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- EMDB-9834: Structure of RyR2 (F/A/C/L-Ca2+/apo-CaM-M dataset) -

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Basic information

Entry
Database: EMDB / ID: EMD-9834
TitleStructure of RyR2 (F/A/C/L-Ca2+/apo-CaM-M dataset)
Map data
Sample
  • Complex: RyR2 in complex with FKBP12.6 and apo-Calmodulin-mimicking mutant
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryr2
    • Protein or peptide: Calmodulin-1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: CAFFEINE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordscryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / response to redox state / Reduction of cytosolic Ca++ levels / protein maturation by protein folding / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / 'de novo' protein folding / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of heart rate / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / FK506 binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of axon regeneration / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / channel regulator activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / smooth muscle contraction / Smooth Muscle Contraction / response to vitamin E / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / eNOS activation / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / release of sequestered calcium ion into cytosol / sperm midpiece / regulation of cytosolic calcium ion concentration / calcium channel complex / sarcoplasmic reticulum membrane / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated vascular permeability / regulation of cytokinesis / VEGFR2 mediated cell proliferation / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of receptor signaling pathway via JAK-STAT / calcium-mediated signaling / RAF activation
Similarity search - Function
: / : / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...: / : / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGong DS / Chi XM
CitationJournal: Nature / Year: 2019
Title: Modulation of cardiac ryanodine receptor 2 by calmodulin.
Authors: Deshun Gong / Ximin Chi / Jinhong Wei / Gewei Zhou / Gaoxingyu Huang / Lin Zhang / Ruiwu Wang / Jianlin Lei / S R Wayne Chen / Nieng Yan /
Abstract: The high-conductance intracellular calcium (Ca) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 ...The high-conductance intracellular calcium (Ca) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 in a Ca-dependent manner. Here we reveal the regulatory mechanism by which porcine RyR2 is modulated by human CaM through the structural determination of RyR2 under eight conditions. Apo-CaM and Ca-CaM bind to distinct but overlapping sites in an elongated cleft formed by the handle, helical and central domains. The shift in CaM-binding sites on RyR2 is controlled by Ca binding to CaM, rather than to RyR2. Ca-CaM induces rotations and intradomain shifts of individual central domains, resulting in pore closure of the PCB95 and Ca-activated channel. By contrast, the pore of the ATP, caffeine and Ca-activated channel remains open in the presence of Ca-CaM, which suggests that Ca-CaM is one of the many competing modulators of RyR2 gating.
History
DepositionFeb 21, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jii
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9834.png

Downloads & links

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Map

FileDownload / File: emd_9834.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 436.4 Å		1.09 Å/pix.
x 400 pix.
= 436.4 Å		1.09 Å/pix.
x 400 pix.
= 436.4 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: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.03578981 - 0.09619624
Average (Standard dev.)0.0007834526 (±0.0050138473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 436.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z436.400436.400436.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0360.0960.001

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Supplemental data

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Sample components

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Entire : RyR2 in complex with FKBP12.6 and apo-Calmodulin-mimicking mutant

EntireName: RyR2 in complex with FKBP12.6 and apo-Calmodulin-mimicking mutant
Components
  • Complex: RyR2 in complex with FKBP12.6 and apo-Calmodulin-mimicking mutant
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryr2
    • Protein or peptide: Calmodulin-1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: CAFFEINE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: RyR2 in complex with FKBP12.6 and apo-Calmodulin-mimicking mutant

SupramoleculeName: RyR2 in complex with FKBP12.6 and apo-Calmodulin-mimicking mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP1B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.798501 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGVEIETISP GDGRTFPKKG QTCVVHYTGM LQNGKKFDSS RDRNKPFKFR IGKQEVIKGF EEGAAQMSLG QRAKLTCTPD VAYGATGHP GVIPPNATLI FDVELLNLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

