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- EMDB-9868: Rabbit Cav1.1-Verapamil Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9868
TitleRabbit Cav1.1-Verapamil Complex
Map dataEM map
Sample
  • Complex: Cav1.1-drug complex
    • Complex: Cav1.1-beta1a-alpha2-delta1-gamma complex
      • Protein or peptide: x 5 types
  • Ligand: x 7 types
KeywordsMembrane protein complex modulated by FDA approved drug. / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of muscle contraction / L-type voltage-gated calcium channel complex / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / cellular response to caffeine / calcium ion import across plasma membrane / calcium channel regulator activity / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / T-tubule ...positive regulation of muscle contraction / L-type voltage-gated calcium channel complex / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / cellular response to caffeine / calcium ion import across plasma membrane / calcium channel regulator activity / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / T-tubule / muscle contraction / calcium ion transmembrane transport / sarcolemma / calcium channel activity / transmembrane transporter binding / calmodulin binding / metal ion binding / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-1 subunit / Voltage-dependent calcium channel, gamma-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S subunit / PMP-22/EMP/MP20/Claudin tight junction / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage-dependent calcium channel, L-type, beta subunit / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit ...Voltage-dependent calcium channel, L-type, beta-1 subunit / Voltage-dependent calcium channel, gamma-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S subunit / PMP-22/EMP/MP20/Claudin tight junction / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage-dependent calcium channel, L-type, beta subunit / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / VWA N-terminal / Voltage-dependent calcium channel, alpha-2/delta subunit, conserved region / VWA N-terminal / Neuronal voltage-dependent calcium channel alpha 2acd / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / von Willebrand factor type A domain / Voltage-dependent channel domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Ion transport domain / Ion transport protein / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit alpha-1S / Voltage-dependent calcium channel subunit alpha-2/delta-1 / Voltage-dependent L-type calcium channel subunit beta-1 / Voltage-dependent calcium channel gamma-1 subunit
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhao Y / Huang G
Funding support China, 6 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500402 China
Ministry of Science and Technology (China)2015CB910101 China
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31630017 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130762 China
National Natural Science Foundation of China81861138009 China
CitationJournal: Cell / Year: 2019
Title: Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca Channel.
Authors: Yanyu Zhao / Gaoxingyu Huang / Jianping Wu / Qiurong Wu / Shuai Gao / Zhen Yan / Jianlin Lei / Nieng Yan /
Abstract: The L-type voltage-gated Ca (Ca) channels are modulated by various compounds exemplified by 1,4-dihydropyridines (DHP), benzothiazepines (BTZ), and phenylalkylamines (PAA), many of which have been ...The L-type voltage-gated Ca (Ca) channels are modulated by various compounds exemplified by 1,4-dihydropyridines (DHP), benzothiazepines (BTZ), and phenylalkylamines (PAA), many of which have been used for characterizing channel properties and for treatment of hypertension and other disorders. Here, we report the cryoelectron microscopy (cryo-EM) structures of Ca1.1 in complex with archetypal antagonistic drugs, nifedipine, diltiazem, and verapamil, at resolutions of 2.9 Å, 3.0 Å, and 2.7 Å, respectively, and with a DHP agonist Bay K 8644 at 2.8 Å. Diltiazem and verapamil traverse the central cavity of the pore domain, directly blocking ion permeation. Although nifedipine and Bay K 8644 occupy the same fenestration site at the interface of repeats III and IV, the coordination details support previous functional observations that Bay K 8644 is less favored in the inactivated state. These structures elucidate the modes of action of different Ca ligands and establish a framework for structure-guided drug discovery.
History
DepositionMar 26, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseJun 12, 2019-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
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  • Surface view colored by height
  • Surface level: 0.025
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  • Surface view with fitted model
  • Atomic models: PDB-6jpa
  • Surface level: 0.025
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9868.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Voxel sizeX=Y=Z: 1.091 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.14246978 - 0.26829797
Average (Standard dev.)0.00007790376 (±0.0051421314)
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/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1420.2680.000

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Supplemental data

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Sample components

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Entire : Cav1.1-drug complex

EntireName: Cav1.1-drug complex
Components
  • Complex: Cav1.1-drug complex
    • Complex: Cav1.1-beta1a-alpha2-delta1-gamma complex
      • Protein or peptide: Voltage-dependent L-type calcium channel subunit alpha-1S
      • Protein or peptide: Voltage-dependent calcium channel gamma-1 subunit
      • Protein or peptide: Voltage-dependent L-type calcium channel subunit beta-1
      • Protein or peptide: Voltage-dependent L-type calcium channel subunit beta-1
      • Protein or peptide: Voltage-dependent calcium channel subunit alpha-2/delta-1Voltage-gated calcium channel
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl)pentanenitrile
  • Ligand: ETHANOLAMINE

