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- EMDB-45165: Cryo-EM structure of native dystrophin-glycoprotein complex (DGC) -

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Basic information

Entry
Database: EMDB / ID: EMD-45165
TitleCryo-EM structure of native dystrophin-glycoprotein complex (DGC)
Map data
Sample
  • Complex: dystrophin-glycoprotein complex (DGC)
    • Protein or peptide: Alpha-dystroglycan
    • Protein or peptide: Dystrophin
    • Protein or peptide: Beta-sarcoglycan
    • Protein or peptide: Sarcospan
    • Protein or peptide: Dystrobrevin
  • Protein or peptide: Beta-dystroglycan
  • Protein or peptide: Alpha-sarcoglycan
  • Protein or peptide: Sarcoglycan delta
  • Protein or peptide: Gamma-sarcoglycan
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsbeta-helix / sarcolemma / glycosylation / muscular dystrophy / membrane protein
Function / homology
Function and homology information


sarcoglycan complex / coronary vasculature morphogenesis / muscle attachment / dystroglycan complex / nerve maturation / retrograde trans-synaptic signaling by trans-synaptic protein complex / contractile ring / morphogenesis of an epithelial sheet / microtubule anchoring / dystrophin-associated glycoprotein complex ...sarcoglycan complex / coronary vasculature morphogenesis / muscle attachment / dystroglycan complex / nerve maturation / retrograde trans-synaptic signaling by trans-synaptic protein complex / contractile ring / morphogenesis of an epithelial sheet / microtubule anchoring / dystrophin-associated glycoprotein complex / laminin-1 binding / photoreceptor ribbon synapse / basement membrane organization / dystroglycan binding / vinculin binding / branching involved in salivary gland morphogenesis / myelination in peripheral nervous system / commissural neuron axon guidance / protein-containing complex localization / node of Ranvier / cardiac muscle cell contraction / cardiac muscle cell development / cardiac muscle tissue development / structural constituent of muscle / muscle organ development / regulation of synapse organization / heart contraction / epithelial tube branching involved in lung morphogenesis / response to muscle activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / alpha-actinin binding / membrane protein ectodomain proteolysis / basement membrane / heart morphogenesis / calcium ion homeostasis / negative regulation of MAPK cascade / tubulin binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / SH2 domain binding / negative regulation of cell migration / sarcoplasmic reticulum / filopodium / calcium-mediated signaling / sarcolemma / GABA-ergic synapse / regulation of synaptic plasticity / cell-cell junction / protein transport / lamellipodium / actin binding / virus receptor activity / postsynaptic membrane / cytoskeleton / intracellular signal transduction / membrane raft / external side of plasma membrane / focal adhesion / calcium ion binding / protein-containing complex binding / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Sarcoglycan complex subunit protein / Sarcoglycan alpha/epsilon / Beta-sarcoglycan / Sarcospan / Sarcoglycan gamma/delta/zeta / : / : / Sarcoglycan complex subunit protein / Sarcoglycan alpha/epsilon N-terminal domain / Sarcoglycan alpha/epsilon second domain ...Sarcoglycan complex subunit protein / Sarcoglycan alpha/epsilon / Beta-sarcoglycan / Sarcospan / Sarcoglycan gamma/delta/zeta / : / : / Sarcoglycan complex subunit protein / Sarcoglycan alpha/epsilon N-terminal domain / Sarcoglycan alpha/epsilon second domain / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Putative Ig domain / CD20-like family / CD20-like family / Cadherin-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sarcoglycan delta / Sarcospan / Beta-sarcoglycan / Gamma-sarcoglycan / Dystroglycan 1 / Alpha-sarcoglycan
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLiu S / Su T / Xia X / Zhou ZH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
CitationJournal: Nature / Year: 2025
Title: Native DGC structure rationalizes muscular dystrophy-causing mutations.
Authors: Shiheng Liu / Tiantian Su / Xian Xia / Z Hong Zhou /
Abstract: Duchenne muscular dystrophy (DMD) is a severe X-linked recessive disorder marked by progressive muscle wasting leading to premature mortality. Discovery of the DMD gene encoding dystrophin both ...Duchenne muscular dystrophy (DMD) is a severe X-linked recessive disorder marked by progressive muscle wasting leading to premature mortality. Discovery of the DMD gene encoding dystrophin both revealed the cause of DMD and helped identify a family of at least ten dystrophin-associated proteins at the muscle cell membrane, collectively forming the dystrophin-glycoprotein complex (DGC). The DGC links the extracellular matrix to the cytoskeleton, but, despite its importance, its molecular architecture has remained elusive. Here we determined the native cryo-electron microscopy structure of rabbit DGC and conducted biochemical analyses to reveal its intricate molecular configuration. An unexpected β-helix comprising β-, γ- and δ-sarcoglycan forms an extracellular platform that interacts with α-dystroglycan, β-dystroglycan and α-sarcoglycan, allowing α-dystroglycan to contact the extracellular matrix. In the membrane, sarcospan anchors β-dystroglycan to the β-, γ- and δ-sarcoglycan trimer, while in the cytoplasm, β-dystroglycan's juxtamembrane fragment binds dystrophin's ZZ domain. Through these interactions, the DGC links laminin 2 to intracellular actin. Additionally, dystrophin's WW domain, along with its EF-hand 1 domain, interacts with α-dystrobrevin. A disease-causing mutation mapping to the WW domain weakens this interaction, as confirmed by deletion of the WW domain in biochemical assays. Our findings rationalize more than 110 mutations affecting single residues associated with various muscular dystrophy subtypes and contribute to ongoing therapeutic developments, including protein restoration, upregulation of compensatory genes and gene replacement.
History
DepositionMay 31, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_45165.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 360 pix.
= 489.6 Å
1.36 Å/pix.
x 360 pix.
= 489.6 Å
1.36 Å/pix.
x 360 pix.
= 489.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.52
Minimum - Maximum-2.8019629 - 4.345665
Average (Standard dev.)-0.00084346376 (±0.045138657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 489.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45165_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_45165_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : dystrophin-glycoprotein complex (DGC)