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Macromolecule #2: Ryr2

MacromoleculeName: Ryr2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 564.905625 KDa
SequenceString: MADGGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVLE QSLSVRALQE MLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI LLRHSYSGMY LCCLSTSRSS TDKLAFDVGL QEDTTGEACW W TIHPASKQ ...String:
MADGGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVLE QSLSVRALQE MLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI LLRHSYSGMY LCCLSTSRSS TDKLAFDVGL QEDTTGEACW W TIHPASKQ RSEGEKVRVG DDLILVSVSS ERYLHLSYGN VSLHVDAAFQ QTLWSVAPIS SGSEAAQGYL IGGDVLRLLH GH MDECLTV PSGEHGEEQR RTVHYEGGAV SVHARSLWRL ETLRVAWSGS HIRWGQPFRL RHVTTGKYLS LMEDKSLLLM DKE KADVKS TAFTFRSSKE KLDVGVRKEV DGMGTSEIKY GDSVCFIQHI GTGLWLTYQS VDVKSVRMGS IQRKAIMHHE GHMD DGLNL SRSQHEESRT ARVIRSTVFL FNRFIRGLDA LSKKAKASTV DLPIESVSLS LQDLIGYFHP PDEHLEHEDK QNRLR ALKN RQNLFQEEGM INLVLECIDR LHVYSSAAHF ADVAGREAGE SWKSILNSLY ELLAALIRGN RKNCAQFSGS LDWLIS RLE RLEASSGILE VLHCVLVESP EALNIIKEGH IKSIISLLDK HGRNHKVLDV LCSLCVCHGV AVRSNQHLIC DNLLPGR DL LLQTRLVNHV SSMRPNIFLG VSEGSAQYKK WYYELMVDHT EPFVTAEATH LRVGWASTEG YSPYPGGGEE WGGNGVGD D LFSYGFDGLH LWSGCIARTV SSPNQHLLRT DDVISCCLDL SAPSISFRIN GQPVQGMFEN FNIDGLFFPV VSFSAGIKV RFLLGGRHGE FKFLPPPGYA PCYEAVLPKE KLKVEHSREY KQERTYTRDL LGPTVSLTQA AFTPIPVDTS QIVLPPHLER IREKLAENI HELWVMNKIE LGWQYGPVRD DNKRQHPCLV EFSKLPEQER NYNLQMSLET LKTLLALGCH VGISDEHAEE K VKKMKLPK NYQLTSGYKP APMDLSFIKL TPSQEAMVDK LAENAHNVWA RDRIRQGWTY GIQQDVKNRR NPRLVPYALL DD RTKKSNK DSLREAVRTL LGYGYNLEAP DQDHAARAEV CSGTGERFRI FRAEKTYAVK AGRWYFEFEA VTAGDMRVGW SRP GCQPDQ ELGSDERAFA FDGFKAQRWH QGNEHYGRSW QAGDVVGCMV DMTEHTMMFT LNGEILLDDS GSELAFKDFD VGDG FIPVC SLGVAQVGRM NFGKDVSTLK YFTICGLQEG YEPFAVNTNR DITMWLSKRL PQFLQVPSSH EHIEVTRIDG TIDSS PCLK VTQKSFGSQN SSTDIMFYRL SMPIECAEVF SKTSAGGIPG ASLFGPKNDL EDYDADSDFE VLMKTAHGHL VPDRVD KDK EATKPEFNNH KDYAQEKPSR LKQRFLLRRT KPDYSTSHSA RLTEDVLADD RDDYDYLMQT STYYYSVRIF PGQEPAN VW VGWITSDFHQ YDTAFDLDRV RTVTVTLGDE KGKVHESIKR SNCYMVCAGE SMSPGQGRNN NGLEIGCVVD AASGLLTF T ANGKDLSTYY QVEPSTKLFP AVFAQATSPN VFQFELGRIK NVMPLSAGLF KSEHKNPVPQ CPPRLHVQFL SHVLWSRMP NQFLKVDVSR ISERQGWLVQ CLEPLQFMSL HIPEENRSVD ILELTEQEEL LKFHYHTLRL YSAVCALGNH RVAHALCSHV DEPQLLYAI ENKYMPGLLR