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Yorodumi- EMDB-35577: Cryo-EM structure of mouse Piezo1-MDFIC complex (composite map) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35577 | |||||||||
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Title | Cryo-EM structure of mouse Piezo1-MDFIC complex (composite map) | |||||||||
Map data | Cryo-EM structure of mouse Piezo1-MDFIC complex (composite map) | |||||||||
Sample |
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Keywords | Piezo1 complex / mechanosensation / mechanotransduction / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information mechanosensitive monoatomic cation channel activity / positive regulation of viral transcription / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / Tat protein binding / regulation of Wnt signaling pathway / negative regulation of protein import into nucleus / positive regulation of myotube differentiation ...mechanosensitive monoatomic cation channel activity / positive regulation of viral transcription / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / Tat protein binding / regulation of Wnt signaling pathway / negative regulation of protein import into nucleus / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / regulation of JNK cascade / monoatomic cation channel activity / regulation of membrane potential / endoplasmic reticulum-Golgi intermediate compartment membrane / cyclin binding / cellular response to mechanical stimulus / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / nucleolus / positive regulation of DNA-templated transcription / endoplasmic reticulum / extracellular region / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
Authors | Zhou Z / Ma X / Lin Y / Cheng D / Bavi N / Li JV / Sutton D / Yao M / Harvey N / Corry B ...Zhou Z / Ma X / Lin Y / Cheng D / Bavi N / Li JV / Sutton D / Yao M / Harvey N / Corry B / Zhang Y / Cox CD | |||||||||
Funding support | Australia, China, 2 items
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Citation | Journal: Science / Year: 2023 Title: MyoD-family inhibitor proteins act as auxiliary subunits of Piezo channels. Authors: Zijing Zhou / Xiaonuo Ma / Yiechang Lin / Delfine Cheng / Navid Bavi / Genevieve A Secker / Jinyuan Vero Li / Vaibhao Janbandhu / Drew L Sutton / Hamish S Scott / Mingxi Yao / Richard P ...Authors: Zijing Zhou / Xiaonuo Ma / Yiechang Lin / Delfine Cheng / Navid Bavi / Genevieve A Secker / Jinyuan Vero Li / Vaibhao Janbandhu / Drew L Sutton / Hamish S Scott / Mingxi Yao / Richard P Harvey / Natasha L Harvey / Ben Corry / Yixiao Zhang / Charles D Cox / Abstract: Piezo channels are critical cellular sensors of mechanical forces. Despite their large size, ubiquitous expression, and irreplaceable roles in an ever-growing list of physiological processes, few ...Piezo channels are critical cellular sensors of mechanical forces. Despite their large size, ubiquitous expression, and irreplaceable roles in an ever-growing list of physiological processes, few Piezo channel-binding proteins have emerged. In this work, we found that MyoD (myoblast determination)-family inhibitor proteins (MDFIC and MDFI) are PIEZO1/2 interacting partners. These transcriptional regulators bind to PIEZO1/2 