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- EMDB-65006: The cryo-EM structure of human Piezo2-MDFIC complex (composite map) -

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Basic information

Entry
Database: EMDB / ID: EMD-65006
TitleThe cryo-EM structure of human Piezo2-MDFIC complex (composite map)
Map dataThe composite map of hPiezo2-hMDFIC complex
Sample
  • Complex: The cryo-EM structure of human Piezo2-MDFIC complex (composite map)
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 2,Green fluorescent protein
    • Protein or peptide: MyoD family inhibitor domain-containing protein
KeywordsPiezo2 / mechanosensitive channel / MDFIC / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic cation channel activity / positive regulation of viral transcription / cuticular plate / detection of mechanical stimulus involved in sensory perception / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / Tat protein binding / stereocilium / regulation of Wnt signaling pathway / regulation of JNK cascade ...mechanosensitive monoatomic cation channel activity / positive regulation of viral transcription / cuticular plate / detection of mechanical stimulus involved in sensory perception / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / Tat protein binding / stereocilium / regulation of Wnt signaling pathway / regulation of JNK cascade / negative regulation of protein import into nucleus / neuronal cell body membrane / monoatomic cation transport / response to mechanical stimulus / monoatomic cation channel activity / cyclin binding / bioluminescence / generation of precursor metabolites and energy / regulation of membrane potential / cellular response to mechanical stimulus / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleolus / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
MyoD family inhibitor / MyoD family inhibitor/MyoD family inhibitor domain-containing protein / Piezo family / Piezo non-specific cation channel, R-Ras-binding domain / Piezo domain / : / : / : / Piezo non-specific cation channel, cap domain / Piezo TM25-28 ...MyoD family inhibitor / MyoD family inhibitor/MyoD family inhibitor domain-containing protein / Piezo family / Piezo non-specific cation channel, R-Ras-binding domain / Piezo domain / : / : / : / Piezo non-specific cation channel, cap domain / Piezo TM25-28 / Piezo1-like, transmembrane helical unit / Piezo TM1-24 / Piezo, THU9 and anchor domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Piezo-type mechanosensitive ion channel component 2 / MyoD family inhibitor domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsZhang Y / Dai F
Funding support China, Australia, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022ZD0207400 China
Australian Research Council (ARC)FT220100159 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: MDFIC2 is a sensory neuron-specific PIEZO channel auxiliary subunit
Authors: Zhang Y / Dai F
History
DepositionJun 9, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65006.png

Downloads & links

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Map

FileDownload / File: emd_65006.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe composite map of hPiezo2-hMDFIC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 422. Å		1.06 Å/pix.
x 400 pix.
= 422. Å		1.06 Å/pix.
x 400 pix.
= 422. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.238
Minimum - Maximum-0.12022175 - 2.9402642
Average (Standard dev.)0.014506393 (±0.050720945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 421.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The cryo-EM structure of human Piezo2-MDFIC complex (composite map)

EntireName: The cryo-EM structure of human Piezo2-MDFIC complex (composite map)
Components
  • Complex: The cryo-EM structure of human Piezo2-MDFIC complex (composite map)
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 2,Green fluorescent protein
    • Protein or peptide: MyoD family inhibitor domain-containing protein

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Supramolecule #1: The cryo-EM structure of human Piezo2-MDFIC complex (composite map)

SupramoleculeName: The cryo-EM structure of human Piezo2-MDFIC complex (composite map)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Piezo-type mechanosensitive ion channel component 2,Green fluores...

