[English] 日本語
Yorodumi
- EMDB-0915: WT transporter state1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0915
TitleWT transporter state1
Map data
Sample
  • Complex: SERCA2b with BeF3
    • Protein or peptide: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
Keywordscalcium / METAL TRANSPORT
Function / homology
Function and homology information


ER-nucleus signaling pathway / longitudinal sarcoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / calcium ion-transporting ATPase complex / T-tubule organization / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential ...ER-nucleus signaling pathway / longitudinal sarcoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / calcium ion-transporting ATPase complex / T-tubule organization / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential / ribbon synapse / platelet dense tubular network membrane / calcium ion import into sarcoplasmic reticulum / Pre-NOTCH Processing in Golgi / P-type Ca2+ transporter / sarcoplasmic reticulum calcium ion transport / negative regulation of heart contraction / transition between fast and slow fiber / P-type calcium transporter activity / regulation of the force of heart contraction / endoplasmic reticulum calcium ion homeostasis / cardiac muscle hypertrophy in response to stress / regulation of cardiac muscle contraction by calcium ion signaling / S100 protein binding / relaxation of cardiac muscle / Reduction of cytosolic Ca++ levels / lncRNA binding / organelle localization by membrane tethering / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / positive regulation of heart rate / positive regulation of cardiac muscle cell apoptotic process / Ion transport by P-type ATPases / autophagosome assembly / regulation of cardiac conduction / epidermis development / Ion homeostasis / sarcoplasmic reticulum membrane / response to endoplasmic reticulum stress / negative regulation of receptor binding / sarcoplasmic reticulum / calcium ion transmembrane transport / intracellular calcium ion homeostasis / neuron cellular homeostasis / cellular response to oxidative stress / monoatomic ion transmembrane transport / transmembrane transporter binding / cell adhesion / calcium ion binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIA, SERCA-type / 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, subfamily IIA, SERCA-type / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhang Y / Tsutsumi A
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structures of SERCA2b reveal the mechanism of regulation by the luminal extension tail.
Authors: Yuxia Zhang / Michio Inoue / Akihisa Tsutsumi / Satoshi Watanabe / Tomohiro Nishizawa / Kazuhiro Nagata / Masahide Kikkawa / Kenji Inaba /
Abstract: Sarco/endoplasmic reticulum Ca ATPase (SERCA) pumps Ca from the cytosol into the ER and maintains the cellular calcium homeostasis. Herein, we present cryo-electron microscopy (cryo-EM) structures of ...Sarco/endoplasmic reticulum Ca ATPase (SERCA) pumps Ca from the cytosol into the ER and maintains the cellular calcium homeostasis. Herein, we present cryo-electron microscopy (cryo-EM) structures of human SERCA2b in E1∙2Ca-adenylyl methylenediphosphonate (AMPPCP) and E2-BeF states at 2.9- and 2.8-Å resolutions, respectively. The structures revealed that the luminal extension tail (LE) characteristic of SERCA2b runs parallel to the lipid-water boundary near the luminal ends of transmembrane (TM) helices TM10 and TM7 and approaches the luminal loop flanked by TM7 and TM8. While the LE served to stabilize the cytosolic and TM domain arrangement of SERCA2b, deletion of the LE rendered the overall conformation resemble that of SERCA1a and SERCA2a and allowed multiple conformations. Thus, the LE appears to play a critical role in conformational regulation in SERCA2b, which likely explains the different kinetic properties of SERCA2b from those of other isoforms lacking the LE.
History
DepositionDec 24, 2019-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6lly
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0915.png

Downloads & links

-
Map

FileDownload / File: emd_0915.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 168 pix.
= 209.16 Å		1.25 Å/pix.
x 168 pix.
= 209.16 Å		1.25 Å/pix.
x 168 pix.
= 209.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.06
Minimum - Maximum-0.39070994 - 0.4854499
Average (Standard dev.)0.00032391635 (±0.01111976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 209.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2451.2451.245
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z209.160209.160209.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.3910.4850.000

