[English] 日本語
Yorodumi
- EMDB-43995: Cryo-EM structure of human Cav3.2 with ACT-709478 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43995
TitleCryo-EM structure of human Cav3.2 with ACT-709478
Map data
Sample
  • Complex: Voltage-dependent T-type calcium channel subunit alpha-1H
    • Protein or peptide: Voltage-dependent T-type calcium channel subunit alpha-1H
  • Ligand: N-{1-[(5-cyanopyridin-2-yl)methyl]-1H-pyrazol-3-yl}-2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}acetamide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate
KeywordsCav3.2 / voltage gated calcium channel / cryo-EM / TRANSPORT PROTEIN / ACT-709478
Function / homology
Function and homology information


low voltage-gated calcium channel activity / aldosterone biosynthetic process / cortisol biosynthetic process / positive regulation of acrosome reaction / cellular response to potassium ion / voltage-gated monoatomic ion channel activity / myoblast fusion / high voltage-gated calcium channel activity / NCAM1 interactions / calcium ion import ...low voltage-gated calcium channel activity / aldosterone biosynthetic process / cortisol biosynthetic process / positive regulation of acrosome reaction / cellular response to potassium ion / voltage-gated monoatomic ion channel activity / myoblast fusion / high voltage-gated calcium channel activity / NCAM1 interactions / calcium ion import / inorganic cation transmembrane transport / regulation of heart contraction / muscle organ development / voltage-gated calcium channel complex / calcium ion import across plasma membrane / Smooth Muscle Contraction / cellular response to hormone stimulus / regulation of membrane potential / muscle contraction / scaffold protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, T-type, 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-1H
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsFan X / Huang J / Yan N
Funding support France, 1 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)LT000754/2020-L France
CitationJournal: Cell Res / Year: 2024
Title: Structural basis for human Ca3.2 inhibition by selective antagonists.
Authors: Jian Huang / Xiao Fan / Xueqin Jin / Chen Lyu / Qinmeng Guo / Tao Liu / Jiaofeng Chen / Amaël Davakan / Philippe Lory / Nieng Yan /
Abstract: The Ca3.2 subtype of T-type calcium channels has been targeted for developing analgesics and anti-epileptics for its role in pain and epilepsy. Here we present the cryo-EM structures of Ca3.2 alone ...The Ca3.2 subtype of T-type calcium channels has been targeted for developing analgesics and anti-epileptics for its role in pain and epilepsy. Here we present the cryo-EM structures of Ca3.2 alone and in complex with four T-type calcium channel selective antagonists with overall resolutions ranging from 2.8 Å to 3.2 Å. The four compounds display two binding poses. ACT-709478 and TTA-A2 both place their cyclopropylphenyl-containing ends in the central cavity to directly obstruct ion flow, meanwhile extending their polar tails into the IV-I fenestration. TTA-P2 and ML218 project their 3,5-dichlorobenzamide groups into the II-III fenestration and place their hydrophobic tails in the cavity to impede ion permeation. The fenestration-penetrating mode immediately affords an explanation for the state-dependent activities of these antagonists. Structure-guided mutational analysis identifies several key residues that determine the T-type preference of these drugs. The structures also suggest the role of an endogenous lipid in stabilizing drug binding in the central cavity.
History
DepositionMar 8, 2024-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43995.png

Downloads & links

-
Map

FileDownload / File: emd_43995.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.
= 265.216 Å		1.04 Å/pix.
x 256 pix.
= 265.216 Å		1.04 Å/pix.
x 256 pix.
= 265.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.036 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.5602884 - 2.2150497
Average (Standard dev.)-0.0000783999 (±0.045642853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 265.216 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_43995_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43995_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Voltage-dependent T-type calcium channel subunit alpha-1H

EntireName: Voltage-dependent T-type calcium channel subunit alpha-1H
Components
  • Complex: Voltage-dependent T-type calcium channel subunit alpha-1H
    • Protein or peptide: Voltage-dependent T-type calcium channel subunit alpha-1H
  • Ligand: N-{1-[(5-cyanopyridin-2-yl)methyl]-1H-pyrazol-3-yl}-2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}acetamide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate

-
Supramolecule #1: Voltage-dependent T-type calcium channel subunit alpha-1H

SupramoleculeName: Voltage-dependent T-type calcium channel subunit alpha-1H
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-1H