EntireName: dystrophin-glycoprotein complex (DGC)
Components
  • Complex: dystrophin-glycoprotein complex (DGC)
    • Protein or peptide: Alpha-dystroglycan
    • Protein or peptide: Dystrophin
    • Protein or peptide: Beta-sarcoglycan
    • Protein or peptide: Sarcospan
    • Protein or peptide: Dystrobrevin
  • Protein or peptide: Beta-dystroglycan
  • Protein or peptide: Alpha-sarcoglycan
  • Protein or peptide: Sarcoglycan delta
  • Protein or peptide: Gamma-sarcoglycan
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: dystrophin-glycoprotein complex (DGC)

SupramoleculeName: dystrophin-glycoprotein complex (DGC) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #5, #8-#9
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Alpha-dystroglycan

MacromoleculeName: Alpha-dystroglycan / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 67.623688 KDa
SequenceString: HWPSEPSEAV RDWENQLEAS MHSVLSDLHE ALPTVVGIPD GTAVVGRSFR VTIPTDLIGS SGEVIKVSTA GKEVLPSWLH WDPQSHTLE GLPLDTDKGV HYISVSAAQL DANGSHIPQT SSVFSIEVYP EDHSEPQSVR AASPDLGEAA ASACAAEEPV T VLTVILDA ...String:
HWPSEPSEAV RDWENQLEAS MHSVLSDLHE ALPTVVGIPD GTAVVGRSFR VTIPTDLIGS SGEVIKVSTA GKEVLPSWLH WDPQSHTLE GLPLDTDKGV HYISVSAAQL DANGSHIPQT SSVFSIEVYP EDHSEPQSVR AASPDLGEAA ASACAAEEPV T VLTVILDA DLTKMTPKQR IDLLHRMQSF SEVELHNMKL VPVVNNRLFD MSAFMAGPGN AKKVVENGAL LSWKLGCSLN QN SVPDIRG VEAPAREGTM SAQLGYPVVG WHIANKKPPL PKRIRRQIHA TPTPVTAIGP PTTAIQEPPS RIVPTPTSPA IAP PTETMA PPVRDPVPGK PTVTTRTRGA IIQTPTLGPI QPTRVSDAGT VVSGQIRATV TIPGYVEPTA VATPPTTTTK KPRV STPKP ATPSTDSSAT TTRRPTKKPR TPRPVPRVTT KAPITRLETA SPPTRIRTTT SGVPRGGEPN QRPELKNHID RVDAW VGTY FEVKIPSDTF YDKEDTTTDK LKLTLKLREQ QLVGEKSWVQ FNSNSQLMYG LPDSSHVGKH EYFMHATDKG GLSAVD AFE IHVHKRPQGD KAPARFKAKF VGDPAPVVND IHKKIALVKK LAFAFGDRNC STVTLQNITR G

