[English] 日本語
Yorodumi
- EMDB-32585: CryoEM structure of human low-voltage activated T-type calcium ch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32585
TitleCryoEM structure of human low-voltage activated T-type calcium channel Cav3.3 in complex with mibefradil (MIB)
Map data
Sample
  • Complex: CaV3.3
    • Protein or peptide: Voltage-dependent T-type calcium channel subunit alpha-1I
  • Ligand: (1S,2S)-2-(2-{[3-(1H-benzimidazol-2-yl)propyl](methyl)amino}ethyl)-6-fluoro-1-(propan-2-yl)-1,2,3,4-tetrahydronaphthalen-2-yl methoxyacetate
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CALCIUM ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMIB / MEMBRANE PROTEIN
Function / homology
Function and homology information


high voltage-gated calcium channel activity / sleep / NCAM1 interactions / voltage-gated calcium channel complex / calcium ion import across plasma membrane / neuronal action potential / Smooth Muscle Contraction / voltage-gated calcium channel activity / signal transduction / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, T-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-dependent T-type calcium channel subunit alpha-1I
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHe L / Yu Z / Dong Y / Chen Q / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2022
Title: Structure, gating, and pharmacology of human Ca3.3 channel.
Authors: Lingli He / Zhuoya Yu / Ze Geng / Zhuo Huang / Changjiang Zhang / Yanli Dong / Yiwei Gao / Yuhang Wang / Qihao Chen / Le Sun / Xinyue Ma / Bo Huang / Xiaoqun Wang / Yan Zhao /
Abstract: The low-voltage activated T-type calcium channels regulate cellular excitability and oscillatory behavior of resting membrane potential which trigger many physiological events and have been ...The low-voltage activated T-type calcium channels regulate cellular excitability and oscillatory behavior of resting membrane potential which trigger many physiological events and have been implicated with many diseases. Here, we determine structures of the human T-type Ca3.3 channel, in the absence and presence of antihypertensive drug mibefradil, antispasmodic drug otilonium bromide and antipsychotic drug pimozide. Ca3.3 contains a long bended S6 helix from domain III, with a positive charged region protruding into the cytosol, which is critical for T-type Ca channel activation at low voltage. The drug-bound structures clearly illustrate how these structurally different compounds bind to the same central cavity inside the Ca3.3 channel, but are mediated by significantly distinct interactions between drugs and their surrounding residues. Phospholipid molecules penetrate into the central cavity in various extent to shape the binding pocket and play important roles in stabilizing the inhibitor. These structures elucidate mechanisms of channel gating, drug recognition, and actions, thus pointing the way to developing potent and subtype-specific drug for therapeutic treatments of related disorders.
History
DepositionJan 13, 2022-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32585.png

Downloads & links

-
Map

FileDownload / File: emd_32585.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-2.3329124 - 3.2744818
Average (Standard dev.)0.009109344 (±0.09386205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : CaV3.3

EntireName: CaV3.3
Components
  • Complex: CaV3.3
    • Protein or peptide: Voltage-dependent T-type calcium channel subunit alpha-1I
  • Ligand: (1S,2S)-2-(2-{[3-(1H-benzimidazol-2-yl)propyl](methyl)amino}ethyl)-6-fluoro-1-(propan-2-yl)-1,2,3,4-tetrahydronaphthalen-2-yl methoxyacetate
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CALCIUM ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: CaV3.3

SupramoleculeName: CaV3.3 / 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-1I

