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- EMDB-29722: Cryo-EM structure of the human cardiac myosin filament -

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Basic information

Entry
Database: EMDB / ID: EMD-29722
TitleCryo-EM structure of the human cardiac myosin filament
Map data
Sample
  • Tissue: Myosin filaments isolated from human cardiac left ventricular muscle
    • Protein or peptide: Myosin-7
    • Protein or peptide: Myosin light chain 3
    • Protein or peptide: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
    • Protein or peptide: Titin
    • Protein or peptide: Myosin-binding protein C, cardiac-type
Keywordscardiac / myosin / filament / complex / CONTRACTILE PROTEIN
Function / homology
Function and homology information


myosin II heavy chain binding / C zone / regulation of muscle filament sliding / muscle cell fate specification / regulation of slow-twitch skeletal muscle fiber contraction / striated muscle myosin thick filament / regulation of the force of skeletal muscle contraction / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding ...myosin II heavy chain binding / C zone / regulation of muscle filament sliding / muscle cell fate specification / regulation of slow-twitch skeletal muscle fiber contraction / striated muscle myosin thick filament / regulation of the force of skeletal muscle contraction / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril / muscle myosin complex / regulation of striated muscle contraction / cardiac myofibril assembly / muscle filament sliding / detection of muscle stretch / muscle alpha-actinin binding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / cardiac muscle tissue morphogenesis / regulation of catalytic activity / myosin II complex / adult heart development / cardiac muscle hypertrophy in response to stress / Striated Muscle Contraction / mitotic chromosome condensation / positive regulation of ATP-dependent activity / cardiac muscle hypertrophy / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / myosin complex / A band / structural constituent of muscle / sarcomere organization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myosin binding / myofibril / myosin heavy chain binding / heart contraction / ATPase activator activity / positive regulation of the force of heart contraction / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle contraction / actin monomer binding / striated muscle contraction / heart morphogenesis / stress fiber / ATP metabolic process / protein kinase A signaling / titin binding / cardiac muscle contraction / regulation of heart rate / sarcomere / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / negative regulation of cell growth / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / actin binding / heart development / protein tyrosine kinase activity / protease binding / cytoskeleton / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand domain pair / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / EF-hand, calcium binding motif / Immunoglobulin V-set domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin light chain 3 / Myosin regulatory light chain 2, ventricular/cardiac muscle isoform / Myosin-7 / Myosin-binding protein C, cardiac-type / Titin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsDutta D / Nguyen V / Padron R / Craig R
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR072036 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL139883 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL164560 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR081941 United States
CitationJournal: Nature / Year: 2023
Title: Cryo-EM structure of the human cardiac myosin filament.
Authors: Debabrata Dutta / Vu Nguyen / Kenneth S Campbell / Raúl Padrón / Roger Craig /
Abstract: Pumping of the heart is powered by filaments of the motor protein myosin that pull on actin filaments to generate cardiac contraction. In addition to myosin, the filaments contain cardiac myosin- ...Pumping of the heart is powered by filaments of the motor protein myosin that pull on actin filaments to generate cardiac contraction. In addition to myosin, the filaments contain cardiac myosin-binding protein C (cMyBP-C), which modulates contractility in response to physiological stimuli, and titin, which functions as a scaffold for filament assembly. Myosin, cMyBP-C and titin are all subject to mutation, which can lead to heart failure. Despite the central importance of cardiac myosin filaments to life, their molecular structure has remained a mystery for 60 years. Here we solve the structure of the main (cMyBP-C-containing) region of the human cardiac filament using cryo-electron microscopy. The reconstruction reveals the architecture of titin and cMyBP-C and shows how myosin's motor domains (heads) form three different types of motif (providing functional flexibility), which interact with each other and with titin and cMyBP-C to dictate filament architecture and function. The packing of myosin tails in the filament backbone is also resolved. The structure suggests how cMyBP-C helps to generate the cardiac super-relaxed state; how titin and cMyBP-C may contribute to length-dependent activation; and how mutations in myosin and cMyBP-C might disturb interactions, causing disease. The reconstruction resolves past uncertainties and integrates previous data on cardiac muscle structure and function. It provides a new paradigm for interpreting structural, physiological and clinical observations, and for the design of potential therapeutic drugs.
History
DepositionFeb 10, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29722.png

