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- EMDB-45178: Cryo-EM structure of Danio rerio voltage-sensing phosphatase (VSP... -

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Basic information

Entry
Database: EMDB / ID: EMD-45178
TitleCryo-EM structure of Danio rerio voltage-sensing phosphatase (VSP) phosphatase domain
Map dataSharpened map
Sample
  • Complex: Voltage-sensing phosphatase (Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2) in lipid nanodisc
    • Protein or peptide: Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2
Keywordsphosphatase / voltage-sensing / MEMBRANE PROTEIN
Function / homology
Function and homology information


phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of endocytosis / monoatomic ion channel activity / protein-tyrosine-phosphatase / cell projection / membrane / cytosol
Similarity search - Function
TPTE, protein tyrosine phosphatase-like catalytic domain / : / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase / Voltage-dependent channel domain superfamily ...TPTE, protein tyrosine phosphatase-like catalytic domain / : / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase / Voltage-dependent channel domain superfamily / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transmembrane phosphatase with tensin homology
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsZhang L / Brohawn SG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145869 United States
CitationJournal: Nat Commun / Year: 2024
Title: Coupling sensor to enzyme in the voltage sensing phosphatase.
Authors: Yawei Yu / Lin Zhang / Baobin Li / Zhu Fu / Stephen G Brohawn / Ehud Y Isacoff /
Abstract: Voltage-sensing phosphatases (VSPs) dephosphorylate phosphoinositide (PIP) signaling lipids in response to membrane depolarization. VSPs possess an S4-containing voltage sensor domain (VSD), ...Voltage-sensing phosphatases (VSPs) dephosphorylate phosphoinositide (PIP) signaling lipids in response to membrane depolarization. VSPs possess an S4-containing voltage sensor domain (VSD), resembling that of voltage-gated cation channels, and a lipid phosphatase domain (PD). The mechanism by which voltage turns on enzyme activity is unclear. Structural analysis and modeling suggest several sites of VSD-PD interaction that could couple voltage sensing to catalysis. Voltage clamp fluorometry reveals voltage-driven rearrangements in three sites implicated earlier in enzyme activation-the VSD-PD linker, gating loop and R loop-as well as the N-terminal domain, which has not yet been explored. N-terminus mutations perturb both rearrangements in the other segments and enzyme activity. Our results provide a model for a dynamic assembly by which S4 controls the catalytic site.
History
DepositionJun 3, 2024-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45178.png

Downloads & links

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Map

FileDownload / File: emd_45178.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 250 pix.
= 278.75 Å		1.12 Å/pix.
x 250 pix.
= 278.75 Å		1.12 Å/pix.
x 250 pix.
= 278.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.115 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-5.5021763 - 7.2796335
Average (Standard dev.)0.0005299548 (±0.10692175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 278.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_45178_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_45178_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45178_half_map_2.map
Projections & Slices
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Sample components

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Entire : Voltage-sensing phosphatase (Phosphatidylinositol-3,4,5-trisphosp...

EntireName: Voltage-sensing phosphatase (Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2) in lipid nanodisc
Components
  • Complex: Voltage-sensing phosphatase (Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2) in lipid nanodisc
    • Protein or peptide: Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2

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Supramolecule #1: Voltage-sensing phosphatase (Phosphatidylinositol-3,4,5-trisphosp...

SupramoleculeName: Voltage-sensing phosphatase (Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2) in lipid nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 119 KDa

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Macromolecule #1: Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2

MacromoleculeName: Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein-tyrosine-phosphatase
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 59.64052 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MTSVHFNPGL DSKEVNGNSV KEEAEVQIGD GKEETKDPDT MYHQVRKKIT PFVMSFGFRV FGLVLIILDI IMVIVDLSLS EKSRDVGGA LETVSLVISF FFLIDVLLRV YVEGFKVYFS SKLNIVDACI VVITLVVTMI YAFSDFSGAS LIPRVVTFLR S LRILILVR ...String:
MTSVHFNPGL DSKEVNGNSV KEEAEVQIGD GKEETKDPDT MYHQVRKKIT PFVMSFGFRV FGLVLIILDI IMVIVDLSLS EKSRDVGGA LETVSLVISF FFLIDVLLRV YVEGFKVYFS SKLNIVDACI VVITLVVTMI YAFSDFSGAS LIPRVVTFLR S LRILILVR IFRLASQKRE LEKVTRRMVS ENKRRYQKDG FDLDLTYVTE RVIAMSFPSS GKQALYRNPI REVVRFLDTK HM DHYKVFN LCSEKGYDPK FFHYRVERVM IDDHNVPSLD DMLRYTACVR DWMAADSRNV IAIHSKGGKG RTGTMVCTWL IDS DQFESA QESLDYFGER RTDKSMSSKF QGVETPSQSR YVGYYEIMKN QYNRQLPPRK SLKIKSIRIH SIAGVGKGNG SDLK LKIIV KHELVFQCVC AKQHNCTVFP DTGSNAVVIS LQDGPIVTGD VKVMFESSAG LPKGYEDCPF YFWFNTSFVE NYRLF LSRE ELDNPHKPKT WDIYKEDFGV TLSFTEPSNS LEVLFQ

UniProtKB: Transmembrane phosphatase with tensin homology

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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

Concentration5.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3TRIS
150.0 mMNaClsodium chloride
5.0 mMEGTAethylene glycol-bis(beta-aminoethyl ether)-N,N,N,N-tetraacetic acid
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV / Details: 3s blot, blot force 1.
DetailsVSP reconstituted in MSP2N2 lipid nanodiscs with 2:1:1:0.2 DOPE:POPS:POPC:Brain PI(3,4)P2

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 208690
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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