MacromoleculeName: Piezo-type mechanosensitive ion channel component 2,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 348.501656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASEVVCGLI FRLLLPICLA VACAFRYNGL SFVYLIYLLL IPLFSEPTKT TMQGHTGRLL KSLCFISLSF LLLHIIFHIT LVSLEAQHR IAPGYNCSTW EKTFRQIGFE SLKGADAGNG IRVFVPDIGM FIASLTIWLL CRNIVQKPVT DEAAQSNPEF E NEELAEGE ...String:
MASEVVCGLI FRLLLPICLA VACAFRYNGL SFVYLIYLLL IPLFSEPTKT TMQGHTGRLL KSLCFISLSF LLLHIIFHIT LVSLEAQHR IAPGYNCSTW EKTFRQIGFE SLKGADAGNG IRVFVPDIGM FIASLTIWLL CRNIVQKPVT DEAAQSNPEF E NEELAEGE KIDSEEALIY EEDFNGGDGV EGELEESTKL KMFRRLASVA SKLKEFIGNM ITTAGKVVVT ILLGSSGMML PS LTSSVYF FVFLGLCTWW SWCRTFDPLL FSCLCVLLAI FTAGHLIGLY LYQFQFFQEA VPPNDYYARL FGIKSVIQTD CSS TWKIIV NPDLSWYHHA NPILLLVMYY TLATLIRIWL QEPLVQDEGT KEEDKALACS PIQITAGRRR SLWYATHYPT DERK LLSMT QDDYKPSDGL LVTVNGNPVD YHTIHPSLPM ENGPGKADLY STPQYRWEPS DESSEKREEE EEEKEEFEEE RSREE KRSI KVHAMVSVFQ FIMKQSYICA LIAMMAWSIT YHSWLTFVLL IWSCTLWMIR NRRKYAMISS PFMVVYGNLL LILQYI WSF ELPEIKKVPG FLEKKEPGEL ASKILFTITF WLLLRQHLTE QKALQEKEAL LSEVKIGSQE NEEKDEELQD IQVEGEP KE EEEEEAKEEK QERKKVEQEE AEEEDEQDIM KVLGNLVVAM FIKYWIYVCG GMFFFVSFEG KIVMYKIIYM VLFLFCVA L YQVHYEWWRK ILKYFWMSVV IYTMLVLIFI YTYQFENFPG LWQNMTGLKK EKLEDLGLKQ FTVAELFTRI FIPTSFLLV CILHLHYFHD RFLELTDLKS IPSKEDNTIY RLAHPEGSLP DLTMMHLTAS LEKPEVRKLA EPGEEKLEGY SEKAQKGDLG KDSEESEED GEEEEESEEE EETSDLRNKW HLVIDRLTVL FLKFLEYFHK LQVFMWWILE LHIIKIVSSY IIWVSVKEVS L FNYVFLIS WAFALPYAKL RRLASSVCTV WTCVIIVCKM LYQLQTIKPE NFSVNCSLPN ENQTNIPFNE LNKSLLYSAP ID PTEWVGL RKSSPLLVYL RNNLLMLAIL AFEVTIYRHQ EYYRGRNNLT APVSRTIFHD ITRLHLDDGL INCAKYFINY FFY KFGLET CFLMSVNVIG QRMDFYAMIH ACWLIAVLYR RRRKAIAEIW PKYCCFLACI ITFQYFICIG IPPAPCRDYP WRFK GASFN DNIIKWLYFP DFIVRPNPVF LVYDFMLLLC ASLQRQIFED ENKAAVRIMA GDNVEICMNL DAASFSQHNP VPDFI HCRS YLDMSKVIIF SYLFWFVLTI IFITGTTRIS IFCMGYLVAC FYFLLFGGDL LLKPIKSILR YWDWLIAYNV FVITMK NIL SIGACGYIGT LVHNSCWLIQ AFSLACTVKG YQMPAANSPC TLPSGEAGII WDSICFAFLL LQRRVFMSYY FLHVVAD IK ASQILASRGA ELFQATIVKA VKARIEEEKK SMDQLKRQMD RIKARQQKYK KGKERMLSLT QEPGEGQDMQ KLSEEDDE R EADKQKAKGK KKQWWRPWVD HASMVRSGDY YLFETDSEEE EEEELKKEDE EPPRRSAFQF VYQAWITDPK TALRQRHKE KKRSAREERK RRRKGSKEGP VEWEDREDEP IKKKSDGPDN IIKRIFNILK FTWVLFLATV DSFTTWLNSI SREHIDISTV LRIERCMLT REIKKGNVPT RESIHMYYQN HIMNLSRESG LDTIDEHPGA ASGAQTAHRM DSLDSHDSIS SEPTQCTMLY S RQGTTETI EEVEAEQEEE AGSTAPEPRE AKEYEATGYD VGAMGAEEAS LTPEEELTQF STLDGDVEAP PSYSKAVSFE HL SFGSQDD SAGKNRMAVS PDDSRTDKLG SSILPPLTHE LTASELLLKK MFHDDELEES EKFYVGQPRF LLLFYAMYNT LVA RSEMVC YFVIILNHMV SASMITLLLP ILIFLWAMLS VPRPSRRFWM MAIVYTEVAI VVKYFFQFGF FPWNKNVEVN KDKP YHPPN IIGVEKKEGY VLYDLIQLLA LFFHRSILKC HGLWDEDDMT ESGMAREESD DELSLGHGRR DSSDSLKSIN LAASV ESVH VTFPEQQTAV RRKRSGSSSE PSQRSSFSSN RSQRGSTSTR NSSQKGSSVL SIKQKGKREL YMEKLQEHLI KAKAFT IKK TLEIYVPIKQ FFYNLIHPEY SAVTDVYVLM FLADTVDFII IVFGFWAFGK HSAAADITSS LSEDQVPGPF LVMVLIQ FG TMVVDRALYL RKTVLGKVIF QVILVFGIHF WMFFILPGVT ERKFSQNLVA QLWYFVKCVY FGLSAYQIRC GYPTRVLG N FLTKSYNYVN LFLFQGFRLV PFLTELRAVM DWVWTDTTLS LSSWICVEDI YAHIFILKCW RESEKRYPQP RGQKKKKVV KYGMGGMIIV LLICIVWFPL LFMSLIKSVA GVINQPLDVS VTITLGGYQP IFTMSAQQSQ LKVMDQQSFN KFIQAFSRDT GAMQFLENY EKEDITVAEL EGNSNSLWTI SPPSKQKMIH ELLDPNSSFS VVFSWSIQRN LSLGAKSEIA TDKLSFPLKN I TRKNIAKM IAGNSTESSK TPVTIEKIYP YYVKAPSDSN SKPIKQLLSE NNFMDITIIL SRDNTTKYNS EWWVLNLTGN RI YNPNSQA LELVVFNDKV SPPSLGFLAG YGIMGLYASV VLVIGKFVRE FFSGISHSIM FEELPNVDRI LKLCTDIFLV RET GELELE EDLYAKLIFL YRSPETMIKW TREKTNSNSL EVLFQGPTAA AAVSKGEELF TGVVPILVEL DGDVNGHKFS VSGE GEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEV KFEG DTLVNRIELK GIDFKEDGNI LGHKLEYNYN SHNVYIMADK QKNGIKVNFK IRHNIEDGSV QLADHYQQNT PIGDGP VLL PDNHYLSTQS KLSKDPNEKR DHMVLLEFVT AAGITLGMDE LYKSGGGHHH HHHHHHH