Downloads & links

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Map

FileDownload / File: emd_29722.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0873 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.015657136 - 2.3601267
Average (Standard dev.)0.004316486 (±0.047680497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 869.83997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_29722_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29722_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29722_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Myosin filaments isolated from human cardiac left ventricular muscle

EntireName: Myosin filaments isolated from human cardiac left ventricular muscle
Components
  • Tissue: Myosin filaments isolated from human cardiac left ventricular muscle
    • Protein or peptide: Myosin-7
    • Protein or peptide: Myosin light chain 3
    • Protein or peptide: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
    • Protein or peptide: Titin
    • Protein or peptide: Myosin-binding protein C, cardiac-type

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Supramolecule #1: Myosin filaments isolated from human cardiac left ventricular muscle

SupramoleculeName: Myosin filaments isolated from human cardiac left ventricular muscle
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Myosin-7

MacromoleculeName: Myosin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 78 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: heart
Molecular weightTheoretical: 223.445984 KDa
SequenceString: MGDSEMAVFG AAAPYLRKSE KERLEAQTRP FDLKKDVFVP DDKQEFVKAK IVSREGGKVT AETEYGKTVT VKEDQVMQQN PPKFDKIED MAMLTFLHEP AVLYNLKDRY GSWMIYTYSG LFCVTVNPYK WLPVYTPEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD ...String:
MGDSEMAVFG AAAPYLRKSE KERLEAQTRP FDLKKDVFVP DDKQEFVKAK IVSREGGKVT AETEYGKTVT VKEDQVMQQN PPKFDKIED MAMLTFLHEP AVLYNLKDRY GSWMIYTYSG LFCVTVNPYK WLPVYTPEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD RENQSILITG ESGAGKTVNT KRVIQYFAVI AAIGDRSKKD QSPGKGTLED QIIQANPALE AFGNAKTVRN DN SSRFGKF IRIHFGATGK LASADIETYL LEKSRVIFQL KAERDYHIFY QILSNKKPEL LDMLLITNNP YDYAFISQGE TTV ASIDDA EELMATDNAF DVLGFTSEEK NSMYKLTGAI MHFGNMKFKL KQREEQAEPD GTEEADKSAY LMGLNSADLL KGLC HPRVK VGNEYVTKGQ NVQQVIYATG ALAKAVYERM FNWMVTRINA TLETKQPRQY FIGVLDIAGF EIFDFNSFEQ LCINF TNEK LQQFFNHHMF VLEQEEYKKE GIEWTFIDFG MDLQACIDLI EKPMGIMSIL EEECMFPKAT DMTFKAKLFD NHLGKS ANF QKPRNIKGKP EAHFSLIHYA GIVDYNIIGW LQKNKDPLNE TVVGLYQKSS LKLLSTLFAN YAGADAPIEK GKGKAKK GS SFQTVSALHR ENLNKLMTNL RSTHPHFVRC IIPNETKSPG VMDNPLVMHQ LRCNGVLEGI RICRKGFPNR ILYGDFRQ R YRILNPAAIP EGQFIDSRKG AEKLLSSLDI DHNQYKFGHT KVFFKAGLLG LLEEMRDERL SRIITRIQAQ SRGVLARME YKKLLERRDS LLVIQWNIRA FMGVKNWPWM KLYFKIKPLL KSAEREKEMA SMKEEFTRLK EALEKSEARR KELEEKMVSL LQEKNDLQL QVQAEQDNLA DAEERCDQLI KNKIQLEAKV KEMNERLEDE EEMNAELTAK KRKLEDECSE LKRDIDDLEL T LAKVEKEK HATENKVKNL TEEMAGLDEI IAKLTKEKKA LQEAHQQALD DLQAEEDKVN TLTKAKVKLE QQVDDLEGSL EQ EKKVRMD LERAKRKLEG DLKLTQESIM DLENDKQQLD ERLKKKDFEL NALNARIEDE QALGSQLQKK LKELQARIEE LEE ELEAER TARAKVEKLR SDLSRELEEI SERLEEAGGA TSVQIEMNKK REAEFQKMRR DLEEATLQHE ATAAALRKKH ADSV AELGE QIDNLQRVKQ KLEKEKSEFK LELDDVTSNM EQIIKAKANL EKMCRTLEDQ MNEHRSKAEE TQRSVNDLTS QRAKL QTEN GELSRQLDEK EALISQLTRG KLTYTQQLED LKRQLEEEVK AKNALAHALQ SARHDCDLLR EQYEEETEAK AELQRV LSK ANSEVAQWRT KYETDAIQRT EELEEAKKKL AQRLQEAEEA VEAVNAKCSS LEKTKHRLQN EIEDLMVDVE RSNAAAA AL DKKQRNFDKI LAEWKQKYEE SQSELESSQK EARSLSTELF KLKNAYEESL EHLETFKREN KNLQEEISDL TEQLGSSG K TIHELEKVRK QLEAEKMELQ SALEEAEASL EHEEGKILRA QLEFNQIKAE IERKLAEKDE EMEQAKRNHL RVVDSLQTS LDAETRSRNE ALRVKKKMEG DLNEMEIQLS HANRMAAEAQ KQVKSLQSLL KDTQIQLDDA VRANDDLKEN IAIVERRNNL LQAELEELR AVVEQTERSR KLAEQELIET SERVQLLHSQ NTSLINQKKK MDADLSQLQT EVEEAVQECR NAEEKAKKAI T DAAMMAEE LKKEQDTSAH LERMKKNMEQ TIKDLQHRLD EAEQIALKGG KKQLQKLEAR VRELENELEA EQKRNAESVK GM RKSERRI KELTYQTEED RKNLLRLQDL VDKLQLKVKA YKRQAEEAEE QANTNLSKFR KVQHELDEAE ERADIAESQV NKL RAKSRD IGTKGLNEE