AGYYDLLIDI HLSSYATARL MMNNEFIVPM TEETKSITLF PDENKKHGLP GIGLSTSLRP R MQFSSPSF VSINNECYQY SPEFPLDILK AKTIQMLTEA VQEGSLHARD PVGGTTEFLF VPLIKLFYTL LIMGIFHNED LK HILQLIE PSVFKEAAGP EEESDTLEKE PCASEDSRLE GPAEEESKGG KRPKEGLLQM KLPEPVKLQM CLLLQYLCDC QVR HRIEAI VAFSDDFVAK LQDNQRFRYN EVMQALNMSA ALTARKTKEF RSPPQEQINM LLNFKDDKSE CPCPEEIRDQ LLDF HEDLM THCGIELDED GSLDGNSDLT IRGRLLSLVE KVTYLKKKQA EKLVESDSKK SSTLQQLISE TMVRWAQESV IEDPE LVRA MFVLLHRQYD GIGGLVRALP KTYTINGVSV EDTINLLASL GQIRSLLSVR MGKEEEKLMI RGLGDIMNNK VFYQHP NLM RALGMHETVM EVMVNVLGGG ESKEITFPKM VANCCRFLCY FCRISRQNQK AMFDHLSYLL ENSSVGLASP AMRGSTP LD VAAASVMDNN ELALALREPD LEKVVRYLAG CGLQSCQMLV SKGYPDIGWN PVEGERYLDF LRFAVFCNGE SVEENANV V VRLLIRRPEC FGPALRGEGG NGLLAAMEEA IKIAEDPSRD GPSPTSGSSK MPDTEGEEDD TIHMGNAIMT FYAALIDLL GRCAPEMHLI HAAKGEAIRI RSILRSLIPL GDLVGVISIA FQMPTIAKDG NVVEPDMSAG FCPDHKAAMV LFLDRVYGIE VQDFLLHLL EVGFLPDLRA AASLDTAALS ATDMALALNR YLCTAVLPLL TRCAPLFAGT EHHASLIDSL LHTVYRLSKG C SLTKAQRD SIEVCLLSIC GQLRPSMMQH LLRRLVFDVP LLNEHAKMPL KLLTNHYERC WKYYCLPGGW GNFGAASEEE LH LSRKLFW GIFDALSQKK YEQELFKLAL PCLSAVAGAL PPDYMESNYV SMMEKQSSMD SEGNFNPQPV DTSNITIPEK LEY FINKYA EHSHDKWSMD KLANGWIYGE IYSDSSKVQP LMKPYKLLSE KEKEIYRWPI KESLKTMLAW GWRIERTREG DSMA LYNRT RRISQTSQVS VDAAHGYSPR AIDMSNVTLS RDLHAMAEMM AENYHNIWAK KKKLELESKG GGNHPLLVPY DTLTA KEKA KDREKAQDIL KFLQINGYAV SRGFKDLELD TPSIEKRFAY SFLQQLIRYV DEAHQYILEF DGGSRSKGEH FPYEQE IKF FAKVVLPLID QYFKNHRLYF LSAASRPLCS GGHASNKEKE MVTSLFCKLG VLVRHRISLF GNDATSIVNC LHILGQT LD ARTVMKTGLE SVKSALRAFL DNAAEDLEKT MENLKQGQFT HTRNQPKGVT QIINYTTVAL LPMLSSLFEH IGQHQFGE D LILEDVQVSC YRILTSLYAL GTSKSIYVER QRSALGECLA AFAGAFPVAF LETHLDKHNI YSIYNTKSSR ERAALNLPT NVEDVCPNIP SLEKLMEEIV DLAESGIRYT QMPHVMEVVL PMLCSYMSRW WEHGPENNPG RAEMCCTALN SEHMNTLLGN ILKIIYNNL GIDEGAWMKR LAVFSQPIIN KVKPQLLKTH FLPLMEKLKK KAAMVVSEED HLKSEVRGDM SEAELLILDE F TTLARDLY AFYPLLIRFV DYNRAKWLKE PNPEAEDLFR MVAEVFIYWS KSHNFKREEQ NFVVQNEINN MSFLITDTKS KM SKAAVSD QERKKMKRKG DRYSMQTSLI VAALKRLLPI GLNICAPGDQ ELIALAKNRF SLKDTEDEVR DIIRSNIHLQ GKL EDPAIR WQMALYKDLP NRTEDTSDPE KTVERVLDIA NVLFHLEQKS TCMRRRYYSL VEHPQRSKKA VWHKLLSKQR KRAV VACFR MAPLYNLPRH RAVNLFLQGY EKSWIETEEH YFEDKLIEDL AKPGAVPPEE DEGTKRVDPL HQLILLFSRT ALTEK CKLE EDFLYMAYAD IMAKSCHDEE DDDGEEEVKS FEEKEMEKQK LLYQQARLHD