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- EMDB-0791: membrane protein -

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Basic information

Entry
Database: EMDB / ID: EMD-0791
Titlemembrane protein
Map data
Sample
  • Complex: membrane protein
    • Protein or peptide: Voltage-dependent T-type calcium channel subunit alpha-1G
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: CHOLESTEROL HEMISUCCINATE
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 / 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 / response to nickel cation ...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 / 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 / response to nickel cation / membrane depolarization during AV node cell action potential / positive regulation of calcium ion-dependent exocytosis / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during action potential / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / NCAM1 interactions / calcium ion import / regulation of monoatomic ion transmembrane transport / voltage-gated sodium channel activity / voltage-gated calcium channel complex / regulation of heart rate by cardiac conduction / neuronal action potential / Smooth Muscle Contraction / regulation of membrane potential / calcium ion transmembrane transport / scaffold protein binding / chemical synaptic transmission / neuron projection / 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: 3.3 Å
AuthorsYan N
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China81861138009 China
National Natural Science Foundation of China31630017 China
Ministry of Science and Technology (China)2016YFA0501100 China
Ministry of Science and Technology (China)2016YFA0500402 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-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kzo
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6kzo
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0791.png

Downloads & links

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Map

FileDownload / File: emd_0791.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.091 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.106609404 - 0.16288418
Average (Standard dev.)0.0000682481 (±0.00326397)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1070.1630.000

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Supplemental data

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Sample components

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Entire : membrane protein

EntireName: membrane protein
Components
  • Complex: membrane protein
    • Protein or peptide: Voltage-dependent T-type calcium channel subunit alpha-1G
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: membrane protein

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

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

MacromoleculeName: 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: 250.506375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDEEEDGAGA EESGQPRSFM RLNDLSGAGG RPGPGSAEKD PGSADSEAEG LPYPALAPVV FFYLSQDSRP RSWCLRTVCN PWFERISML VILLNCVTLG MFRPCEDIAC DSQRCRILQA FDDFIFAFFA VEMVVKMVAL GIFGKKCYLG DTWNRLDFFI V IAGMLEYS ...String:
MDEEEDGAGA EESGQPRSFM RLNDLSGAGG RPGPGSAEKD PGSADSEAEG LPYPALAPVV FFYLSQDSRP RSWCLRTVCN PWFERISML VILLNCVTLG MFRPCEDIAC DSQRCRILQA FDDFIFAFFA VEMVVKMVAL GIFGKKCYLG DTWNRLDFFI V IAGMLEYS LDLQNVSFSA VRTVRVLRPL RAINRVPSMR ILVTLLLDTL PMLGNVLLLC FFVFFIFGIV GVQLWAGLLR NR CFLPENF SLPLSVDLER YYQTENEDES PFICSQPREN GMRSCRSVPT LRGDGGGGPP CGLDYEAYNS SSNTTCVNWN QYY TNCSAG EHNPFKGAIN FDNIGYAWIA IFQVITLEGW VDIMYFVMDA HSFYNFIYFI LLIIVGSFFM INLCLVVIAT QFSE TKQRE SQLMREQRVR FLSNASTLAS FSEPGSCYEE LLKYLVYILR KAARRLAQVS RAAGVRVGLL SSPAPLGGQE TQPSS SCSR SHRRLSVHHL VHHHHHHHHH YHLGNGTLRA PRASPEIQDR DANGSRRLML PPPSTPALSG APPGGAESVH SFYHAD CHL EPVRCQAPPP RSPSEASGRT VGSGKVYPTV HTSPPPETLK EKALVEVAAS SGPPTLTSLN IPPGPYSSMH KLLETQS TG ACQSSCKISS PCLKADSGAC GPDSCPYCAR AGAGEVELAD REMPDSDSEA VYEFTQDAQH SDLRDPHSRR QRSLGPDA E PSSVLAFWRL ICDTFRKIVD SKYFGRGIMI AILVNTLSMG IEYHEQPEEL TNALEISNIV FTSLFALEML LKLLVYGPF GYIKNPYNIF DGVIVVISVW EIVGQQGGGL SVLRTFRLMR VLKLVRFLPA LQRQLVVLMK TMDNVATFCM LLMLFIFIFS ILGMHLFGC KFASERDGDT LPDRKNFDSL LWAIVTVFQI LTQEDWNKVL YNGMASTSSW AALYFIALMT FGNYVLFNLL V AILVEGFQ AEGDANKSES EPDFFSPSLD GDGDRKKCLA LVSLGEHPEL RKSLLPPLII HTAATPMSLP KSTSTGLGEA LG PASRRTS SSGSAEPGAA HEMKSPPSAR SSPHSPWSAA SSWTSRRSSR NSLGRAPSLK RRSPSGERRS LLSGEGQESQ DEE ESSEEE RASPAGSDHR HRGSLEREAK SSFDLPDTLQ VPGLHRTASG RGSASEHQDC NGKSASGRLA RALRPDDPPL DGDD ADDEG NLSKGERVRA WIRARLPACC LERDSWSAYI FPPQSRFRLL CHRIITHKMF DHVVLVIIFL NCITIAMERP KIDPH SAER IFLTLSNYIF TAVFLAEMTV KVVALGWCFG EQAYLRSSWN VLDGLLVLIS VIDILVSMVS DSGTKILGML RVLRLL RTL RPLRVISRAQ GLKLVVETLM SSLKPIGNIV VICCAFFIIF GILGVQLFKG KFFVCQGEDT RNITNKSDCA EASYRWV RH KYNFDNLGQA LMSLFVLASK DGWVDIMYDG LDAVGVDQQP IMNHNPWMLL YFISFLLIVA FFVLNMFVGV VVENFHKC R QHQEEEEARR REEKRLRRLE KKRRNLMLDD VIASGSSASA ASEAQCKPYY SDYSRFRLLV HHLCTSHYLD LFITGVIGL NVVTMAMEHY QQPQILDEAL KICNYIFTVI FVLESVFKLV AFGFRRFFQD RWNQLDLAIV LLSIMGITLE EIEVNASLPI NPTIIRIMR VLRIARVLKL LKMAVGMRAL LDTVMQALPQ VGNLGLLFML LFFIFAALGV ELFGDLECDE THPCEGLGRH A TFRNFGMA FLTLFRVSTG DNWNGIMKDT LRDCDQESTC YNTVISPIYF VSFVLTAQFV LVNVVIAVLM KHLEESNKEA KE EAELEAE LELEMKTLSP QPHSPLGSPF LWPGVEGPDS PDSPKPGALH PAAHARSASH FSLEHPTMQP HPTELPGPDL LTV RKSGVS RTHSLPNDSY MCRHGSTAEG PLGHRGWGLP KAQSGSVLSV HSQPADTSYI LQLPKDAPHL LQPHSAPTWG TIPK LPPPG RSPLAQRPLR RQAAIRTDSL DVQGLGSRED LLAEVSGPSP PLARAYSFWG QSSTQAQQHS RSHSKISKHM TPPAP CPGP EPNWGKGPPE TRSSLELDTE LSWISGDLLP PGGQEEPPSP RDLKKCYSVE AQSCQRRPTS WLDEQRRHSI AVSCLD SGS QPHLGTDPSN LGGQPLGGPG SRPKKKLSPP SITIDPPESQ GPRTPPSPGI CLRRRAPSSD SKDPLASGPP DSMAASP SP KKDVLSLSGL SSDPADLDP

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Macromolecule #2: CALCIUM ION

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

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 4 / Number of copies: 13 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105559

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