UniProtKB: Myosin-7

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Macromolecule #2: Myosin light chain 3

MacromoleculeName: Myosin light chain 3 / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: heart
Molecular weightTheoretical: 21.962068 KDa
SequenceString: MAPKKPEPKK DDAKAAPKAA PAPAPPPEPE RPKEVEFDAS KIKIEFTPEQ IEEFKEAFML FDRTPKCEMK ITYGQCGDVL RALGQNPTQ AEVLRVLGKP RQEELNTKMM DFETFLPMLQ HISKNKDTGT YEDFVEGLRV FDKEGNGTVM GAELRHVLAT L GERLTEDE ...String:
MAPKKPEPKK DDAKAAPKAA PAPAPPPEPE RPKEVEFDAS KIKIEFTPEQ IEEFKEAFML FDRTPKCEMK ITYGQCGDVL RALGQNPTQ AEVLRVLGKP RQEELNTKMM DFETFLPMLQ HISKNKDTGT YEDFVEGLRV FDKEGNGTVM GAELRHVLAT L GERLTEDE VEKLMAGQED SNGCINYEAF VKHIMSS

UniProtKB: Myosin light chain 3

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Macromolecule #3: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform

MacromoleculeName: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: heart
Molecular weightTheoretical: 18.813273 KDa
SequenceString:
MAPKKAKKRA GGANSNVFSM FEQTQIQEFK EAFTIMDQNR DGFIDKNDLR DTFAALGRVN VKNEEIDEMI KEAPGPINFT VFLTMFGEK LKGADPEETI LNAFKVFDPE GKGVLKADYV REMLTTQAER FSKEEVDQMF AAFPPDVTGN LDYKNLVHII T HGEEKD

