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- EMDB-25137: Consensus structure of ATP7B -

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Basic information

Entry
Database: EMDB / ID: EMD-25137
TitleConsensus structure of ATP7B
Map dataXenopus ATP7B in E2-Pi state
Sample
  • Complex: ATP7B
    • Protein or peptide: P-type Cu(+) transporter
  • Ligand: MAGNESIUM ION
  • Ligand: TETRAFLUOROALUMINATE ION
KeywordsCopper transport / Wilson disease / METAL TRANSPORT / METAL TRANSPORT-Translocase complex
Function / homology
Function and homology information


Ion transport by P-type ATPases / P-type Cu+ transporter / P-type monovalent copper transporter activity / trans-Golgi network / copper ion binding / ATP hydrolysis activity / ATP binding / membrane
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
P-type Cu(+) transporter
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsBitter RM / Oh SC
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS109307 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA008748 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure of the Wilson disease copper transporter ATP7B.
Authors: Ryan M Bitter / SeCheol Oh / Zengqin Deng / Suhaila Rahman / Richard K Hite / Peng Yuan /
Abstract: ATP7A and ATP7B, two homologous copper-transporting P1B-type ATPases, play crucial roles in cellular copper homeostasis, and mutations cause Menkes and Wilson diseases, respectively. ATP7A/B contains ...ATP7A and ATP7B, two homologous copper-transporting P1B-type ATPases, play crucial roles in cellular copper homeostasis, and mutations cause Menkes and Wilson diseases, respectively. ATP7A/B contains a P-type ATPase core consisting of a membrane transport domain and three cytoplasmic domains, the A, P, and N domains, and a unique amino terminus comprising six consecutive metal-binding domains. Here, we present a cryo-electron microscopy structure of frog ATP7B in a copper-free state. Interacting with both the A and P domains, the metal-binding domains are poised to exert copper-dependent regulation of ATP hydrolysis coupled to transmembrane copper transport. A ring of negatively charged residues lines the cytoplasmic copper entrance that is presumably gated by a conserved basic residue sitting at the center. Within the membrane, a network of copper-coordinating ligands delineates a stepwise copper transport pathway. This work provides the first glimpse into the structure and function of ATP7 proteins and facilitates understanding of disease mechanisms and development of rational therapies.
History
DepositionOct 12, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7si3
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25137.png

Downloads & links

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Map

FileDownload / File: emd_25137.map.gz / Format: CCP4 / Size: 8.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationXenopus ATP7B in E2-Pi state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 112 pix.
= 95.2 Å		0.85 Å/pix.
x 110 pix.
= 93.5 Å		0.85 Å/pix.
x 173 pix.
= 147.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-13.338737 - 21.202873
Average (Standard dev.)-0.00000000001955 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin135122129
Dimensions110173112
Spacing112110173
CellA: 95.200005 Å / B: 93.5 Å / C: 147.05 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z112110173
origin x/y/z0.0000.0000.000
length x/y/z95.20093.500147.050
α/β/γ90.00090.00090.000
start NX/NY/NZ129135122
NX/NY/NZ112110173
MAP C/R/S321
start NC/NR/NS122135129
NC/NR/NS173110112
D min/max/mean-13.33921.203-0.000

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Supplemental data

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Sample components

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Entire : ATP7B

EntireName: ATP7B
Components
  • Complex: ATP7B
    • Protein or peptide: P-type Cu(+) transporter
  • Ligand: MAGNESIUM ION
  • Ligand: TETRAFLUOROALUMINATE ION

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Supramolecule #1: ATP7B

SupramoleculeName: ATP7B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)

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Macromolecule #1: P-type Cu(+) transporter