channels, regulating channel inactivation. Using single-particle cryogenic electron microscopy, we mapped the interaction site in MDFIC to a lipidated, C-terminal helix that inserts laterally into the PIEZO1 pore module. These Piezo-interacting proteins fit all the criteria for auxiliary subunits, contribute to explaining the vastly different gating kinetics of endogenous Piezo channels observed in many cell types, and elucidate mechanisms potentially involved in human lymphatic vascular disease. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35577.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-35577-v30.xml emd-35577.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
Images | emd_35577.png | 138.9 KB | ||
Others | emd_35577_additional_1.map.gz emd_35577_additional_2.map.gz emd_35577_additional_3.map.gz | 10.9 MB 229.9 MB 230.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35577 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35577 | HTTPS FTP |
-Related structure data
Related structure data | 8imzMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35577.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of mouse Piezo1-MDFIC complex (composite map) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Local refinement of the transmembrane domain
File | emd_35577_additional_1.map | ||||||||||||
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Annotation | Local refinement of the transmembrane domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local refinement of the cap domain
File | emd_35577_additional_2.map | ||||||||||||
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Annotation | Local refinement of the cap domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The consensus map without local masked refinement
File | emd_35577_additional_3.map | ||||||||||||
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Annotation | The consensus map without local masked refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Piezo1 in complex with MDFIC
Entire | Name: Piezo1 in complex with MDFIC |
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Components |
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-Supramolecule #1: Piezo1 in complex with MDFIC
Supramolecule | Name: Piezo1 in complex with MDFIC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Piezo-type mechanosensitive ion channel component 1
Macromolecule | Name: Piezo-type mechanosensitive ion channel component 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 292.320656 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEPHVLGAGL YWLLLPCTLL AASLLRFNAL SLVYLLFLLL LPWLPGPSRH SIPGHTGRLL RALLCLSLLF LVAHLAFQIC LHTVPHLDQ FLGQNGSLWV KVSQHIGVTR LDLKDIFNTT RLVAPDLGVL LASSLCLGLC GRLTRKAGQS RRTQELQDDD D DDDDDDED ...String: MEPHVLGAGL YWLLLPCTLL AASLLRFNAL SLVYLLFLLL LPWLPGPSRH SIPGHTGRLL RALLCLSLLF LVAHLAFQIC LHTVPHLDQ FLGQNGSLWV KVSQHIGVTR LDLKDIFNTT RLVAPDLGVL LASSLCLGLC GRLTRKAGQS RRTQELQDDD D DDDDDDED IDAAPAVGLK GAPALATKRR LWLASRFRVT AHWLLMTSGR TLVIVLLALA GIAHPSAFSS IYLVVFLAIC TW WSCHFPL SPLGFNTLCV MVSCFGAGHL ICLYCYQTPF IQDMLPPGNI WARLFGLKNF VDLPNYSSPN ALVLNTKHAW PIY VSPGIL LLLYYTATSL LKLHKSCPSE LRKETPREDE EHELELDHLE PEPQARDATQ GEMPMTTEPD LDNCTVHVLT SQSP VRQRP VRPRLAELKE