[English] 日本語
Yorodumi
- EMDB-6987: Cryo-EM structure of a P-type ATPase -

+
Open data


ID or keywords:

Loading...

-
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 1
    • Protein or peptide: Neuroplastin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMembrane protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


calcium ion export across plasma membrane / regulation of receptor localization to synapse / calcium ion transmembrane transporter activity / type 1 fibroblast growth factor receptor binding / regulation of vascular associated smooth muscle contraction / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity ...calcium ion export across plasma membrane / regulation of receptor localization to synapse / calcium ion transmembrane transporter activity / type 1 fibroblast growth factor receptor binding / regulation of vascular associated smooth muscle contraction / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / photoreceptor ribbon synapse / P-type Ca2+ transporter / P-type calcium transporter activity / GABA receptor activation / positive regulation of calcium ion transport / Sensory processing of sound by inner hair cells of the cochlea / Reduction of cytosolic Ca++ levels / negative regulation of cytokine production / negative regulation of cytosolic calcium ion concentration / molecular function inhibitor activity / homophilic cell adhesion via plasma membrane adhesion molecules / Ion transport by P-type ATPases / immunological synapse / regulation of cardiac conduction / regulation of cytosolic calcium ion concentration / positive regulation of bone mineralization / Ion homeostasis / cell adhesion molecule binding / regulation of cellular response to insulin stimulus / axon guidance / cell projection / positive regulation of neuron projection development / regulation of blood pressure / long-term synaptic potentiation / intracellular calcium ion homeostasis / synaptic vesicle membrane / positive regulation of protein phosphorylation / presynaptic membrane / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / basolateral plasma membrane / calmodulin binding / postsynaptic density / axon / intracellular membrane-bounded organelle / glutamatergic synapse / cell surface / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / 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 / Cation transport ATPase (P-type) / E1-E2 ATPase ...Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / 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 / Cation transport ATPase (P-type) / 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 / Immunoglobulin domain / haloacid dehalogenase-like hydrolase / Immunoglobulin I-set / Immunoglobulin I-set domain / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsGong DS / Chi XM
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-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

-
Structure visualization

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

emd_6987.png

Downloads & links

-
Map

FileDownload / File: emd_6987.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 200 pix.
= 218.2 Å		1.09 Å/pix.
x 200 pix.
= 218.2 Å		1.09 Å/pix.
x 200 pix.
= 218.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Sample components

-
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 1
    • Protein or peptide: Neuroplastin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
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)

-
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: Ca2+-transporting ATPase
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

UniProtKB: Plasma membrane calcium-transporting ATPase 1

-
Macromolecule #2: Neuroplastin

MacromoleculeName: Neuroplastin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (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

UniProtKB: Neuroplastin

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

+
Image processing

Startup modelType of model: OTHER
Details: 10 good 2D classes were used to generate an initial model using e2initialmodel.py
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
Initial angle assignmentType: PROJECTION MATCHING / Software - Version: Relion 2.0
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Version: Relion 2.0
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more