UniProtKB: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform

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Macromolecule #4: Titin

MacromoleculeName: Titin / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human) / Tissue: heart
Molecular weightTheoretical: 119.771961 KDa
SequenceString: PPEIELDADL RKVVTIRACC TLRLFVPIKG RPAPEVKWAR DHGESLDKAS IESTSSYTLL IVGNVNRFDS GKYILTVENS SGSKSAFVN VRVLDTPGPP QDLKVKEVTK TSVTLTWDPP LLDGGSKIKN YIVEKRESTR KAYSTVATNC HKTSWKVDQL Q EGCSYYFR ...String:
PPEIELDADL RKVVTIRACC TLRLFVPIKG RPAPEVKWAR DHGESLDKAS IESTSSYTLL IVGNVNRFDS GKYILTVENS SGSKSAFVN VRVLDTPGPP QDLKVKEVTK TSVTLTWDPP LLDGGSKIKN YIVEKRESTR KAYSTVATNC HKTSWKVDQL Q EGCSYYFR VLAENEYGIG LPAETAESVK ASERPLPPGK ITLMDVTRNS VSLSWEKPEH DGGSRILGYI VEMQTKGSDK WA TCATVKV TEATITGLIQ GEEYSFRVSA QNEKGISDPR QLSVPVIAKD LVIPPAFKLL FNTFTVLAGE DLKVDVPFIG RPT PAVTWH KDNVPLKQTT RVNAESTENN SLLTIKDACR EDVGHYVVKL TNSAGEAIET LNVIVLDKPG PPTGPVKMDE VTAD SITLS WGPPKYDGGS SINNYIVEKR DTSTTTWQIV SATVARTTIK ACRLKTGCEY QFRIAAENRY GKSTYLNSEP TVAQY PFKV PGPPGTPVVT LSSRDSMEVQ WNEPISDGGS RVIGYHLERK ERNSILWVKL NKTPIPQTKF KTTGLEEGVE YEFRVS AEN IVGIGKPSKV SECYVARDPC DPPGRPEAII VTRNSVTLQW KKPTYDGGSK ITGYIVEKKE LPEGRWMKAS FTNIIDT HF EVTGLVEDHR YEFRVIARNA AGVFSEPSES TGAITARDEV DPPRISMDPK YKDTIVVHAG ESFKVDADIY GKPIPTIQ W IKGDQELSNT ARLEIKSTDF ATSLSVKDAV RVDSGNYILK AKNVAGERSV TVNVKVLDRP GPPEGPVVIS GVTAEKCTL AWKPPLQDGG SDIINYIVER RETSRLVWTV VDANVQTLSC KVTKLLEGNE YTFRIMAVNK YGVGEPLESE PVVAKNPFVV PDAPKAPEV TTVTKDSMIV VWERPASDGG SEILGYVLEK RDKEGIRWTR CHKRLIGELR LRVTGLIENH DYEFRVSAEN A AGLSEPSP PSAYQKACDP IYKPGPPNNP KVIDITRSSV FLSWSKPIYD GGCEIQGYIV EKCDVSVGEW TMCTPPTGIN KT NIEVEKL LEKHEYNFRI CAINKAGVGE HADVPGPIIV EEKLEAP

UniProtKB: Titin

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Macromolecule #5: Myosin-binding protein C, cardiac-type