UniProtKB: Dystroglycan 1

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Macromolecule #2: Beta-dystroglycan

MacromoleculeName: Beta-dystroglycan / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 15.714142 KDa
SequenceString:
SIVVEWTNNT LPLEPCPKEQ ITGLSRRIAE DNGQPRPAFT NALEPDFKAT SIAITGSGSC RHLQFIPVAP PGIPSSVTPP TEVPDRDPE KSSEDDVYLH TVIPAVVVAA ILLIAGIIAM ICYRKKRKGK LTLEDQATFI KKGVPI

UniProtKB: Dystroglycan 1

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Macromolecule #3: Dystrophin

MacromoleculeName: Dystrophin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 427.942781 KDa
SequenceString: MLWWEEVEDC YEREDVQKKT FTKWINAQFS KFGKQHIENL FSDLQDGRRL LDLLEGLTGQ QLPKEKGSTR VHALNNVNKA LRVLQKNNV DLVNIGSTDI VDGNHKLTLG LIWNIILHWQ VKNVMKNIMA GLQQTNSEKI LLSWVRQSTR NYSQVNVINF T TSWSDGLA ...String:
MLWWEEVEDC YEREDVQKKT FTKWINAQFS KFGKQHIENL FSDLQDGRRL LDLLEGLTGQ QLPKEKGSTR VHALNNVNKA LRVLQKNNV DLVNIGSTDI VDGNHKLTLG LIWNIILHWQ VKNVMKNIMA GLQQTNSEKI LLSWVRQSTR NYSQVNVINF T TSWSDGLA LNALIHSHRP DLFDWNSVVC QQSATQRLEH AFNIAKCQLG IEKLLDPEDV ATTYPDKKSI LMYITSLFQV LP QQVSIEA IQEVELLPRP SKVTREEHFQ LHHQMHYSQQ ITVSLAQGYE RTSSPKPRFK SYAYTQAAYV STSDPTRSPF PSQ HLEAPG DKSFGSSLME TEVSLDSYQT ALEEVLSWLL SAEDTLQAQK EISSDVEEVK EQFHTHEGYM MDLTSHQGRV GNVL QLGSQ LIRTGKLSEE EETEVQEQMN LLNSRWECLR VASMEKQSNL HKVLMDLQNQ KLKELNDWLT KTEERTRKME EEPLG PDLE DLKRQVQQHK VLQEDLEQEQ VRVNSLTHMV VVVDESSGEH ATAALEEQLK VLGDRWANIC RWTEDRWVLL QDILLK WQR FTEEQCLFST WLSEKEDAVN KIHTTGFKDQ NEMLSSLHKL TVLKTDLEKK KQSMDKLSSL NQALLSTLKN KSVTQKM EA WLENFALRWD NLVQKLEKSS AQISQAVTTT QPSLTQTTVM ETVTMVTTRE QILVKHAQEE LPPPPPQKKR QIIVDSEI R KRLDVDITEL HSWITRSEAV LQSPEFAIYR KEGNFSDLKE KVNAIEREKA EKFRKLQDAS RSAQALVEQM VNEGVNADS IKQALEQLNS RWIEFCQLLS ERLHWLEYQN SIITFYNQLQ QLEQMITTAE NWLKTQPTTA SEPTAIKSQL KMCKDEVNRL SALQPQIER LKIQSTALKE KGQGPMFLDA DFVAFTNHFN QVFADAQARE KELQTIFDTL PPTRYQETIS TIRTWIQQSE P KLSIPQLS VTEYEIMEQR LGELQALQSS LQEQQSGLTY LSTTVKEMAK KAPSEISRKY QSEFEEIEGH WKKLSYQLVD HC QKLEEQM NKLRKIQNHI KTLKKWMAEV DVFLKEEWPA LGDSEILKKQ LKQCRLLVND IQTIQPSLNS VNESGQKIKN EAE PEFASR LETELRELNS QWDHMCRQVY TRKDALKAGL DKTLSLQKDL SEMHEWMTQA EEEYLERDFE YKTPDELQTA VEEM KRAKE EAQQKESKVK LLTESVNSVI AQAPPAAQEA LKKELDTLTT NYQWLCTRLN GKCKTLEEVW ACWHELLSYL EKANK WLNE VEVKLKTTET LPGGAEEISE VLDSLENLMQ HSEDNPNQIR ILAQTLTDGG VMDELINEEL ETFNSRWREL HEEAVR RQK LLEQSIQSAQ EIEKSLHLIQ ESLAFIDKQL AAYIADKVDA AQMPQEAQKI QSDLTSHEIS LEEMKKHNQG KEAAQRV LS QIDVAQKKLQ DVSMKFRLFQ KPANFEQRLE ESKMILDEVK