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- PDB-8q74: Copper-transporting ATPase HMA4 in E1 state with Cu -

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Basic information

Entry
Database: PDB / ID: 8q74
TitleCopper-transporting ATPase HMA4 in E1 state with Cu
ComponentsCopper-transporting ATPase HMA4
KeywordsTRANSPORT PROTEIN / P-ATPase
Function / homology
Function and homology information


P-type monovalent copper transporter activity / P-type Cu+ transporter / 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 (II) ION / Copper-transporting ATPase HMA4
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsGuo, Z. / Gourdon, P. / Wang, K.
Funding support Denmark, 2items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-transporting ATPase HMA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3002
Polymers105,2361
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Copper-transporting ATPase HMA4


Mass: 105236.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: HMA4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q6H7M3
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5 / Details: 20mM tris-hcl, 150mM NaCl, o.5mM CuCl2, 1mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethaneTris1
2150 mMSodium chlorideNaCl1
30.5 mMcupric chlorideCuCl21
41 mMTris (2-carboxyethyl) phosphineTCEP1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246045 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046057
ELECTRON MICROSCOPYf_angle_d0.8838226
ELECTRON MICROSCOPYf_dihedral_angle_d6.38826
ELECTRON MICROSCOPYf_chiral_restr0.048974
ELECTRON MICROSCOPYf_plane_restr0.0081041

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