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- EMDB-18205: Copper-transporting ATPase HMA4 in E2P state with BeF -

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Basic information

Entry
Database: EMDB / ID: EMD-18205
TitleCopper-transporting ATPase HMA4 in E2P state with BeF
Map data
Sample
  • Complex: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
    • Protein or peptide: Copper-transporting ATPase HMA4
  • Ligand: MAGNESIUM ION
KeywordsP-ATPase / TRANSPORT PROTEIN
Function / homology
Function and homology information


P-type Cu+ transporter / P-type monovalent copper transporter activity / vacuolar membrane / copper ion binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Copper-transporting ATPase HMA4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Oryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsGuo Z / Gourdon P / Wang K
Funding support Denmark, 2 items
OrganizationGrant numberCountry
LundbeckfondenR133-A12689 Denmark
LundbeckfondenR324-2019-1855 Denmark
CitationJournal: Nat Commun / Year: 2024
Title: Diverse roles of the metal binding domains and transport mechanism of copper transporting P-type ATPases.
Authors: Zongxin Guo / Fredrik Orädd / Viktoria Bågenholm / Christina Grønberg / Jian Feng Ma / Peter Ott / Yong Wang / Magnus Andersson / Per Amstrup Pedersen / Kaituo Wang / Pontus Gourdon /
Abstract: Copper transporting P-type (P-) ATPases are essential for cellular homeostasis. Nonetheless, the E1-E1P-E2P-E2 states mechanism of P-ATPases remains poorly understood. In particular, the role of the ...Copper transporting P-type (P-) ATPases are essential for cellular homeostasis. Nonetheless, the E1-E1P-E2P-E2 states mechanism of P-ATPases remains poorly understood. In particular, the role of the intrinsic metal binding domains (MBDs) is enigmatic. Here, four cryo-EM structures and molecular dynamics simulations of a P-ATPase are combined to reveal that in many eukaryotes the MBD immediately prior to the ATPase core, MBD, serves a structural role, remodeling the ion-uptake region. In contrast, the MBD prior to MBD, MBD, likely assists in copper delivery to the ATPase core. Invariant Tyr, Asn and Ser residues in the transmembrane domain assist in positioning sulfur-providing copper-binding amino acids, allowing for copper uptake, binding and release. As such, our findings unify previously conflicting data on the transport and regulation of P-ATPases. The results are critical for a fundamental understanding of cellular copper homeostasis and for comprehension of the molecular bases of P-disorders and ongoing clinical trials.
History
DepositionAug 15, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18205.png

Downloads & links

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Map

FileDownload / File: emd_18205.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.0060433 - 1.9397873
Average (Standard dev.)-0.0017096911 (±0.04703988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18205_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_18205_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 : Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica

EntireName: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
Components
  • Complex: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
    • Protein or peptide: Copper-transporting ATPase HMA4
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica

SupramoleculeName: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Copper-transporting ATPase HMA4

MacromoleculeName: Copper-transporting ATPase HMA4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 105.301398 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MEQNGENHLK DPLLQADGGG SGASPAGASP RKERKTRKVM FNVRGISCAS CAVSIETVVA GLKGVESVSV SPLQGQAVVQ YRPEEADAR TIKEAIEGLN FEVDELQEQE IAVCRLQIKG MACTSCSESV ERALQMVPGV KKAAVGLALE EAKVHFDPNI T SRDLIIEA ...String:
MEQNGENHLK DPLLQADGGG SGASPAGASP RKERKTRKVM FNVRGISCAS CAVSIETVVA GLKGVESVSV SPLQGQAVVQ YRPEEADAR TIKEAIEGLN FEVDELQEQE IAVCRLQIKG MACTSCSESV ERALQMVPGV KKAAVGLALE EAKVHFDPNI T SRDLIIEA IEDAGFGADL ISSGDDVNKV HLKLEGVSSP EDIKLIQSRL ESVEGVNNVE CDTAGQTIIV AYDPDVTGPR LL IQCIQDA AQPPKYFNAS LYSPPKQREA ERHHEIRNYR NQFLWSCLFS VPVFMFSMVL PMISPFGDWL FYKVCNNMTI GML LRWLLC SPVQFIIGWR FYVGAYHALK RGYSNMDVLV ALGTNAAYFY SVYIVLKALT SESFEGQDFF ETSAMLISFI LLGK YLEVV AKGKTSDALS KLTELAPETA CLLTLDKDGN AISETEISTQ LLQRNDVIKI VPGEKVPVDG VVIKGQSHVN ESMIT GEAR PIAKKPGDKV IGGTVNDNGC IIVKVTHVGS ETALSQIVQL VEAAQLARAP VQKLADRISR FFVPTVVVAA FLTWLG WFV AGQFDIYPRE WIPKAMDSFE LALQFGISVL VVACPCALGL ATPTAVMVAT GKGASQGVLI KGGNALEKAH KVKAIIF (BFD)K TGTLTVGKPS VVQTKVFSKI PLLELCDLAA GAEANSEHPL SKAIVEYTKK LREQYGSHSD HIMESKDFEV HPGA GVSAN VEGKLVLVGN KRLMQEFEVP ISSEVEGHMS ETEELARTCV LVAIDRTICG ALSVSDPLKP EAGRAISYLS SMGIS SIMV TGDNWATAKS IAKEVGIGTV FAEIDPVGKA EKIKDLQMKG LTVAMVGDGI NDSPALAAAD VGLAIGAGTD VAIEAA DIV LMRSSLEDVI TAIDLSRKTL SRIRLNYVWA LGYNVLGMPV AAGVLFPFTG IRLPPWLAGA CMAASSVSVV CSSLLLQ LY KKPLHVEEVA AGPKNDPDLV

UniProtKB: Copper-transporting ATPase HMA4

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mM(HOCH2)3CNH2tris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride

Details: 20mM Tris-HCl, 150mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216389
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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