MHLPALETKS VEQEVVQSQL NHCVNLYKSL SEVKSEVE M VIKTGRQIVQ KKQTENPKEL DERVTALKLH YNELGAKVTE RKQQLEKCLK LSRKMRKEMN ALTEWLAATD MELTKRSAV EGMPSNLDAE IAWGKATQKE VEKQKAHLKS VIELGEALKT VLGKKETLVE DKLSLLNSNW VAVTSRAEEW LNLLLEYQKH METFDQNVD HITKWIIQAD TLLDESEKKK PQQKEDVLKR LKAEMNDIRP KVDSIRDQAA NLMANRGDHC RKVVEPKISE L NHRFAAIS HRIKTGKASI PLKELEQFNS DIQKLLEPLE AEIQQGVNLK EEDFNKDMSE DNEGTVKELL QRGDNLHERI TD ERKREEI KIKQQLLQTK HNALKDLRSQ RRKKALEISH QWYQYKRQAD DLLKCLDDIE KKLASLPDPK DERKIKEIDR ELQ KKKEEL NAVHRQAEGL SEDGAAMAVE PIQIQLSKRW REIESKFAQF RRLNFAQIHT VREETMVVMT EDMPLEISYV PSTY LTEIT HVSQALSEVD QLLNAPDLSA KDFEDLFKQE ESLKNIKECM QQISGRIDVI HNKKAAALQS ATAAERVKLQ EALAQ LDSQ WEKVNKMYKD RQGRFDRSVE KWRRFHYDMK IFNQWLTEAE QFLKKTQIPE NWEHAKYKWY LKELQDGIGQ RQTVVR TLN TTGEEIIQQS SKTDANILQE KLGNLNLRWQ EVCKQLAERR KRLEEQKNIL SEFQRDLNEF VLWLEEADNI TSIPLEP GN EQQLKEKLEQ VKLLAEELPL RQGILKQLNE AGGTALVSAP ISPEEQDKLE NKLKQTNLQW IKVSKALPEK QEEIVAHV K ELGQLEEQLN HLLLWLTPIR NQLEIYNQPN QTGPFDIKET EVAVQAKQPD VERILSKGQH LYKEKPATQP VKRKLEDLS SEWKVVNYLL QELRAKRPDL PPGPATIGAS PSQTVTLVTQ TVVTKEISLS ELEMPSSLLL EVPALADFNR AWTELTDWLS LLDRVLKSQ QVIVGDLEDI NEMIIKQKAT LQELEQRRPQ LEELITAAQN LKNKTSNQEA RTIITDRIER IQNQWDEVQE H LQNRRQQL NEMLKDSTQW LEAKEEAEQV LGQARAKLES WKEGPYTMDA LQKKIEETKQ LAKDLRQWQI NVDVANDLAL KL LRDYSAD DTRKVHMITE NINASWGSIH KRVNEREATL EEAYRLLQQF PLDLEKFLAW LTEAETTANV LQDATHKERL PED SKGVRE LMKQWQDLQG EIEAHTDIYH NLDENGQKIL RSLEGSDEAV LLQRRLDNMN FKWSELRKKS LNIRSHLEAS SDQW KRLHL SLQELLVWLQ LKDDELNRQA PVGGDFPAVQ KQNDVHRAFK RELKTKEPVI MSTLETVRIF LTEQPLGGLE KLYQE PREL PPDERAQNVT RLLRKQAEEV NAEWEKLNLH STDWQRKLDE ALERLQELQE ATDELDLKLR QAEVIKGSWQ PVGDLL IDS LQDHLEKVKA LRGEIAPLKE NVSHVNDLGR QLTTLGIQLS PYNLSTLEDL NTRWKLLQVA VEDRIRQLHE AHRDFGP AS QHFLSTSVQG PWERAISPNK VPYYINHETQ TTCWDHPKMT ELYQSLADLN NVRFSAYRTA MKLRRLQKAL CLDLLTLS A ACDALDQHNL KQNDQPMDIL QIINCLTTVY DRLEQEHNNL VNVPLCVDMC LNWLLNVYDT GRTGRIRVLS FKTGIISLC KAHLEDKYRY LFKQVASSTG FCDQRRLGLL LHDSIQIPRQ LGEVASFGGS NIEPSVRSCF QFANNKPEIE AALFLDWMRL EPQSMVWLP VLHRVAAAET AKHQAKCNIC KECPIIGFRY RSLKHFNYDI CQSCFFSGRV AKGHKMHYPM VEYCTPTTSG E DVRDFAKV LKNKFRTKRY FAKHPRMGYL PVQTVLEGDN METPVTLINF WPVDSAPASS PQLSHDDTHS RIEHYASRLA EM ENSNGSY LNDSISPNES IDDEHLLIQH YCQSLNQDSP LSQPRSPAQI LISLESEERG ELERILADLE EENRNLQAEY DRL KQQHEH KGLSPLPSPP EMMPTSPQSP RDAELIAEAK LLRQHKGRLE ARMQILEDHN KQLESQLHRL RQLLEQPQAE AKVN GTTVS SPSTSLQRSD SSQPMLLRVV GSQTSESMGE EDLPSPPQDT STGLEEVMEQ LNNSFPSSRG HNVGSLFHMA DDLGR AMES LVSVMTDEEG AE