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Supramolecule #1: Cav1.1-drug complex

SupramoleculeName: Cav1.1-drug complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#5

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Supramolecule #2: Cav1.1-beta1a-alpha2-delta1-gamma complex

SupramoleculeName: Cav1.1-beta1a-alpha2-delta1-gamma complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Voltage-dependent L-type calcium channel subunit alpha-1S

MacromoleculeName: Voltage-dependent L-type calcium channel subunit alpha-1S
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 172.146531 KDa
SequenceString: MEPSSPQDEG LRKKQPKKPL PEVLPRPPRA LFCLTLQNPL RKACISIVEW KPFETIILLT IFANCVALAV YLPMPEDDNN SLNLGLEKL EYFFLTVFSI EAAMKIIAYG FLFHQDAYLR SGWNVLDFII VFLGVFTAIL EQVNVIQSNT APMSSKGAGL D VKALRAFR ...String:
MEPSSPQDEG LRKKQPKKPL PEVLPRPPRA LFCLTLQNPL RKACISIVEW KPFETIILLT IFANCVALAV YLPMPEDDNN SLNLGLEKL EYFFLTVFSI EAAMKIIAYG FLFHQDAYLR SGWNVLDFII VFLGVFTAIL EQVNVIQSNT APMSSKGAGL D VKALRAFR VLRPLRLVSG VPSLQVVLNS IFKAMLPLFH IALLVLFMVI IYAIIGLELF KGKMHKTCYY IGTDIVATVE NE KPSPCAR TGSGRPCTIN GSECRGGWPG PNHGITHFDN FGFSMLTVYQ CITMEGWTDV LYWVNDAIGN EWPWIYFVTL ILL GSFFIL NLVLGVLSGE FTKEREKAKS RGTFQKLREK QQLEEDLRGY MSWITQGEVM DVEDLREGKL SLEEGGSDTE SLYE IEGLN KIIQFIRHWR QWNRVFRWKC HDLVKSRVFY WLVILIVALN TLSIASEHHN QPLWLTHLQD IANRVLLSLF TIEML LKMY GLGLRQYFMS IFNRFDCFVV CSGILELLLV ESGAMTPLGI SVLRCIRLLR LFKITKYWTS LSNLVASLLN SIRSIA SLL LLLFLFIIIF ALLGMQLFGG RYDFEDTEVR RSNFDNFPQA LISVFQVLTG EDWNSVMYNG IMAYGGPSYP GVLVCIY FI ILFVCGNYIL LNVFLAIAVD NLAEAESLTS AQKAKAEERK RRKMSRGLPD KTEEEKSVMA KKLEQKPKGE GIPTTAKL K VDEFESNVNE VKDPYPSADF PGDDEEDEPE IPVSPRPRPL AELQLKEKAV PIPEASSFFI FSPTNKVRVL CHRIVNATW FTNFILLFIL LSSAALAAED PIRAESVRNQ ILGYFDIAFT SVFTVEIVLK MTTYGAFLHK GSFCRNYFNI LDLLVVAVSL ISMGLESST ISVVKILRVL RVLRPLRAIN RAKGLKHVVQ CVFVAIRTIG NIVLVTTLLQ FMFACIGVQL FKGKFFSCND L SKMTEEEC RGYYYVYKDG DPTQMELRPR QWIHNDFHFD NVLSAMMSLF TVSTFEGWPQ LLYRAIDSNE EDMGPVYNNR VE MAIFFII YIILIAFFMM NIFVGFVIVT FQEQGETEYK NCELDKNQRQ CVQYALKARP LRCYIPKNPY QYQVWYVVTS SYF EYLMFA LIMLNTICLG MQHYHQSEEM NHISDILNVA FTIIFTLEMI LKLLAFKARG YFGDPWNVFD FLIVIGSIID VILS EIDTF LASSGGLYCL GGGCGNVDPD ESARISSAFF RLFRVMRLIK LLSRAEGVRT LLWTFIKSFQ ALPYVALLIV MLFFI YAVI GMQMFGKIAL VDGTQINRNN NFQTFPQAVL LLFRCATGEA WQEILLACSY GKLCDPESDY APGEEYTCGT NFAYYY FIS FYMLCAFLII NLFVAVIMDN FDYLTRDWSI LGPHHLDEFK AIWAEYDPEA KGRIKHLDVV TLLRRIQPPL GFGKFCP HR VACKRLVGMN MPLNSDGTVT FNATLFALVR TALKIKTEGN FEQANEELRA IIKKIWKRTS MKLL