MSPLHGLGHL IMDQSYVCAL IAMMVWSIMY HSWLTFVLLL WACLIWTVRS RHQLAMLCSP CILLY GLTL CCLRYVWAME LPELPTTLGP VSLHQLGLEH TRYPCLDLGA MLLYLLTFWL LLRQFVKEKL LKKQKVPAAL LEVTVA DTE PTQTQTLLRS LGELVTGIYV KYWIYVCAGM FIVVSFAGRL VVYKIVYMFL FLLCLTLFQV YYTLWRKLLR VFWWLVV AY TMLVLIAVYT FQFQDFPTYW RNLTGFTDEQ LGDLGLEQFS VSELFSSILI PGFFLLACIL QLHYFHRPFM QLTDLEHV P PPGTRHPRWA HRQDAVSEAP LLEHQEEEEV FREDGQSMDG PHQATQVPEG TASKWGLVAD RLLDLAASFS AVLTRIQVF VRRLLELHVF KLVALYTVWV ALKEVSVMNL LLVVLWAFAL PYPRFRPMAS CLSTVWTCII IVCKMLYQLK IVNPHEYSSN CTEPFPNNT NLQPLEINQS LLYRGPVDPA NWFGVRKGYP NLGYIQNHLQ ILLLLVFEAV VYRRQEHYRR QHQQAPLPAQ A VCADGTRQ RLDQDLLSCL KYFINFFFYK FGLEICFLMA VNVIGQRMNF MVILHGCWLV AILTRRRREA IARLWPNYCL FL TLFLLYQ YLLCLGMPPA LCIDYPWRWS KAIPMNSALI KWLYLPDFFR APNSTNLISD FLLLLCASQQ WQVFSAERTE EWQ RMAGIN TDHLEPLRGE PNPIPNFIHC RSYLDMLKVA VFRYLFWLVL VVVFVAGATR ISIFGLGYLL ACFYLLLFGT TLLQ KDTRA QLVLWDCLIL YNVTVIISKN MLSLLSCVFV EQMQSNFCWV IQLFSLVCTV KGYYDPKEMM TRDRDCLLPV EEAGI IWDS ICFFFLLLQR RIFLSHYFLH VSADLKATAL QASRGFALYN AANLKSINFH RQIEEKSLAQ LKRQMKRIRA KQEKYR QSQ ASRGQLQSKD PQDPSQEPGP DSPGGSSPPR RQWWRPWLDH ATVIHSGDYF LFESDSEEEE EALPEDPRPA AQSAFQM AY QAWVTNAQTV LRQRRERARQ ERAEQLASGG DLNPDVEPVD VPEDEMAGRS HMMQRVLSTM QFLWVLGQAT VDGLTRWL R AFTKHHRTMS DVLCAERYLL TQELLRVGEV RRGVLDQLYV GEDEATLSGP VETRDGPSTA SSGLGAEEPL SSMTDDTSS PLSTGYNTRS GSEEIVTDAG DLQAGTSLHG SQELLANART RMRTASELLL DRRLHIPELE EAERFEAQQG RTLRLLRAGY QCVAAHSEL LCYFIIILNH MVTASAASLV LPVLVFLWAM LTIPRPSKRF WMTAIVFTEV MVVTKYLFQF GFFPWNSYVV L RRYENKPY FPPRILGLEK TDSYIKYDLV QLMALFFHRS QLLCYGLWDH EEDRYPKDHC RSSVKDREAK EEPEAKLESQ SE TGTGHPK EPVLAGTPRD HIQGKGSIRS KDVIQDPPED LKPRHTRHIS IRFRRRKETP GPKGTAVMET EHEEGEGKET TER KRPRHT QEKSKFRERM KAAGRRLQSF CVSLAQSFYQ PLQRFFHDIL HTKYRAATDV YALMFLADIV DIIIIIFGFW AFGK HSAAT DIASSLSDDQ VPQAFLFMLL VQFGTMVIDR ALYLRKTVLG KLAFQVVLVV AIHIWMFFIL PAVTERMFSQ NAVAQ LWYF VKCIYFALSA YQIRCGYPTR ILGNFLTKKY NHLNLFLFQG FRLVPFLVEL RAVMDWVWTD TTLSLSNWMC VEDIYA NIF IIKCSRETEK KYPQPKGQKK KKIVKYGMGG LIILFLIAII WFPLLFMSLI RSVVGVVNQP IDVTVTLKLG GYEPLFT MS AQQPSIVPFT PQAYEELSQQ FDPYPLAMQF ISQYSPEDIV TAQIEGSSGA LWRISPPSRA QMKQELYNGT ADITLRFT W NFQRDLAKGG TVEYTNEKHT LELAPNSTAR RQLAQLLEGR PDQSVVIPHL FPKYIRAPNG PEANPVKQLQ PDEEEDYLG VRIQLRREQV GTGASGEQAG TKASDFLEWW VIELQDCKAD CNLLPMVIFS DKVSPPSLGF LAGYGIVGLY VSIVLVVGKF VRGFFSEIS HSIMFEELPC VDRILKLCQD IFLVRETREL ELEEELYAKL IFLYRSPETM IKWTRERE UniProtKB: Piezo-type mechanosensitive ion channel component 1 |
-Macromolecule #2: MyoD family inhibitor domain-containing protein
Macromolecule | Name: MyoD family inhibitor domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 26.122732 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSCAGEALAP GPAEQQCPVE AGGGRLGSPA HEACNEDNTE KDKRPATSGH TRCGLMRDQS IWPNPSAGEL VRTQPERLPQ LQTSAQEPG KEETGKIKNG GHTRMSNGNG IPHGAKHVSV ENHKISAPVS QKMHRKIQSS LSVNNDISKK SKVNAVFSPK A ASSPEDCC ...String: MSCAGEALAP GPAEQQCPVE AGGGRLGSPA HEACNEDNTE KDKRPATSGH TRCGLMRDQS IWPNPSAGEL VRTQPERLPQ LQTSAQEPG KEETGKIKNG GHTRMSNGNG IPHGAKHVSV ENHKISAPVS QKMHRKIQSS LSVNNDISKK SKVNAVFSPK A ASSPEDCC VHCILACLFC EFLTLCNIVL GQASCGICTS EACCCCCGDE MGDDCSCPCD MDCGIMDACC ESSDCLEICM EC CGICFPS UniProtKB: MyoD family inhibitor domain-containing protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102644 |