RGAAEMVLQT ISASKGETGP MVAATL KLG IAILNGGNST VQQKMLEYLK EKKDVGFFQS LAGLMQSCSV LDLNAFERQN KAEGLGMVTE EGSGEKVLQD DEFTCDL FR FLQLLCEGHN SDFQNYLRTQ TGNNTTVNII ISTVDYLLRV QESISDFYWY YSGKDVIDEQ GQRNFSKAIQ VAKQVFNT L TEYIQGPCTG NQQSLAHSRL WDAVVGFLHV FAHMQMKLSQ DSSQIELLKE LMDLQKDMVV MLLSMLEGNV VNGTIGKQM VDMLVESSNN VEMILKFFDM FLKLKDLTSS DTFKEYDPDG KGVISKRDFH KAMESHKHYT QSETEFLLSC AETDENETLD YEEFVKRFH EPAKDIGFNV AVLLTNLSEH MPNDTRLQTF LELAESVLNY FQPFLGRIEI MGSAKRIERV YFEISESSRT Q WEKPQVKE SKRQFIFDVV NEGGEKEKME LFVNFCEDTI FEMQLAAQIS ESDLNERSAN KEESEKEKPE EQGPRMGFFS LV TVRSALL ALRYNVLTLM RMLSLKSLKK QMKKVKKMTV RDMVTAFFTS YWSVFMTLLH FAASVSRGFS RIIGGLLLGG SLV EGAKKI KVAELLANMP DPTQDEVRGD GDEGERKVLE GTLPSEDLTD LKELTEESDL LSDIFGLDLK REGGQYKLIP HNPN AGLSD LMSSPAPIPE VQEKFQEQKA KEEEKEEKEE NKSEPEKAEG EDGEKEEKAK EDKGKQKLRQ LHTHRYGEPE VPESA FWKK IIAYQQKLLN YFARNFYNMR MLALFVAFAI NFILLFYKVS TSSVVEGKEL PTRSSSENAN FGSLDSSSPR IIAVHY VLE ESSGYMEPTL RILAILHTVI SFFCIIGYYC LKVPLVIFKR EKEVARKLEF DGLYITEQPS EDDIKGQWDR LVINTQS FP NNYWDKFVKR KVMDKYGEFY GRDRISELLG MDKAALDFSD AREKKKPKKD SSLSAVLNSI DVKYQMWKLG VVFTDNSF L YLAWYMTMSV LGHYNNFFFA AHLLDIAMGF KTLRTILSSV THNGKQLVLT VGLLAVVVYL YTVVAFNFFR KFYNKSEDG DTPDMKCDDM LTCYMFHMYV GVRAGGGIGD EIEDPAGDEY EIYRIIFDIT FFFFVIVILL AIIQGLIIDA FGELRDQQEQ VKEDMETKC FICGIGNDYF DTVPHGFETH TLQEHNLANY LFFLMYLINK DETEHTGQES YVWKMYQERC WEFFPAGDCF R KQYEDQLN

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Macromolecule #3: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.620402 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KALGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPAFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAALRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EAFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: CAFFEINE

MacromoleculeName: CAFFEINE / type: ligand / ID: 6 / Number of copies: 4 / Formula: CFF
Molecular weightTheoretical: 194.191 Da
Chemical component information

ChemComp-CFF:
CAFFEINE / medication*YM

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 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

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 69556
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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