UniProtKB: Voltage-dependent L-type calcium channel subunit alpha-1S

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Macromolecule #2: Voltage-dependent calcium channel gamma-1 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-1 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 25.082254 KDa
SequenceString: MSPTEAPKVR VTLFCILVGI VLAMTAVVSD HWAVLSPHME NHNTTCEAAH FGLWRICTKR IALGEDRSCG PITLPGEKNC SYFRHFNPG ESSEIFEFTT QKEYSISAAA ISVFSLGFLI MGTICALMAF RKKRDYLLRP ASMFYVFAGL CLFVSLEVMR Q SVKRMIDS ...String:
MSPTEAPKVR VTLFCILVGI VLAMTAVVSD HWAVLSPHME NHNTTCEAAH FGLWRICTKR IALGEDRSCG PITLPGEKNC SYFRHFNPG ESSEIFEFTT QKEYSISAAA ISVFSLGFLI MGTICALMAF RKKRDYLLRP ASMFYVFAGL CLFVSLEVMR Q SVKRMIDS EDTVWIEYYY SWSFACACAA FVLLFLGGIS LLLFSLPRMP QNPWESCMDA EPEH

UniProtKB: Voltage-dependent calcium channel gamma-1 subunit

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Macromolecule #3: Voltage-dependent L-type calcium channel subunit beta-1

MacromoleculeName: Voltage-dependent L-type calcium channel subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 49.64243 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QGPHMALRKE AERQALAQLE KAKTKPVAFA VRTNVGYNPS PGDEVPVEGV AITFEPKDFL HIKEKYNNDW WIGRLVKEGC EVGFIPSPV KLDSLRLLQE QKLRQSRLSS SKSGDNSSSS LGDVVTGTRR PTPPASGNEM TNLAFELEPL DLEEDEAELG E QSGSAKTS ...String:
QGPHMALRKE AERQALAQLE KAKTKPVAFA VRTNVGYNPS PGDEVPVEGV AITFEPKDFL HIKEKYNNDW WIGRLVKEGC EVGFIPSPV KLDSLRLLQE QKLRQSRLSS SKSGDNSSSS LGDVVTGTRR PTPPASGNEM TNLAFELEPL DLEEDEAELG E QSGSAKTS VSSVTTPPPH GTRIPFFKKT EHVPPYDVVP SMRPIILVGP SLKGYEVTDM MQKALFDFLK HLFDGRISIT RV TADISLA KRSVLNNPSK HIIIERSNTR SSLAEVQSEI ERIFELARTL QLVALDADTI NHPAQLSKTS LAPIIVYIKI TSP KVLQRL IKSRGKSQSK HLNVQIAASE KLAQCPPEMF DIILDENQLE DACEHLAEYL EAYWKATHPP SSTPPNPLLN RTMA TAALA ASPAPVSNLQ VQVLTSLRRN LSFWGGLETS QRGGGAVPQQ QEHAM

UniProtKB: Voltage-dependent L-type calcium channel subunit beta-1

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Macromolecule #4: Voltage-dependent L-type calcium channel subunit beta-1

MacromoleculeName: Voltage-dependent L-type calcium channel subunit beta-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 57.898285 KDa
SequenceString: MVQKTSMSRG PYPPSQEIPM EVFDPSPQGK YSKRKGRFKR SDGSTSSDTT SNSFVRQGSA ESYTSRPSDS DVSLEEDREA LRKEAERQA LAQLEKAKTK PVAFAVRTNV GYNPSPGDEV PVEGVAITFE PKDFLHIKEK YNNDWWIGRL VKEGCEVGFI P SPVKLDSL ...String:
MVQKTSMSRG PYPPSQEIPM EVFDPSPQGK YSKRKGRFKR SDGSTSSDTT SNSFVRQGSA ESYTSRPSDS DVSLEEDREA LRKEAERQA LAQLEKAKTK PVAFAVRTNV GYNPSPGDEV PVEGVAITFE PKDFLHIKEK YNNDWWIGRL VKEGCEVGFI P SPVKLDSL RLLQEQKLRQ SRLSSSKSGD NSSSSLGDVV TGTRRPTPPA SGNEMTNLAF ELEPLDLEED EAELGEQSGS AK TSVSSVT TPPPHGTRIP FFKKTEHVPP YDVVPSMRPI ILVGPSLKGY EVTDMMQKAL FDFLKHLFDG RISITRVTAD ISL AKRSVL NNPSKHIIIE RSNTRSSLAE VQSEIERIFE LARTLQLVAL DADTINHPAQ LSKTSLAPII VYIKITSPKV LQRL IKSRG KSQSKHLNVQ IAASEKLAQC PPEMFDIILD ENQLEDACEH LAEYLEAYWK ATHPPSSTPP NPLLNRTMAT AALAA SPAP VSNLQVQVLT SLRRNLSFWG GLETSQRGGG AVPQQQEHAM

