[English] 日本語
Yorodumi
- EMDB-29722: Cryo-EM structure of the human cardiac myosin filament -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of the force of skeletal muscle contraction / striated muscle myosin thick filament / 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 / regulation of the force of skeletal muscle contraction / striated muscle myosin thick filament / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril / regulation of striated muscle contraction / cardiac myofibril assembly / muscle myosin complex / muscle filament sliding / muscle alpha-actinin binding / detection of muscle stretch / transition between fast and slow fiber / regulation of the force of heart contraction / cardiac muscle tissue morphogenesis / myosin filament / adult heart development / protein kinase regulator activity / positive regulation of ATP-dependent activity / cardiac muscle hypertrophy / mitotic chromosome condensation / cardiac muscle hypertrophy in response to stress / actinin binding / Striated Muscle Contraction / myosin II complex / M band / I band / myosin complex / cardiac muscle cell development / A band / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / microfilament motor activity / myosin binding / myofibril / heart contraction / myosin heavy chain binding / positive regulation of the force of heart contraction / skeletal muscle thin filament assembly / striated muscle thin filament / ATPase activator activity / skeletal muscle contraction / actin monomer binding / heart morphogenesis / cardiac muscle contraction / stress fiber / striated muscle contraction / ATP metabolic process / titin binding / muscle contraction / protein kinase A signaling / regulation of heart rate / sarcomere / condensed nuclear chromosome / positive regulation of protein secretion / negative regulation of cell growth / Z disc / response to calcium ion / actin filament binding / Platelet degranulation / heart development / actin binding / protease binding / protein tyrosine kinase activity / cytoskeleton / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / 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 ...: / 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. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Immunoglobulin I-set / Kinesin motor domain superfamily / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / EF-hand domain pair / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29722.png

Downloads & links

-
Map

FileDownload / File: emd_29722.map.gz / Format: CCP4 / Size: 1.9 GB / 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 800 pix.
= 869.84 Å		1.09 Å/pix.
x 800 pix.
= 869.84 Å		1.09 Å/pix.
x 800 pix.
= 869.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0873 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Additional map: #1

Fileemd_29722_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29722_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_29722_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

-
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

-
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

-
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

-
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

-
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

+
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