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- EMDB-6987: Cryo-EM structure of a P-type ATPase -

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Basic information

Entry
Database: EMDB / ID: EMD-6987
TitleCryo-EM structure of a P-type ATPase
Map data
Sample
  • Complex: complex of one PMCA1 molecular with one NPTN molecular
    • Protein or peptide: Plasma membrane calcium-transporting ATPase 1ATP2B1
    • Protein or peptide: NeuroplastinNPTN
  • Ligand: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine
Function / homology
Function and homology information


P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration / regulation of receptor localization to synapse / calcium ion export across plasma membrane / calcium ion transmembrane transporter activity / : / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / regulation of vascular associated smooth muscle contraction / : / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly ...P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration / regulation of receptor localization to synapse / calcium ion export across plasma membrane / calcium ion transmembrane transporter activity / : / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / regulation of vascular associated smooth muscle contraction / : / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / cellular response to corticosterone stimulus / : / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / inhibitory synapse / GABA receptor activation / neural retina development / P-type Ca2+ transporter / P-type calcium transporter activity / cellular response to vitamin D / ATPase-coupled monoatomic cation transmembrane transporter activity / positive regulation of calcium ion transport / dendritic spine membrane / negative regulation of cytokine production / Reduction of cytosolic Ca++ levels / neuronal cell body membrane / positive regulation of protein localization / negative regulation of cytosolic calcium ion concentration / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / Ion transport by P-type ATPases / immunological synapse / regulation of cardiac conduction / GABA-ergic synapse / positive regulation of bone mineralization / regulation of cellular response to insulin stimulus / Ion homeostasis / regulation of cytosolic calcium ion concentration / response to cold / monoatomic ion transmembrane transport / cell adhesion molecule binding / long-term synaptic potentiation / positive regulation of long-term synaptic potentiation / PDZ domain binding / axon guidance / brain development / Schaffer collateral - CA1 synapse / visual learning / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / intracellular calcium ion homeostasis / regulation of blood pressure / presynaptic membrane / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / positive regulation of protein phosphorylation / membrane raft / apical plasma membrane / axon / intracellular membrane-bounded organelle / dendrite / glutamatergic synapse / cell surface / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Plasma membrane calcium-transporting ATPase 1 / Neuroplastin / Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / Basigin-like / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal ...Plasma membrane calcium-transporting ATPase 1 / Neuroplastin / Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / Basigin-like / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / 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 / HAD superfamily / HAD-like superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Plasma membrane calcium-transporting ATPase 1 / Neuroplastin
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsGong DS / Chi XM / Ren K / Huang GXY / Zhou GW / Yan N / Lei JL / Zhou Q
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the human plasma membrane Ca-ATPase 1 in complex with its obligatory subunit neuroplastin.
Authors: Deshun Gong / Ximin Chi / Kang Ren / Gaoxingyu Huang / Gewei Zhou / Nieng Yan / Jianlin Lei / Qiang Zhou /
Abstract: Plasma membrane Ca-ATPases (PMCAs) are key regulators of global Ca homeostasis and local intracellular Ca dynamics. Recently, Neuroplastin (NPTN) and basigin were identified as previously ...Plasma membrane Ca-ATPases (PMCAs) are key regulators of global Ca homeostasis and local intracellular Ca dynamics. Recently, Neuroplastin (NPTN) and basigin were identified as previously unrecognized obligatory subunits of PMCAs that dramatically increase the efficiency of PMCA-mediated Ca clearance. Here, we report the cryo-EM structure of human PMCA1 (hPMCA1) in complex with NPTN at a resolution of 4.1 Å for the overall structure and 3.9 Å for the transmembrane domain. The single transmembrane helix of NPTN interacts with the TM-linker and TM10 of hPMCA1. The subunits are required for the hPMCA1 functional activity. The NPTN-bound hPMCA1 closely resembles the E1-Mg structure of endo(sarco)plasmic reticulum Ca ATPase and the Ca site is exposed through a large open cytoplasmic pathway. This structure provides insight into how the subunits bind to the PMCAs and serves as an important basis for understanding the functional mechanisms of this essential calcium pump family.
History
DepositionJun 27, 2018-
Header (metadata) releaseSep 19, 2018-
Map releaseSep 19, 2018-
UpdateSep 19, 2018-
Current statusSep 19, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6a69
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6987.png

Downloads & links

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Map

FileDownload / File: emd_6987.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.091 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.04
Minimum - Maximum-0.15821315 - 0.23960134
Average (Standard dev.)0.00071353745 (±0.008618075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 218.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z218.200218.200218.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1580.2400.001

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Supplemental data

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Sample components

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Entire : complex of one PMCA1 molecular with one NPTN molecular

EntireName: complex of one PMCA1 molecular with one NPTN molecular
Components
  • Complex: complex of one PMCA1 molecular with one NPTN molecular
    • Protein or peptide: Plasma membrane calcium-transporting ATPase 1ATP2B1
    • Protein or peptide: NeuroplastinNPTN
  • Ligand: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine

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Supramolecule #1: complex of one PMCA1 molecular with one NPTN molecular

SupramoleculeName: complex of one PMCA1 molecular with one NPTN molecular
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Plasma membrane calcium-transporting ATPase 1

