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- EMDB-35208: Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc... -

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Basic information

Entry
Database: EMDB / ID: EMD-35208
TitleCryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
Map data
Sample
  • Complex: Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 1
    • Protein or peptide: Vacuolar transporter chaperone 3 complex subunit 3
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 4
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: PHOSPHATE ION
  • Ligand: TRIPHOSPHATE
  • Ligand: MANGANESE (II) ION
  • Ligand: water
Keywordspolyphosphate polymerase / VTC complex / coupled synthesis and translocation / MEMBRANE 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 (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsMayer A / Wu S / Ye S
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908500 China
Ministry of Science and Technology (MoST, China)2020YFA0908400 China
National Natural Science Foundation of China (NSFC)31971127 China
National Natural Science Foundation of China (NSFC)31900930 China
CitationJournal: EMBO J / Year: 2023
Title: Cryo-EM structure of the polyphosphate polymerase VTC reveals coupling of polymer synthesis to membrane transit.
Authors: Wei Liu / Jiening Wang / Véronique Comte-Miserez / Mengyu Zhang / Xuejing Yu / Qingfeng Chen / Henning Jacob Jessen / Andreas Mayer / Shan Wu / Sheng Ye /
Abstract: The eukaryotic vacuolar transporter chaperone (VTC) complex acts as a polyphosphate (polyP) polymerase that synthesizes polyP from adenosine triphosphate (ATP) and translocates polyP across the ...The eukaryotic vacuolar transporter chaperone (VTC) complex acts as a polyphosphate (polyP) polymerase that synthesizes polyP from adenosine triphosphate (ATP) and translocates polyP across the vacuolar membrane to maintain an intracellular phosphate (P ) homeostasis. To discover how the VTC complex performs its function, we determined a cryo-electron microscopy structure of an endogenous VTC complex (Vtc4/Vtc3/Vtc1) purified from Saccharomyces cerevisiae at 3.1 Å resolution. The structure reveals a heteropentameric architecture of one Vtc4, one Vtc3, and three Vtc1 subunits. The transmembrane region forms a polyP-selective channel, likely adopting a resting state conformation, in which a latch-like, horizontal helix of Vtc4 limits the entrance. The catalytic Vtc4 central domain is located on top of the pseudo-symmetric polyP channel, creating a strongly electropositive pathway for nascent polyP that can couple synthesis to translocation. The SPX domain of the catalytic Vtc4 subunit positively regulates polyP synthesis by the VTC complex. The noncatalytic Vtc3 regulates VTC through a phosphorylatable loop. Our findings, along with the functional data, allow us to propose a mechanism of polyP channel gating and VTC complex activation.
History
DepositionJan 29, 2023-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35208.png

Downloads & links

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Map

FileDownload / File: emd_35208.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.851 Å
Density
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.09325098 - 0.15957512
Average (Standard dev.)0.000060211412 (±0.0035143248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_35208_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35208_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35208_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc...

EntireName: Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
Components
  • Complex: Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 1
    • Protein or peptide: Vacuolar transporter chaperone 3 complex subunit 3
    • Protein or peptide: Vacuolar transporter chaperone complex subunit 4
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: PHOSPHATE ION
  • Ligand: TRIPHOSPHATE
  • Ligand: MANGANESE (II) ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc...

SupramoleculeName: Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: Vacuolar transporter chaperone complex subunit 1

MacromoleculeName: Vacuolar transporter chaperone complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 14.388053 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSSAPLLQRT PGKKIALPTR VEPKVFFANE RTFLSWLNFT VMLGGLGVGL LNFGDKIGRV SAGLFTFVAM GTMIYALVTY HWRAAAIRR RGSGPYDDRL GPTLLCFFLL VAVIINFILR LKYNDANTKL

UniProtKB: Vacuolar transporter chaperone complex subunit 1

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Macromolecule #2: Vacuolar transporter chaperone 3 complex subunit 3