MacromoleculeName: Voltage-dependent T-type calcium channel subunit alpha-1I
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 245.373031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAESASPPSS SAAAPAAEPG VTTEQPGPRS PPSSPPGLEE PLDGADPHVP HPDLAPIAFF CLRQTTSPRN WCIKMVCNPW FECVSMLVI LLNCVTLGMY QPCDDMDCLS DRCKILQVFD DFIFIFFAME MVLKMVALGI FGKKCYLGDT WNRLDFFIVM A GMVEYSLD ...String:
MAESASPPSS SAAAPAAEPG VTTEQPGPRS PPSSPPGLEE PLDGADPHVP HPDLAPIAFF CLRQTTSPRN WCIKMVCNPW FECVSMLVI LLNCVTLGMY QPCDDMDCLS DRCKILQVFD DFIFIFFAME MVLKMVALGI FGKKCYLGDT WNRLDFFIVM A GMVEYSLD LQNINLSAIR TVRVLRPLKA INRVPSMRIL VNLLLDTLPM LGNVLLLCFF VFFIFGIIGV QLWAGLLRNR CF LEENFTI QGDVALPPYY QPEEDDEMPF ICSLSGDNGI MGCHEIPPLK EQGRECCLSK DDVYDFGAGR QDLNASGLCV NWN RYYNVC RTGSANPHKG AINFDNIGYA WIVIFQVITL EGWVEIMYYV MDAHSFYNFI YFILLIIVGS FFMINLCLVV IATQ FSETK QREHRLMLEQ RQRYLSSSTV ASYAEPGDCY EEIFQYVCHI LRKAKRRALG LYQALQSRRQ ALGPEAPAPA KPGPH AKEP RHYHGKTKGQ GDEGRHLGSR HCQTLHGPAS PGNDHSGREL CPQHSPLDAT PHTLVQPIPA TLASDPASCP CCQHED GRR PSGLGSTDSG QEGSGSGSSA GGEDEADGDG ARSSEDGASS ELGKEEEEEE QADGAVWLCG DVWRETRAKL RGIVDSK YF NRGIMMAILV NTVSMGIEHH EQPEELTNIL EICNVVFTSM FALEMILKLA AFGLFDYLRN PYNIFDSIIV IISIWEIV G QADGGLSVLR TFRLLRVLKL VRFMPALRRQ LVVLMKTMDN VATFCMLLML FIFIFSILGM HIFGCKFSLR TDTGDTVPD RKNFDSLLWA IVTVFQILTQ EDWNVVLYNG MASTSPWASL YFVALMTFGN YVLFNLLVAI LVEGFQAEGD ANRSYSDEDQ SSSNIEEFD KLQEGLDSSG DPKLCPIPMT PNGHLDPSLP LGGHLGPAGA AGPAPRLSLQ PDPMLVALGS RKSSVMSLGR M SYDQRSLS SSRSSYYGPW GRSAAWASRR SSWNSLKHKP PSAEHESLLS AERGGGARVC EVAADEGPPR AAPLHTPHAH HI HHGPHLA HRHRHHRRTL SLDNRDSVDL AELVPAVGAH PRAAWRAAGP APGHEDCNGR MPSIAKDVFT KMGDRGDRGE DEE EIDYTL CFRVRKMIDV YKPDWCEVRE DWSVYLFSPE NRFRVLCQTI IAHKLFDYVV LAFIFLNCIT IALERPQIEA GSTE RIFLT VSNYIFTAIF VGEMTLKVVS LGLYFGEQAY LRSSWNVLDG FLVFVSIIDI VVSLASAGGA KILGVLRVLR LLRTL RPLR VISRAPGLKL VVETLISSLK PIGNIVLICC AFFIIFGILG VQLFKGKFYH CLGVDTRNIT NRSDCMAANY RWVHHK YNF DNLGQALMSL FVLASKDGWV NIMYNGLDAV AVDQQPVTNH NPWMLLYFIS FLLIVSFFVL NMFVGVVVEN FHKCRQH QE AEEARRREEK RLRRLEKKRR KAQRLPYYAT YCHTRLLIHS MCTSHYLDIF ITFIICLNVV TMSLEHYNQP TSLETALK Y CNYMFTTVFV LEAVLKLVAF GLRRFFKDRW NQLDLAIVLL SVMGITLEEI EINAALPINP TIIRIMRVLR IARVLKLLK MATGMRALLD TVVQALPQVG NLGLLFMLLF FIYAALGVEL FGKLVCNDEN PCEGMSRHAT FENFGMAFLT LFQVSTGDNW NGIMKDTLR DCTHDERSCL SSLQFVSPLY FVSFVLTAQF VLINVVVAVL MKHLDDSNKE AQEDAEMDAE LELEMAHGLG P GPRLPTGS PGAPGRGPGG AGGGGDTEGG LCRRCYSPAQ ENLWLDSVSL IIKDSLEGEL TIIDNLSGSI FHHYSSPAGC KK CHHDKQE VQLAETEAFS LNSDRSSSIL LGDDLSLEDP TACPPGRKDS KGELDPPEPM RVGDLGECFF PLSSTAVSPD PEN FLCEME EIPFNPVRSW LKHDSSQAPP SPFSPDASSP LLPMPAEFFH PAVSASQKGP EKGTGTGTLP KIALQGSWAS LRSP RVNCT LLRQATGSDT SLDASPSSSA GSLQTTLEDS LTLSDSPRRA LGPPAPAPGP RAGLSPAARR RLSLRGRGLF SLRGL RAHQ RSHSSGGSTS PGCTHHDSMD PSDEEGRGGA GGGGAGSEHS ETLSSLSLTS LFCPPPPPPA PGLTPARKFS STSSLA APG RPHAAALAHG LARSPSWAAD RSKDPPGRAP LPMGLGPLAP PPQPLPGELE PGDAASKRKR

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

-
Macromolecule #2: (1S,2S)-2-(2-{[3-(1H-benzimidazol-2-yl)propyl](methyl)amino}ethyl...

MacromoleculeName: (1S,2S)-2-(2-{[3-(1H-benzimidazol-2-yl)propyl](methyl)amino}ethyl)-6-fluoro-1-(propan-2-yl)-1,2,3,4-tetrahydronaphthalen-2-yl methoxyacetate
type: ligand / ID: 2 / Number of copies: 1 / Formula: MWV
Molecular weightTheoretical: 495.629 Da
Chemical component information

ChemComp-MWV:
(1S,2S)-2-(2-{[3-(1H-benzimidazol-2-yl)propyl](methyl)amino}ethyl)-6-fluoro-1-(propan-2-yl)-1,2,3,4-tetrahydronaphthalen-2-yl methoxyacetate / channel blocker*YM

-
Macromolecule #3: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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

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

-
Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / 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: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 9.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kzo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151492
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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