolar transporter chaperone 3 complex subunit 3

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Macromolecule #4: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #5: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #6: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 734934
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC

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