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Macromolecule #4: Alpha-sarcoglycan

MacromoleculeName: Alpha-sarcoglycan / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 35.969039 KDa
SequenceString: QQTTLYPLVG RVFVHTLEPA SFLHLPEHAA PATIPVTYHA HLQGHPDLPR WLRYTQRSPH HPGFLYGAAT PEDRGRQVIE VTAYNRDSF DTAGQSLVLL IRDPEGSPLP YQTEFLVRSH DVEEVLPPTP ASHFLTALAG LWEPGELKLL NITSALDRGG R VPLPIGGQ ...String:
QQTTLYPLVG RVFVHTLEPA SFLHLPEHAA PATIPVTYHA HLQGHPDLPR WLRYTQRSPH HPGFLYGAAT PEDRGRQVIE VTAYNRDSF DTAGQSLVLL IRDPEGSPLP YQTEFLVRSH DVEEVLPPTP ASHFLTALAG LWEPGELKLL NITSALDRGG R VPLPIGGQ KEGVYIKVGS ASPFSTCLKM VASPDSHARC ARGQPPLLSC YDTLAPHFRV DWCNVSLVDT SVPEPVDEVP TP GDGILEH DPFFCPPTEA TARDFLADAL VTLLVPLLVA LLLALLLAYI MCCRREGRLK RDLATSDIQM VHHCTIHENT EEL RQMAAS

UniProtKB: Alpha-sarcoglycan

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Macromolecule #5: Beta-sarcoglycan

MacromoleculeName: Beta-sarcoglycan / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 34.768695 KDa
SequenceString: MAAAAAAAAE QQSSNGPVKK SMREKAVERR NVNKEHNSNF KAGYIPIDED RLHKTGLRGR KGNLAICVIV LLFLLAVINL IITLVIWAV IRIGPNGCDS MEFHESGLLR FKQVSDMGVI HPLYKSTVGG RRNENLVITG NNQPIVFQQG TTKLSVEKNK T SITSDIGM ...String:
MAAAAAAAAE QQSSNGPVKK SMREKAVERR NVNKEHNSNF KAGYIPIDED RLHKTGLRGR KGNLAICVIV LLFLLAVINL IITLVIWAV IRIGPNGCDS MEFHESGLLR FKQVSDMGVI HPLYKSTVGG RRNENLVITG NNQPIVFQQG TTKLSVEKNK T SITSDIGM QFFDPRTQNI LFSTDYETHE FHLPSGVKSL NVQKASTERI TSNATSDLNI KVDGRAIVRG NEGVFIMGKT IE FHMGGNM ELKAENSIIL NGTVMVSTTR LPSSSSADQL GGGDWVRYKL CMCADGTLFK VQVTGQNVGC QVSDNPCGNT H

UniProtKB: Beta-sarcoglycan

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Macromolecule #6: Sarcoglycan delta

