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- EMDB-36219: Cryo-EM structure of RDGC/Ca2+-CaM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36219
TitleCryo-EM structure of RDGC/Ca2+-CaM complex
Map data
Sample
  • Complex: Cryo-EM structure of RDGC/Ca2+-CaM complex
    • Protein or peptide: AT15141p
    • Protein or peptide: Serine/threonine-protein phosphatase rdgC
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: FE (III) ION
  • Ligand: PHOSPHATE ION
KeywordsPhosphatase / metal binding. / HYDROLASE
Function / homology
Function and homology information


detection of stimulus involved in sensory perception / negative regulation of opsin-mediated signaling pathway / calcium-dependent protein serine/threonine phosphatase activity / thermotaxis / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity ...detection of stimulus involved in sensory perception / negative regulation of opsin-mediated signaling pathway / calcium-dependent protein serine/threonine phosphatase activity / thermotaxis / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phototransduction / visual perception / calcium-mediated signaling / manganese ion binding / calmodulin binding / iron ion binding / calcium ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein phosphatase with EF-hands / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / IQ motif profile. ...Serine/threonine-protein phosphatase with EF-hands / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / IQ motif profile. / Metallo-dependent phosphatase-like / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
AT15141p / Serine/threonine-protein phosphatase rdgC
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsLiu ZM / Liu W / Wu C / Liu J
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of RDGC/Ca2+-CaM complex
Authors: Liu ZM / Liu W / Wu C / Liu J
History
DepositionMay 19, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36219.png

Downloads & links

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Map

FileDownload / File: emd_36219.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 328.32 Å		0.86 Å/pix.
x 384 pix.
= 328.32 Å		0.86 Å/pix.
x 384 pix.
= 328.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-0.9746241 - 1.6087819
Average (Standard dev.)0.00042282243 (±0.030805273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 328.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36219_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36219_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 : Cryo-EM structure of RDGC/Ca2+-CaM complex

EntireName: Cryo-EM structure of RDGC/Ca2+-CaM complex
Components
  • Complex: Cryo-EM structure of RDGC/Ca2+-CaM complex
    • Protein or peptide: AT15141p
    • Protein or peptide: Serine/threonine-protein phosphatase rdgC
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: FE (III) ION
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Cryo-EM structure of RDGC/Ca2+-CaM complex

SupramoleculeName: Cryo-EM structure of RDGC/Ca2+-CaM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: AT15141p

MacromoleculeName: AT15141p / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 16.82552 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG FISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVTMMTSK

UniProtKB: AT15141p

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Macromolecule #2: Serine/threonine-protein phosphatase rdgC

MacromoleculeName: Serine/threonine-protein phosphatase rdgC / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 68.828453 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDENAIRAAI FIQKWYRRHQ ARREMQRRCN WQIFQNLEYA SEQDQAELYK FFNDLIKHMP QAAGRKNQYQ GSDDKDDLVE EFGDIVNAK IELPIRKNHI DLLIDVFRKK RGNRLHPKYV ALILREAAKS LKQLPNISPV STAVSQQVTV CGDLHGKLDD L LVVLHKNG ...String:
MDENAIRAAI FIQKWYRRHQ ARREMQRRCN WQIFQNLEYA SEQDQAELYK FFNDLIKHMP QAAGRKNQYQ GSDDKDDLVE EFGDIVNAK IELPIRKNHI DLLIDVFRKK RGNRLHPKYV ALILREAAKS LKQLPNISPV STAVSQQVTV CGDLHGKLDD L LVVLHKNG LPSSSNPYVF NGDFVDRGKR GLEVLLLLLS LYLAFPNAVF LNRGNHEDSV MNARYGFIRE VESKYPRNHK RI LAFIDEV YRWLPLGSVL NSRVLIVHGG FSDSTSLDLI KSIDRGKYVS ILRPPLTDGE PLDKTEWQQI FDIMWSDPQA TMG CVPNTL RGAGVWFGPD VTDNFLQRHR LSYVIRSHEC KPNGHEFMHD NKIITIFSAS NYYAIGSNKG AYIRLNNQLM PHFV QYISA ASQTKRLSFK QRMGIVESSA LKELAVRMRD HRDELEDEFR KYDPKDSGYI SISHWCKVME NVTKLGLPWR LLRDK LAPG TDSQKVNYNR TLDLLDTDVI LEAEADGMSV MDALYANKAS LVAIFNIIDA DNSGEITLDE FETAIDLLVA HMPGAY SKA EMLEKCRMMD LNGDGKVDLN EFLEAFRLSD LHRKEQ

UniProtKB: Serine/threonine-protein phosphatase rdgC

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 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: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56344
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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