MacromoleculeName: Myosin-binding protein C, cardiac-type / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: heart
Molecular weightTheoretical: 140.947172 KDa
SequenceString: MPEPGKKPVS AFSKKPRSVE VAAGSPAVFE AETERAGVKV RWQRGGSDIS ASNKYGLATE GTRHTLTVRE VGPADQGSYA VIAGSSKVK FDLKVIEAEK AEPMLAPAPA PAEATGAPGE APAPAAELGE SAPSPKGSSS AALNGPTPGA PDDPIGLFVM R PQDGEVTV ...String:
MPEPGKKPVS AFSKKPRSVE VAAGSPAVFE AETERAGVKV RWQRGGSDIS ASNKYGLATE GTRHTLTVRE VGPADQGSYA VIAGSSKVK FDLKVIEAEK AEPMLAPAPA PAEATGAPGE APAPAAELGE SAPSPKGSSS AALNGPTPGA PDDPIGLFVM R PQDGEVTV GGSITFSARV AGASLLKPPV VKWFKGKWVD LSSKVGQHLQ LHDSYDRASK VYLFELHITD AQPAFTGSYR CE VSTKDKF DCSNFNLTVH EAMGTGDLDL LSAFRRTSLA GGGRRISDSH EDTGILDFSS LLKKRDSFRT PRDSKLEAPA EED VWEILR QAPPSEYERI AFQYGVTDLR GMLKRLKGMR RDEKKSTAFQ KKLEPAYQVS KGHKIRLTVE LADHDAEVKW LKNG QEIQM SGSKYIFESI GAKRTLTISQ CSLADDAAYQ CVVGGEKCST ELFVKEPPVL ITRPLEDQLV MVGQRVEFEC EVSEE GAQV KWLKDGVELT REETFKYRFK KDGQRHHLII NEAMLEDAGH YALCTSGGQA LAELIVQEKK LEVYQSIADL MVGAKD QAV FKCEVSDENV RGVWLKNGKE LVPDSRIKVS HIGRVHKLTI DDVTPADEAD YSFVPEGFAC NLSAKLHFME VKIDFVP RQ EPPKIHLDCP GRIPDTIVVV AGNKLRLDVP ISGDPAPTVI WQKAITQGNK APARPAPDAP EDTGDSDEWV FDKKLLCE T EGRVRVETTK DRSIFTVEGA EKEDEGVYTV TVKNPVGEDQ VNLTVKVIDV PDAPAAPKIS NVGEDSCTVQ WEPPAYDGG QPILGYILER KKKKSYRWMR LNFDLIQELS HEARRMIEGV VYEMRVYAVN AIGMSRPSPA SQPFMPIGPP SEPTHLAVED VSDTTVSLK WRPPERVGAG GLDGYSVEYC PEGCSEWVAA LQGLTEHTSI LVKDLPTGAR LLFRVRAHNM AGPGAPVTTT E PVTVQEIL QRPRLQLPRH LRQTIQKKVG EPVNLLIPFQ GKPRPQVTWT KEGQPLAGEE VSIRNSPTDT ILFIRAARRV HS GTYQVTV RIENMEDKAT LVLQVVDKPS PPQDLRVTDA WGLNVALEWK PPQDVGNTEL WGYTVQKADK KTMEWFTVLE HYR RTHCVV PELIIGNGYY FRVFSQNMVG FSDRAATTKE PVFIPRPGIT YEPPNYKALD FSEAPSFTQP LVNRSVIAGY TAML CCAVR GSPKPKISWF KNGLDLGEDA RFRMFSKQGV LTLEIRKPCP FDGGIYVCRA TNLQGEARCE CRLEVRVPQ

UniProtKB: Myosin-binding protein C, cardiac-type

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102581
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8g4l:
Cryo-EM structure of the human cardiac myosin filament

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Atomic model buiding 2

Initial model
PDB IDChain

5n69

source_name: PDB, initial_model_type: experimental model

2fxo

source_name: PDB, initial_model_type: experimental model

l_v1

source_name: AlphaFold, initial_model_type: in silico model

l_v3

source_name: AlphaFold, initial_model_type: in silico model

wz42

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-8g4l:
Cryo-EM structure of the human cardiac myosin filament

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Atomic model buiding 3

Initial model
PDB IDChain

5n69

source_name: PDB, initial_model_type: experimental model

2fxo

source_name: PDB, initial_model_type: experimental model

l_v1

source_name: AlphaFold, initial_model_type: in silico model

l_v3

source_name: AlphaFold, initial_model_type: in silico model

wz42

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-8g4l:
Cryo-EM structure of the human cardiac myosin filament

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Atomic model buiding 4

Initial model
PDB IDChain

5n69

source_name: PDB, initial_model_type: experimental model

2fxo

source_name: PDB, initial_model_type: experimental model

l_v1

source_name: AlphaFold, initial_model_type: in silico model

l_v3

source_name: AlphaFold, initial_model_type: in silico model

wz42

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-8g4l:
Cryo-EM structure of the human cardiac myosin filament

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Atomic model buiding 5

Initial model
PDB IDChain

5n69

source_name: PDB, initial_model_type: experimental model

2fxo

source_name: PDB, initial_model_type: experimental model

l_v1

source_name: AlphaFold, initial_model_type: in silico model

l_v3

source_name: AlphaFold, initial_model_type: in silico model

wz42

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-8g4l:
Cryo-EM structure of the human cardiac myosin filament

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Atomic model buiding 6

Initial model
PDB IDChain

5n69

source_name: PDB, initial_model_type: experimental model

2fxo

source_name: PDB, initial_model_type: experimental model

l_v1

source_name: AlphaFold, initial_model_type: in silico model

l_v3

source_name: AlphaFold, initial_model_type: in silico model

wz42

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-8g4l:
Cryo-EM structure of the human cardiac myosin filament

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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

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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

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