MacromoleculeName: Voltage-dependent T-type calcium channel subunit alpha-1H
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 234.853609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMTEGARA ADEVRVPLGA PPPGPAALVG ASPESPGAPG REAERGSEL GVSPSESPAA ERGAELGADE EQRVPYPALA ATVFFCLGQT TRPRSWCLRL VCNPWFEHVS MLVIMLNCVT L GMFRPCED ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMTEGARA ADEVRVPLGA PPPGPAALVG ASPESPGAPG REAERGSEL GVSPSESPAA ERGAELGADE EQRVPYPALA ATVFFCLGQT TRPRSWCLRL VCNPWFEHVS MLVIMLNCVT L GMFRPCED VECGSERCNI LEAFDAFIFA FFAVEMVIKM VALGLFGQKC YLGDTWNRLD FFIVVAGMME YSLDGHNVSL SA IRTVRVL RPLRAINRVP SMRILVTLLL DTLPMLGNVL LLCFFVFFIF GIVGVQLWAG LLRNRCFLDS AFVRNNNLTF LRP YYQTEE GEENPFICSS RRDNGMQKCS HIPGRRELRM PCTLGWEAYT QPQAEGVGAA RNACINWNQY YNVCRSGDSN PHNG AINFD NIGYAWIAIF QVITLEGWVD IMYYVMDAHS FYNFIYFILL IIVGSFFMIN LCLVVIATQF SETKQRESQL MREQR ARHL SNDSTLASFS EPGSCYEELL KYVGHIFRKV KRRSLRLYAR WQSRWRKKVD PGWMGRLWVT FSGKLRRIVD SKYFSR GIM MAILVNTLSM GVEYHEQPEE LTNALEISNI VFTSMFALEM LLKLLACGPL GYIRNPYNIF DGIIVVISVW EIVGQAD GG LSVLRTFRLL RVLKLVRFLP ALRRQLVVLV KTMDNVATFC TLLMLFIFIF SILGMHLFGC KFSLKTDTGD TVPDRKNF D SLLWAIVTVF QILTQEDWNV VLYNGMASTS SWAALYFVAL MTFGNYVLFN LLVAILVEGF QAEGDANRSD TDEDKTSVH FEEDFHKLRE LQTTELKMCS LAVTPNGHLE GRGSLSPPLI MCTAATPMPT PKSSPFLDAA PSLPDSRRGS SSSGDPPLGD QKPPASLRS SPCAPWGPSG AWSSRRSSWS SLGRAPSLKR RGQCGERESL LSGEGKGSTD DEAEDGRAAP GPRATPLRRA E SLDPRPLR PAALPPTKCR DRDGQVVALP SDFFLRIDSH REDAAELDDD SEDSCCLRLH KVLEPYKPQW CRSREAWALY LF SPQNRFR VSCQKVITHK MFDHVVLVFI FLNCVTIALE RPDIDPGSTE RVFLSVSNYI FTAIFVAEMM VKVVALGLLS GEH AYLQSS WNLLDGLLVL VSLVDIVVAM ASAGGAKILG VLRVLRLLRT LRPLRVISRA PGLKLVVETL ISSLRPIGNI VLIC CAFFI IFGILGVQLF KGKFYYCEGP DTRNISTKAQ CRAAHYRWVR RKYNFDNLGQ ALMSLFVLSS KDGWVNIMYD GLDAV GVDQ QPVQNHNPWM LLYFISFLLI VSFFVLNMFV GVVVENFHKC RQHQEAEEAR RREEKRLRRL ERRRRSTFPS PEAQRR PYY ADYSPTRRSI HSLCTSHYLD LFITFIICVN VITMSMEHYN QPKSLDEALK YCNYVFTIVF VFEAALKLVA FGFRRFF KD RWNQLDLAIV LLSLMGITLE EIEMSAALPI NPTIIRIMRV LRIARVLKLL KMATGMRALL DTVVQALPQV GNLGLLFM L LFFIYAALGV ELFGRLECSE DNPCEGLSRH ATFSNFGMAF LTLFRVSTGD NWNGIMKDTL RECSREDKHC LSYLPALSP VYFVTFVLVA QFVLVNVVVA VLMKHLEESN KEAREDAELD AEIELEMAQG PGSARRVDAD RPPLPQESPG ARDAPNLVAR KVSVSRMLS LPNDSYMFRP VVPASAPHPR PLQEVEMETY GAGTPLGSVA SVHSPPAESC ASLQIPLAVS SPARSGEPLH A LSPRGTAR SPSLSRLLCR QEAVHTDSLE GKIDSPRDTL DPAEPGEKTP VRPVTQGGSL QSPPRSPRPA SVRTRKHTFG QR CVSSRPA APGGEEAEAS DPADEEVSHI TSSACPWQPT AEPHGPEASP VAGGERDLRR LYSVDAQGFL DKPGRADEQW RPS AELGSG EPGEAKAWGP EAEPALGARR KKKMSPPCIS VEPPAEDEGS ARPSAAEGGS TTLRRRTPSC EATPHRDSLE PTEG SGAGG DPAAKGERWG QASCRAEHLT VPSFAFEPLD LGVPSGDPFL DGSHSVTPES RASSSGAIVP LEPPESEPPM PVGDP PEKR RGLYLTVPQC PLEKPGSPSA TPAPGGGADD PV

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

-
Macromolecule #2: N-{1-[(5-cyanopyridin-2-yl)methyl]-1H-pyrazol-3-yl}-2-{4-[1-(trif...

MacromoleculeName: N-{1-[(5-cyanopyridin-2-yl)methyl]-1H-pyrazol-3-yl}-2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}acetamide
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1AHK
Molecular weightTheoretical: 425.406 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: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Macromolecule #4: CALCIUM ION

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

-
Macromolecule #5: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: LPE
Molecular weightTheoretical: 510.708 Da
Chemical component information

ChemComp-LPE:
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

-
Macromolecule #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #7: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoy...

MacromoleculeName: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate
type: ligand / ID: 7 / Number of copies: 4 / Formula: JL3
Molecular weightTheoretical: 663.906 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188950
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