UniProtKB: Piezo-type mechanosensitive ion channel component 2, Green fluorescent protein

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Macromolecule #2: MyoD family inhibitor domain-containing protein

MacromoleculeName: MyoD family inhibitor domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.114574 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG LEVLFQGPGS SMSGAGEALA PGPVGPQRVA EAGGGQLGST AQGKCDKDNT EKDITQATNS HFTHGEMQDQ SIWGNPSDG ELIRTQPQRL PQLQTSAQVP SGEEIGKIKN GHTGLSNGNG IHHGAKHGSA DNRKLSAPVS QKMHRKIQSS L SVNSDISK ...String:
MDYKDDDDKG LEVLFQGPGS SMSGAGEALA PGPVGPQRVA EAGGGQLGST AQGKCDKDNT EKDITQATNS HFTHGEMQDQ SIWGNPSDG ELIRTQPQRL PQLQTSAQVP SGEEIGKIKN GHTGLSNGNG IHHGAKHGSA DNRKLSAPVS QKMHRKIQSS L SVNSDISK KSKVNAVFSQ KTGSSPEDCC VHCILACLFC EFLTLCNIVL GQASCGICTS EACCCCCGDE MGDDCNCPCD MD CGIMDAC CESSDCLEIC MECCGICFPS

UniProtKB: MyoD family inhibitor domain-containing protein

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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: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: AF2 predicted
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83949
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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