[English] 日本語
Yorodumi
- EMDB-0792: calcium channel-ligand -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0792
Titlecalcium channel-ligand
Map data
Sample
  • Complex: membrane protein-ligand
    • Protein or peptide: Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordschannel / blocker / MEMBRANE PROTEIN
Function / homology
Function and homology information


SA node cell to atrial cardiac muscle cell signaling / AV node cell to bundle of His cell signaling / voltage-gated calcium channel activity involved SA node cell action potential / sinoatrial node development / low voltage-gated calcium channel activity / response to nickel cation / voltage-gated calcium channel activity involved in AV node cell action potential / AV node cell action potential / SA node cell action potential / membrane depolarization during SA node cell action potential ...SA node cell to atrial cardiac muscle cell signaling / AV node cell to bundle of His cell signaling / voltage-gated calcium channel activity involved SA node cell action potential / sinoatrial node development / low voltage-gated calcium channel activity / response to nickel cation / voltage-gated calcium channel activity involved in AV node cell action potential / AV node cell action potential / SA node cell action potential / membrane depolarization during SA node cell action potential / membrane depolarization during AV node cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / NCAM1 interactions / cardiac muscle cell action potential involved in contraction / calcium ion import / voltage-gated calcium channel complex / regulation of heart rate by cardiac conduction / calcium ion import across plasma membrane / Smooth Muscle Contraction / voltage-gated calcium channel activity / regulation of membrane potential / calcium ion transmembrane transport / scaffold protein binding / chemical synaptic transmission / synapse / plasma membrane / cytoplasm
Similarity search - Function
Voltage-dependent calcium channel, T-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit / : / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-dependent T-type calcium channel subunit alpha-1G
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYan N
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31800628 China
National Natural Science Foundation of China81920108015 China
Ministry of Science and Technology (China)2016YFA0500402 China
Ministry of Science and Technology (China)2016YFA0501100 China
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures of apo and antagonist-bound human Ca3.1.
Authors: Yanyu Zhao / Gaoxingyu Huang / Qiurong Wu / Kun Wu / Ruiqi Li / Jianlin Lei / Xiaojing Pan / Nieng Yan /
Abstract: Among the ten subtypes of mammalian voltage-gated calcium (Ca) channels, Ca3.1-Ca3.3 constitute the T-type, or the low-voltage-activated, subfamily, the abnormal activities of which are associated ...Among the ten subtypes of mammalian voltage-gated calcium (Ca) channels, Ca3.1-Ca3.3 constitute the T-type, or the low-voltage-activated, subfamily, the abnormal activities of which are associated with epilepsy, psychiatric disorders and pain. Here we report the cryo-electron microscopy structures of human Ca3.1 alone and in complex with a highly Ca3-selective blocker, Z944, at resolutions of 3.3 Å and 3.1 Å, respectively. The arch-shaped Z944 molecule reclines in the central cavity of the pore domain, with the wide end inserting into the fenestration on the interface between repeats II and III, and the narrow end hanging above the intracellular gate like a plug. The structures provide the framework for comparative investigation of the distinct channel properties of different Ca subfamilies.
History
DepositionSep 25, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseDec 18, 2019-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6kzp
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0792.png

Downloads & links

-
Map

FileDownload / File: emd_0792.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 349.12 Å		1.09 Å/pix.
x 320 pix.
= 349.12 Å		1.09 Å/pix.
x 320 pix.
= 349.12 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: 0.035
Minimum - Maximum-0.14650272 - 0.25729814
Average (Standard dev.)0.00008795772 (±0.004930761)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 349.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z349.120349.120349.120
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/NS320320320
D min/max/mean-0.1470.2570.000

-
Supplemental data

-
Mask #1

Fileemd_0792_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : membrane protein-ligand

EntireName: membrane protein-ligand
Components
  • Complex: membrane protein-ligand
    • Protein or peptide: Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CHOLESTEROL HEMISUCCINATE

-
Supramolecule #1: membrane protein-ligand

SupramoleculeName: membrane protein-ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage...