-
Supplemental data

-
Mask #1

Fileemd_0915_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: no sharpen map

Fileemd_0915_additional.map
Annotationno sharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: no sharpen map

Fileemd_0915_additional_1.map
Annotationno sharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: unfiltered half1 map

Fileemd_0915_half_map_1.map
Annotationunfiltered half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: unfiltered half2 map

Fileemd_0915_half_map_2.map
Annotationunfiltered half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SERCA2b with BeF3

EntireName: SERCA2b with BeF3
Components
  • Complex: SERCA2b with BeF3
    • Protein or peptide: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: SERCA2b with BeF3

SupramoleculeName: SERCA2b with BeF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110 kDa/nm

-
Macromolecule #1: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2

MacromoleculeName: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Ca2+ transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 117.764875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGVAMPGAE DDVVRENLYF QGKDGLAAME NAHTKTVEEV LGHFGVNEST GLSLEQVKKL KERWGSNELP AEEGKTLLEL VIEQFEDLL VRILLLAACI SFVLAWFEEG EETITAFVEP FVILLILVAN AIVGVWQERN AENAIEALKE YEPEMGKVYR Q DRKSVQRI ...String:
MGGVAMPGAE DDVVRENLYF QGKDGLAAME NAHTKTVEEV LGHFGVNEST GLSLEQVKKL KERWGSNELP AEEGKTLLEL VIEQFEDLL VRILLLAACI SFVLAWFEEG EETITAFVEP FVILLILVAN AIVGVWQERN AENAIEALKE YEPEMGKVYR Q DRKSVQRI KAKDIVPGDI VEIAVGDKVP ADIRLTSIKS TTLRVDQSIL TGESVSVIKH TDPVPDPRAV NQDKKNMLFS GT NIAAGKA MGVVVATGVN TEIGKIRDEM VATEQERTPL QQKLDEFGEQ LSKVISLICI AVWIINIGHF NDPVHGGSWI RGA IYYFKI AVALAVAAIP EGLPAVITTC LALGTRRMAK KNAIVRSLPS VETLGCTSVI CSDKTGTLTT NQMSVCRMFI LDRV EGDTC SLNEFTITGS TYAPIGEVHK DDKPVNCHQY DGLVELATIC ALCNDSALDY NEAKGVYEKV GEATETALTC LVEKM NVFD TELKGLSKIE RANACNSVIK QLMKKEFTLE FSRDRKSMSV YCTPNKPSRT SMSKMFVKGA PEGVIDRCTH IRVGST KVP MTSGVKQKIM SVIREWGSGS DTLRCLALAT HDNPLRREEM HLEDSANFIK YETNLTFVGC VGMLDPPRIE VASSVKL CR QAGIRVIMIT GDNKGTAVAI CRRIGIFGQD EDVTSKAFTG REFDELNPSA QRDACLNARC FARVEPSHKS KIVEFLQS F DEITAMTGDG VNDAPALKKA EIGIAMGSGT AVAKTASEMV LADDNFSTIV AAVEEGRAIY NNMKQFIRYL ISSNVGEVV CIFLTAALGF PEALIPVQLL WVNLVTDGLP ATALGFNPPD LDIMNKPPRN PKEPLISGWL FFRYLAIGCY VGAATVGAAA WWFIAADGG PRVSFYQLSH FLQCKEDNPD FEGVDCAIFE SPYPMTMALS VLVTIEMCNA LNSLSENQSL LRMPPWENIW L VGSICLSM SLHFLILYVE PLPLIFQITP LNVTQWLMVL KISLPVILMD ETLKFVARNY LEPGKECVQP ATKSCSFSAC TD GISWPFV LLIMPLVIWV YSTDTNFSDM FWS

UniProtKB: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2

-
Macromolecule #2: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 623250
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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