UniProtKB: Voltage-dependent L-type calcium channel subunit beta-1

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Macromolecule #5: Voltage-dependent calcium channel subunit alpha-2/delta-1

MacromoleculeName: Voltage-dependent calcium channel subunit alpha-2/delta-1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 118.641398 KDa
SequenceString: FPSAVTIKSW VDKMQEDLVT LAKTASGVHQ LVDIYEKYQD LYTVEPNNAR QLVEIAARDI EKLLSNRSKA LVRLALEAEK VQAAHQWRE DFASNEVVYY NAKDDLDPEK NDSEPGSQRI KPVFIDDANF RRQVSYQHAA VHIPTDIYEG STIVLNELNW T SALDDVFK ...String:
FPSAVTIKSW VDKMQEDLVT LAKTASGVHQ LVDIYEKYQD LYTVEPNNAR QLVEIAARDI EKLLSNRSKA LVRLALEAEK VQAAHQWRE DFASNEVVYY NAKDDLDPEK NDSEPGSQRI KPVFIDDANF RRQVSYQHAA VHIPTDIYEG STIVLNELNW T SALDDVFK KNREEDPSLL WQVFGSATGL ARYYPASPWV DNSRTPNKID LYDVRRRPWY IQGAASPKDM LILVDVSGSV SG LTLKLIR TSVSEMLETL SDDDFVNVAS FNSNAQDVSC FQHLVQANVR NKKVLKDAVN NITAKGITDY KKGFSFAFEQ LLN YNVSRA NCNKIIMLFT DGGEERAQEI FAKYNKDKKV RVFTFSVGQH NYDRGPIQWM ACENKGYYYE IPSIGAIRIN TQEY LDVLG RPMVLAGDKA KQVQWTNVYL DALELGLVIT GTLPVFNITG QFENKTNLKN QLILGVMGVD VSLEDIKRLT PRFTL CPNG YYFAIDPNGY VLLHPNLQPK PIGVGIPTIN LRKRRPNVQN PKSQEPVTLD FLDAELENDI KVEIRNKMID GESGEK TFR TLVKSQDERY IDKGNRTYTW TPVNGTDYSL ALVLPTYSFY YIKAKIEETI TQARYSETLK PDNFEESGYT FLAPRDY CS DLKPSDNNTE FLLNFNEFID RKTPNNPSCN TDLINRVLLD AGFTNELVQN YWSKQKNIKG VKARFVVTDG GITRVYPK E AGENWQENPE TYEDSFYKRS LDNDNYVFTA PYFNKSGPGA YESGIMVSKA VEIYIQGKLL KPAVVGIKID VNSWIENFT KTSIRDPCAG PVCDCKRNSD VMDCVILDDG GFLLMANHDD YTNQIGRFFG EIDPSLMRHL VNISVYAFNK SYDYQSVCEP GAAPKQGAG HRSAYVPSIA DILQIGWWAT AAAWSILQQF LLSLTFPRLL EAADMEDDDF TASMSKQSCI TEQTQYFFDN D SKSFSGVL DCGNCSRIFH VEKLMNTNLI FIMVESKGTC PCDTRLLIQA EQTSDGPDPC DMVKQPRYRK GPDVCFDNNV LE DYTDCG

UniProtKB: Voltage-dependent calcium channel subunit alpha-2/delta-1

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 8 / 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 #10: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 10 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #11: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 11 / Number of copies: 8 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

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Macromolecule #12: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 12 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #13: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...

MacromoleculeName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
type: ligand / ID: 13 / Number of copies: 1 / Formula: 9Z9
Molecular weightTheoretical: 544.805 Da
Chemical component information

ChemComp-9Z9:
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergent*YM

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Macromolecule #14: (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](me...

MacromoleculeName: (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl)pentanenitrile
type: ligand / ID: 14 / Number of copies: 2 / Formula: 4YH
Molecular weightTheoretical: 454.602 Da
Chemical component information

ChemComp-4YH:
(2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl)pentanenitrile

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Macromolecule #15: ETHANOLAMINE

MacromoleculeName: ETHANOLAMINE / type: ligand / ID: 15 / Number of copies: 1 / Formula: ETA
Molecular weightTheoretical: 61.083 Da
Chemical component information

ChemComp-ETA:
ETHANOLAMINE / Ethanolamine

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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
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 433477

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  • 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

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