MacromoleculeName: Vacuolar transporter chaperone 3 complex subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 96.684312 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLFGIKLAND VYPPWKDSYI DYERLKKLLK ESVIHDGRSS VDSWSERNES DFVEALDKEL EKVYTFQISK YNAVLRKLDD LEENTKSAE KIQKINSEQF KNTLEECLDE AQRLDNFDRL NFTGFIKIVK KHDKLHPNYP SVKSLLQVRL KELPFNNSEE Y SPLLYRIS ...String:
MLFGIKLAND VYPPWKDSYI DYERLKKLLK ESVIHDGRSS VDSWSERNES DFVEALDKEL EKVYTFQISK YNAVLRKLDD LEENTKSAE KIQKINSEQF KNTLEECLDE AQRLDNFDRL NFTGFIKIVK KHDKLHPNYP SVKSLLQVRL KELPFNNSEE Y SPLLYRIS YLYEFLRSNY DHPNTVSKSL ASTSKLSHFS NLEDASFKSY KFWVHDDNIM EVKARILRHL PALVYASVPN EN DDFVDNL ESDVRVQPEA RLNIGSKSNS LSSDGNSNQD VEIGKSKSVI FPQSYDPTIT TLYFDNDFFD LYNNRLLKIS GAP TLRLRW IGKLLDKPDI FLEKRTFTEN TETGNSSFEE IRLQMKAKFI NNFIFKNDPS YKNYLINQLR ERGTQKEELE KLSR DFDNI QNFIVEEKLQ PVLRATYNRT AFQIPGDQSI RVTIDSNIMY IREDSLDKNR PIRNPENWHR DDIDSNIPNP LRFLR AGEY SKFPYSVMEI KVINQDNSQM PNYEWIKDLT NSHLVNEVPK FSLYLQGVAS LFGEDDKYVN ILPFWLPDLE TDIRKN PQE AYEEEKKTLQ KQKSIHDKLD NMRRLSKISV PDGKTTERQG QKDQNTRHVI ADLEDHESSD EEGTALPKKS AVKKGKK FK TNAAFLKILA GKNISENGND PYSDDTDSAS SFQLPPGVKK PVHLLKNAGP VKVEAKVWLA NERTFNRWLS VTTLLSVL T FSIYNSVQKA EFPQLADLLA YVYFFLTLFC GVWAYRTYLK RLTLIKGRSG KHLDAPVGPI LVAVVLIVTL VVNFSVAFK EAARRERGLV NVSSQPSLPR TLKPIQDFIF NLVGE

UniProtKB: Vacuolar transporter chaperone 3 complex subunit 3

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Macromolecule #3: Vacuolar transporter chaperone complex subunit 4

MacromoleculeName: Vacuolar transporter chaperone complex subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ATP-polyphosphate phosphotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 83.268664 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKFGEHLSKS LIRQYSYYYI SYDDLKTELE DNLSKNNGQW TQELETDFLE SLEIELDKVY TFCKVKHSEV FRRVKEVQEQ VQHTVRLLD SNNPPTQLDF EILEEELSDI IADVHDLAKF SRLNYTGFQK IIKKHDKKTG FILKPVFQVR LDSKPFFKEN Y DELVVKIS ...String:
MKFGEHLSKS LIRQYSYYYI SYDDLKTELE DNLSKNNGQW TQELETDFLE SLEIELDKVY TFCKVKHSEV FRRVKEVQEQ VQHTVRLLD SNNPPTQLDF EILEEELSDI IADVHDLAKF SRLNYTGFQK IIKKHDKKTG FILKPVFQVR LDSKPFFKEN Y DELVVKIS QLYDIARTSG RPIKGDSSAG GKQQNFVRQT TKYWVHPDNI TELKLIILKH LPVLVFNTNK EFEREDSAIT SI YFDNENL DLYYGRLRKD EGAEAHRLRW YGGMSTDTIF VERKTHREDW TGEKSVKARF ALKERHVNDF LKGKYTVDQV FAK MRKEGK KPMNEIENLE ALASEIQYVM LKKKLRPVVR SFYNRTAFQL PGDARVRISL DTELTMVRED NFDGVDRTHK NWRR TDIGV DWPFKQLDDK DICRFPYAVL EVKLQTQLGQ EPPEWVRELV GSHLVEPVPK FSKFIHGVAT LLNDKVDSIP FWLPQ MDVD IRKPPLPTNI EITRPGRSDN EDNDFDEDDE DDAALVAAMT NAPGNSLDIE ESVGYGATSA PTSNTNHVVE SANAAY YQR KIRNAENPIS KKYYEIVAFF DHYFNGDQIS KIPKGTTFDT QIRAPPGKTI CVPVRVEPKV YFATERTYLS WLSISIL LG GVSTTLLTYG SPTAMIGSIG FFITSLAVLI RTVMVYAKRV VNIRLKRAVD YEDKIGPGMV SVFLILSILF SFFCNLVA K

UniProtKB: Vacuolar transporter chaperone complex subunit 4

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Macromolecule #4: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 4 / Number of copies: 1 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #6: TRIPHOSPHATE

MacromoleculeName: TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: 3PO
Molecular weightTheoretical: 257.955 Da
Chemical component information

ChemComp-3PO:
TRIPHOSPHATE

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Macromolecule #7: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.4
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: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1042873
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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