MacromoleculeName: Plasma membrane calcium-transporting ATPase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ec: 3.6.3.8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140.987844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDMANNSVA YSGVKNSLKE ANHDGDFGIT LAELRALMEL RSTDALRKIQ ESYGDVYGIC TKLKTSPNEG LSGNPADLER REAVFGKNF IPPKKPKTFL QLVWEALQDV TLIILEIAAI VSLGLSFYQP PEGDNALCGE VSVGEEEGEG ETGWIEGAAI L LSVVCVVL ...String:
MGDMANNSVA YSGVKNSLKE ANHDGDFGIT LAELRALMEL RSTDALRKIQ ESYGDVYGIC TKLKTSPNEG LSGNPADLER REAVFGKNF IPPKKPKTFL QLVWEALQDV TLIILEIAAI VSLGLSFYQP PEGDNALCGE VSVGEEEGEG ETGWIEGAAI L LSVVCVVL VTAFNDWSKE KQFRGLQSRI EQEQKFTVIR GGQVIQIPVA DITVGDIAQV KYGDLLPADG ILIQGNDLKI DE SSLTGES DHVKKSLDKD PLLLSGTHVM EGSGRMVVTA VGVNSQTGII FTLLGAGGEE EEKKDEKKKE KKNKKQDGAI ENR NKAKAQ DGAAMEMQPL KSEEGGDGDE KDKKKANLPK KEKSVLQGKL TKLAVQIGKA GLLMSAITVI ILVLYFVIDT FWVQ KRPWL AECTPIYIQY FVKFFIIGVT VLVVAVPEGL PLAVTISLAY SVKKMMKDNN LVRHLDACET MGNATAICSD KTGTL TMNR MTVVQAYINE KHYKKVPEPE AIPPNILSYL VTGISVNCAY TSKILPPEKE GGLPRHVGNK TECALLGLLL DLKRDY QDV RNEIPEEALY KVYTFNSVRK SMSTVLKNSD GSYRIFSKGA SEIILKKCFK ILSANGEAKV FRPRDRDDIV KTVIEPM AS EGLRTICLAF RDFPAGEPEP EWDNENDIVT GLTCIAVVGI EDPVRPEVPD AIKKCQRAGI TVRMVTGDNI NTARAIAT K CGILHPGEDF LCLEGKDFNR RIRNEKGEIE QERIDKIWPK LRVLARSSPT DKHTLVKGII DSTVSDQRQV VAVTGDGTN DGPALKKADV GFAMGIAGTD VAKEASDIIL TDDNFTSIVK AVMWGRNVYD SISKFLQFQL TVNVVAVIVA FTGACITQDS PLKAVQMLW VNLIMDTLAS LALATEPPTE SLLLRKPYGR NKPLISRTMM KNILGHAFYQ LVVVFTLLFA GEKFFDIDSG R NAPLHAPP SEHYTIVFNT FVLMQLFNEI NARKIHGERN VFEGIFNNAI FCTIVLGTFV VQIIIVQFGG KPFSCSELSI EQ WLWSIFL GMGTLLWGQL ISTIPTSRLK FLKEAGHGTQ KEEIPEEELA EDVEEIDHAE RELRRGQILW FRGLNRIQTQ MDV VNAFQS GSSIQGALRR QPSIASQHHD VTNISTPTHI RVVNAFRSSL YEGLEKPESR SSIHNFMTHP EFRIEDSEPH IPLI DDTDA EDDAPTKRNS SPPPSPNKNN NAVDSGIHLT IEMNKSATSS SPGSPLHSLE TSLHHHHHHL EDYKDDDDK

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Macromolecule #2: Neuroplastin

MacromoleculeName: Neuroplastin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 31.3284 KDa
SequenceString: MSGSSLPSAL ALSLLLVSGS LLPGPGAAQN EPRIVTSEEV IIRDSPVLPV TLQCNLTSSS HTLTYSYWTK NGVELSATRK NASNMEYRI NKPRAEDSGE YHCVYHFVSA PKANATIEVK AAPDITGHKR SENKNEGQDA TMYCKSVGYP HPDWIWRKKE N GMPMDIVN ...String:
MSGSSLPSAL ALSLLLVSGS LLPGPGAAQN EPRIVTSEEV IIRDSPVLPV TLQCNLTSSS HTLTYSYWTK NGVELSATRK NASNMEYRI NKPRAEDSGE YHCVYHFVSA PKANATIEVK AAPDITGHKR SENKNEGQDA TMYCKSVGYP HPDWIWRKKE N GMPMDIVN TSGRFFIINK ENYTELNIVN LQITEDPGEY ECNATNAIGS ASVVTVLRVR SHLAPLWPFL GILAEIIILV VI IVVYEKR KRPDEVPDDD EPAGPMKTNS TNNHKDKNLR QRNTN

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Macromolecule #3: N-ACETYL-D-GLUCOSAMINE

MacromoleculeName: N-ACETYL-D-GLUCOSAMINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Version: gctf
Startup modelType of model: OTHER
Details: 10 good 2D classes were used to generate an initial model using e2initialmodel.py
Initial angle assignmentType: PROJECTION MATCHING / Software - Version: Relion 2.0
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Version: Relion 2.0
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Version: Relion 2.0 / Number images used: 105188
FSC plot (resolution estimation)

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