MacromoleculeName: Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 238.874984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHG DYKDDDDKGT DEEEDGAGAE ESGQPRSFMR LNDLSGAGGR PGPGSAEKDP GSADSEAEGL PYPALAPVVF FYLSQDSRP RSWCLRTVCN PWFERISMLV ILLNCVTLGM FRPCEDIACD SQRCRILQAF DDFIFAFFAV EMVVKMVALG I FGKKCYLG ...String:
MHHHHHHHHG DYKDDDDKGT DEEEDGAGAE ESGQPRSFMR LNDLSGAGGR PGPGSAEKDP GSADSEAEGL PYPALAPVVF FYLSQDSRP RSWCLRTVCN PWFERISMLV ILLNCVTLGM FRPCEDIACD SQRCRILQAF DDFIFAFFAV EMVVKMVALG I FGKKCYLG DTWNRLDFFI VIAGMLEYSL DLQNVSFSAV RTVRVLRPLR AINRVPSMRI LVTLLLDTLP MLGNVLLLCF FV FFIFGIV GVQLWAGLLR NRCFLPENFS LPLSVDLERY YQTENEDESP FICSQPRENG MRSCRSVPTL RGDGGGGPPC GLD YEAYNS SSNTTCVNWN QYYTNCSAGE HNPFKGAINF DNIGYAWIAI FQVITLEGWV DIMYFVMDAH SFYNFIYFIL LIIV GSFFM INLCLVVIAT QFSETKQRES QLMREQRVRF LSNASTLASF SEPGSCYEEL LKYLVYILRK AARRLAQVSR AAGVR VGLL SSPAPLGGQE TQPSSSCSRS HRRLSVHHLV HHHHHHHHHY HLGACQSSCK ISSPCLKADS GACGPDSCPY CARAGA GEV ELADREMPDS DSEAVYEFTQ DAQHSDLRDP HSRRQRSLGP DAEPSSVLAF WRLICDTFRK IVDSKYFGRG IMIAILV NT LSMGIEYHEQ PEELTNALEI SNIVFTSLFA LEMLLKLLVY GPFGYIKNPY NIFDGVIVVI SVWEIVGQQG GGLSVLRT F RLMRVLKLVR FLPALQRQLV VLMKTMDNVA TFCMLLMLFI FIFSILGMHL FGCKFASERD GDTLPDRKNF DSLLWAIVT VFQILTQEDW NKVLYNGMAS TSSWAALYFI ALMTFGNYVL FNLLVAILVE GFQAEGDANK SESEPDFFSP SLDGDGDRKK CLALVSLGE HPELRKSLLP PLIIHTAATP MSLPKSTSTG LGEALGPASR RTSSSGSAEP GAAHEMKSPP SARSSPHSPW S AASSWTSR RSSRNSLGRA PSLKRRSPSG ERRSLLSGEG QESQDEEESS EEERASPAGS DHRHRGSLER EAKSSFDLPD TL QVPGLHR TASGRGSASE HQDCNGKSAS GRLARALRPD DPPLDGDDAD DEGNLSKGER VRAWIRARLP ACCLERDSWS AYI FPPQSR FRLLCHRIIT HKMFDHVVLV IIFLNCITIA MERPKIDPHS AERIFLTLSN YIFTAVFLAE MTVKVVALGW CFGE QAYLR SSWNVLDGLL VLISVIDILV SMVSDSGTKI LGMLRVLRLL RTLRPLRVIS RAQGLKLVVE TLMSSLKPIG NIVVI CCAF FIIFGILGVQ LFKGKFFVCQ GEDTRNITNK SDCAEASYRW VRHKYNFDNL GQALMSLFVL ASKDGWVDIM YDGLDA VGV DQQPIMNHNP WMLLYFISFL LIVAFFVLNM FVGVVVENFH KCRQHQEEEE ARRREEKRLR RLEKKRRNLM LDDVIAS GS SASAASEAQC KPYYSDYSRF RLLVHHLCTS HYLDLFITGV IGLNVVTMAM EHYQQPQILD EALKICNYIF TVIFVLES V FKLVAFGFRR FFQDRWNQLD LAIVLLSIMG ITLEEIEVNA SLPINPTIIR IMRVLRIARV LKLLKMAVGM RALLDTVMQ ALPQVGNLGL LFMLLFFIFA ALGVELFGDL ECDETHPCEG LGRHATFRNF GMAFLTLFRV STGDNWNGIM KDTLRDCDQE STCYNTVIS PIYFVSFVLT AQFVLVNVVI AVLMKHLEES NKEAKEEAEL EAELELEMKT LSPQPHSPLG SPFLWPGVEG P DSPDSPKP GALHPAAHAR SASHFSLEHP TMQPHPTELP GPDLLTVRKS GVSRTHSLPN DSYMCRHGST AEGPLGHRGW GL PKAQSGS VLSVHSQPAD TSYILQLPKD APHLLQPHSA PTWGTIPKLP PPGRSPLAQR PLRRQAAIRT DSLDVQGLGS RED LLAEVS GPSPPLARAY SFWGQSSTQA QQHSRSHSKI SKHMTPPAPC PGPEPNWGKG PPETRSSLEL DTELSWISGD LLPP GGQEE PPSPRDLKKC YSVEAQSCQR RPTSWLDEQR RHSIAVSCLD SGSQPHLGTD PSNLGGQPLG GPGSRPKKKL SPPSI TIDP PESQGPRTPP SPGICLRRRA PSSDSKDPLA SGPPDSMAAS PSPKKDVLSL SGLSSDPADL DP

UniProtKB: Voltage-dependent T-type calcium channel subunit alpha-1G, Voltage-dependent T-type calcium channel subunit alpha-1G

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #4: ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-...

MacromoleculeName: ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: DZR
Molecular weightTheoretical: 383.888 Da
Chemical component information

ChemComp-DZR:
~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide / Z944*YM

-
Macromolecule #5: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 5 / Number of copies: 8 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

-
Macromolecule #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
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: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138449
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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