[English] 日本語
Yorodumi
- SASDEU4: ACA8 complex with Calmodulin (hydrogenated) in stealth nanodisc (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDEU4
SampleACA8 complex with Calmodulin (hydrogenated) in stealth nanodisc (SANS, 100% D2O)
  • Membrane scaffold protein 1D1 (deuterated, 75%) (protein), d75-msp1d1
  • 1-palmitoyl-2-palmitoleoyl-sn-glycero-3-phosphocholine (deuteration: 78% head, 92% acyl) (other), d(78,92)-POPC, Escherichia coli. (AL95 strain)
  • Calcium-transporting ATPase 8, plasma membrane-type (protein), ACA8, Arabidopsis thaliana
  • Calmodulin-7 (protein), Cam7, Arabidopsis thaliana
Biological speciesEscherichia coli. (AL95 strain)
Arabidopsis thaliana (thale cress)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: ACA8 complex with Calmodulin (hydrogenated) in stealth nanodisc (SANS, 100% D2O)
Contrast: -3.32 / Specific vol: 0.744 / Specimen concentration: 3 mg/ml / Concentration method: A280 / Entity id: 1017 / 1018 / 1312 / 1314
BufferName: 30 mM Tris, 150 mM NaCl, 1mM MgCl2, 1 mM CaCl2 / pH: 7.5
Entity #1017Name: d75-msp1d1 / Type: protein
Description: Membrane scaffold protein 1D1 (deuterated, 75%)
Formula weight: 24.661 / Num. of mol.: 2
Sequence: GHHHHHHHDY DIPTTENLYF QGSTFSKLRE QLGPVTQEFW DNLEKETEGL RQEMSKDLEE VKAKVQPYLD DFQKKWQEEM ELYRQKVEPL RAELQEGARQ KLHELQEKLS PLGEEMRDRA RAHVDALRTH LAPYSDELRQ RLAARLEALK ENGGARLAEY HAKATEHLST ...Sequence:
GHHHHHHHDY DIPTTENLYF QGSTFSKLRE QLGPVTQEFW DNLEKETEGL RQEMSKDLEE VKAKVQPYLD DFQKKWQEEM ELYRQKVEPL RAELQEGARQ KLHELQEKLS PLGEEMRDRA RAHVDALRTH LAPYSDELRQ RLAARLEALK ENGGARLAEY HAKATEHLST LSEKAKPALE DLRQGLLPVL ESFKVSFLSA LEEYTKKLNT Q
Entity #1018Name: d(78,92)-POPC / Type: other
Description: 1-palmitoyl-2-palmitoleoyl-sn-glycero-3-phosphocholine (deuteration: 78% head, 92% acyl)
Formula weight: 0.76 / Source: Escherichia coli. (AL95 strain)
Sequence:
C42H82NO8P
Entity #1312Name: ACA8 / Type: protein
Description: Calcium-transporting ATPase 8, plasma membrane-type
Formula weight: 118.209 / Num. of mol.: 1 / Source: Arabidopsis thaliana
Sequence: HHHHHHHHEN LYFQGSMTSL LKSSPGRRRG GDVESGKSEH ADSDSDTFYI PSKNASIERL QQWRKAALVL NASRRFRYTL DLKKEQETRE MRQKIRSHAH ALLAANRFMD MGRESGVEKT TGPATPAGDF GITPEQLVIM SKDHNSGALE QYGGTQGLAN LLKTNPEKGI ...Sequence:
HHHHHHHHEN LYFQGSMTSL LKSSPGRRRG GDVESGKSEH ADSDSDTFYI PSKNASIERL QQWRKAALVL NASRRFRYTL DLKKEQETRE MRQKIRSHAH ALLAANRFMD MGRESGVEKT TGPATPAGDF GITPEQLVIM SKDHNSGALE QYGGTQGLAN LLKTNPEKGI SGDDDDLLKR KTIYGSNTYP RKKGKGFLRF LWDACHDLTL IILMVAAVAS LALGIKTEGI KEGWYDGGSI AFAVILVIVV TAVSDYKQSL QFQNLNDEKR NIHLEVLRGG RRVEISIYDI VVGDVIPLNI GNQVPADGVL ISGHSLALDE SSMTGESKIV NKDANKDPFL MSGCKVADGN GSMLVTGVGV NTEWGLLMAS ISEDNGEETP LQVRLNGVAT FIGSIGLAVA AAVLVILLTR YFTGHTKDNN GGPQFVKGKT KVGHVIDDVV KVLTVAVTIV VVAVPEGLPL AVTLTLAYSM RKMMADKALV RRLSACETMG SATTICSDKT GTLTLNQMTV VESYAGGKKT DTEQLPATIT SLVVEGISQN TTGSIFVPEG GGDLEYSGSP TEKAILGWGV KLGMNFETAR SQSSILHAFP FNSEKKRGGV AVKTADGEVH VHWKGASEIV LASCRSYIDE DGNVAPMTDD KASFFKNGIN DMAGRTLRCV ALAFRTYEAE KVPTGEELSK WVLPEDDLIL LAIVGIKDPC RPGVKDSVVL CQNAGVKVRM VTGDNVQTAR AIALECGILS SDADLSEPTL IEGKSFREMT DAERDKISDK ISVMGRSSPN DKLLLVQSLR RQGHVVAVTG DGTNDAPALH EADIGLAMGI AGTEVAKESS DIIILDDNFA SVVKVVRWGR SVYANIQKFI QFQLTVNVAA LVINVVAAIS SGDVPLTAVQ LLWVNLIMDT LGALALATEP PTDHLMGRPP VGRKEPLITN IMWRNLLIQA IYQVSVLLTL NFRGISILGL EHEVHEHATR VKNTIIFNAF VLCQAFNEFN ARKPDEKNIF KGVIKNRLFM GIIVITLVLQ VIIVEFLGKF ASTTKLNWKQ WLICVGIGVI SWPLALVGKF IPVPAAPISN KLKVLKFWGK KKNSSGEGSL
Entity #1314Name: Cam7 / Type: protein / Description: Calmodulin-7 / Num. of mol.: 1 / Source: Arabidopsis thaliana

-
Experimental information

BeamInstrument name: Heinz Maier-Leibnitz Zentrum SANS-1 / City: Garching / 国: Germany / Type of source: neutron source / Wavelength: 5 Å / Dist. spec. to detc.: 5.5 mm
DetectorName: MLZ / Type: Array of 128 3-He position sensitive tubes / Pixsize x: 8 mm
ScanTitle: ACA8 + Cam7 in stealth nanodisc (SANS, 100% D2O) / Measurement date: Aug 28, 2017 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 7200 sec. / Number of frames: 1 / Unit: 1/A /
MinMax
Q0.0119 0.2336
ResultType of curve: single_conc
Comments: 'ACA8 protein complex with Calmodulin encapsulated in a partially deuterated
ExperimentalExperimental errorPorodPorod error
MW186 kDa20 186 kDa20
Volume--297 nm330

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.15 0.001 0.15 0.001
Radius of gyration, Rg5.29 nm0.01 4.78 nm0.01

MinMaxError
D-18 0.5
Guinier point4 9 -

+
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