MacromoleculeName: P-type Cu(+) transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Cu+ transporter
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 159.678672 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MFPKRILDEE EGVQLLSTEN EKCSTKRRSS PQFCVNNTFS DSPVSVWKEA KKPSCAFDNR GYEGSPDDLC SLPDDVGSVV VAIQGMTCQ SCVQSIEGRI SKVSGVVGIN VCLEQNNAIV NYLQTEITPH KICEEIEDMG FDASLSEQSG MPSSVKSSYY G DNVIKIRV ...String:
MFPKRILDEE EGVQLLSTEN EKCSTKRRSS PQFCVNNTFS DSPVSVWKEA KKPSCAFDNR GYEGSPDDLC SLPDDVGSVV VAIQGMTCQ SCVQSIEGRI SKVSGVVGIN VCLEQNNAIV NYLQTEITPH KICEEIEDMG FDASLSEQSG MPSSVKSSYY G DNVIKIRV EGMTCQSCVN TIEGKIGKIQ GVQKIKVSLT GQEAVITYQS HIIQAEDLRK YIEDMGFEAS IKNKPDPTKL GT IDIERLQ NSIAENHSGH TNSNTVTLGI DGMHCKSCVH NIEGYVSGLA GIQSIRVSLK NKNAVVCLSQ GSTSLLSLKE SIE NLPPGK FKVTLPVGVE KGQSLARNST HSSHRDQSMG GNIAIISIGG MTCQSCVSSI ENMISQRKGV LHILVSLDEG NGNI FYNPC ETNAEELRAA IEDMGFHSTL VSDNSPSISC SEYNSKEEEN KQTPPKATRQ ISGSRDYILD VLPKKSHPDF ANEKY DTAP EKCFLQITGM TCISCVSNIE RNLKKKDGIV SVLVALMSGK AEVKFYPDRI EPLEIAQLVE DLGFGASVME DYTASD GNV ELIITGMTCA SCVHNIESRL MRTPGILQAS VALATCKAQV KFDPEIVGPR DIIRIIEGIG FQASLAKRDP TAHKLDH KE EIKQWRNSFL FSLLFGIPVI ILMIYMLAAN KDHHNTMVLD RNIVPGLSII NLVFFILCTF VQTLGGRYFY VQAYKSLK H KATNMDVLIV LATTIAYIYS VVILTVAMVE KADKSPETFF DTPPMLFMFI ALGRWLEHIA KSKTSEALAK LISLQATEA AVVTFGANQI ILREEQVAVE LVQRGDIVKV VPGGKFPVDG KVIEGTSMAD ESLITGEPMP VRKKPGSMVI AGSINAHGTV LVEATHVGS ETTLAQIVKL VEEAQMSKAP IQQLADKISG YFVPFIIIIS VVTLVTWIII GFVNFDIIIK YFPSYSKNIS K TEVIIRVA FQTSITVLSI ACPCALGLAT PTAVMVGTGV AAQNGILIKG GEPLEMAHKI KAVMFDKTGT ITHGVPKVMR VL LLGDVVK MPLKRMLAVV GTAEASSEHP LGMAVTKYCK EELGTELLGY CTDFQAVPGC GISCKVNNIE SVLVQNEEGL NEQ NSYRNS LIGTTDSSLI ITPELLGAQA PLAHTVLIGN REWMRRNGLH ISTDVDEAMS SHEMKGQTAV LVAIDGELCG MIAI ADTVK QEAALAVHTL KSMGIDVVLI TGDNRKTAKA IATQVGIKKV FAEVLPSHKV AKVQALQSDN KRVAMVGDGV NDSPA LARA DVGIAIGTGT DVAIEAADIV LIRNDLLDVV ASIHLSKRTV RRIRLNFVFA LIYNLLGIPI AAGVFMPAGL VLQPWM GSA AMAASSVSVV LSSLQLKCYR KPDSDRYEAR AQGHMKPLTP SQISVHIGMD DRWRDLPKTK AWDQISYISQ VSRASQK PK RHGSLVEQQD KWSLLINETH EDQMI

UniProtKB: P-type Cu(+) transporter

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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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Macromolecule #3: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE 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

Concentration7 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMNaCl
5.0 mMMgCl2
10.0 mMNaF
0.5 mMADP
1.0 mMAlCl3
40.0 micromolarGDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1889296
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 257208
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationDetails: Iterative heterogeneous classification in cryosparc.

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Atomic model buiding 1

Initial modelPDB ID:

3rfu


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7si3:
Consensus structure of ATP7B

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