MacromoleculeName: Sarcoglycan delta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 32.14235 KDa
SequenceString: MPQEQYTHHR STMPSAEGPQ VYKVGIYGWR KRCLYFFVLL LMILILVNLA MTIWILKVMN FTIDGMGNLR ITEKGLKLEG DSEFLQPLY AKEIQSRPGN ALYFKSARNV TVNILNDQTK VLTQLITGPK AVEAYGKKFE VKTVSGKLLF SADDNEVVVG A ERLRVLGA ...String:
MPQEQYTHHR STMPSAEGPQ VYKVGIYGWR KRCLYFFVLL LMILILVNLA MTIWILKVMN FTIDGMGNLR ITEKGLKLEG DSEFLQPLY AKEIQSRPGN ALYFKSARNV TVNILNDQTK VLTQLITGPK AVEAYGKKFE VKTVSGKLLF SADDNEVVVG A ERLRVLGA EGTVFPKSIE TPNVRADPFK ELRLESPTRA LVMEAPKGVE INAEAGNMEA TCRTELRLES KDGEIKLDAA KI KLPRLPH GSYTPTGTRQ KVFEICVCAN GRLFLSQAGT GSTCQINTSV CL

UniProtKB: Sarcoglycan delta

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Macromolecule #7: Gamma-sarcoglycan

MacromoleculeName: Gamma-sarcoglycan / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 32.005486 KDa
SequenceString: MAGEQYLTAT EGTHIERPEN QCVYKIGIYG WRKRCLYLLV LLLLIILVVN LALTIWILKV MWFSPTGMGH LHVTKDGLRL EGESEFLFP LYAKEIHSRV DSSLLLQSTQ NVTVNARNSD GEVTGRLKVG PQMVEVQSQQ FQINSREGKS LFTVDEEEVV V GTDRLRVT ...String:
MAGEQYLTAT EGTHIERPEN QCVYKIGIYG WRKRCLYLLV LLLLIILVVN LALTIWILKV MWFSPTGMGH LHVTKDGLRL EGESEFLFP LYAKEIHSRV DSSLLLQSTQ NVTVNARNSD GEVTGRLKVG PQMVEVQSQQ FQINSREGKS LFTVDEEEVV V GTDRLRVT GPEGALFEHS VETPLVTADP FQDLRLESPT RSLSMDAPRG VHIEAHAGEV EALSQMDIVL HSSDGTLVLD AE TVCLPKL LQGTQAASGS SQGLYEICVC PDGKLYLSVA GAGTTCQEHS HICL

UniProtKB: Gamma-sarcoglycan

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Macromolecule #8: Sarcospan

MacromoleculeName: Sarcospan / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 26.058631 KDa
SequenceString: MGKDRQPRGQ QRQGDAAGPD DPGPKKGAGT REQRGEEEAQ TCCGCRFPLL LALLQLALGV AVTVVGFLMA SVSSSLLVRA TPYWAGIIV CVVAYLGLFM LCVSYQVDER TCIQFSMKLL YFVLSALGLV VCVLAVAFAA HHYSLLTHLT CENAPDSCQC K LPSSEPLS ...String:
MGKDRQPRGQ QRQGDAAGPD DPGPKKGAGT REQRGEEEAQ TCCGCRFPLL LALLQLALGV AVTVVGFLMA SVSSSLLVRA TPYWAGIIV CVVAYLGLFM LCVSYQVDER TCIQFSMKLL YFVLSALGLV VCVLAVAFAA HHYSLLTHLT CENAPDSCQC K LPSSEPLS RTFVYRDVTD CTSITGTFQV FLLVQMVLNL VCGLVCLVAC FVMWKHRYQV FYVGVRMCPL SASEGQQQKV

UniProtKB: Sarcospan

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Macromolecule #9: Dystrobrevin

MacromoleculeName: Dystrobrevin / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 92.647117 KDa
SequenceString: MIEDSGKRGN TMAERRQLFA EMRAQDLDRI RLSTYRTACK LRFVQKKCNL HLVDIWNVIE ALRENALNNL DPNTELNVAR LEAVLSTIF YQLNKRMPTT HQIHVEQSIS LLLNFLLAAF DPEGHGKISV FAVKMALATL CGGKIMDKLR YIFSMISDSS G VMVYGRYD ...String:
MIEDSGKRGN TMAERRQLFA EMRAQDLDRI RLSTYRTACK LRFVQKKCNL HLVDIWNVIE ALRENALNNL DPNTELNVAR LEAVLSTIF YQLNKRMPTT HQIHVEQSIS LLLNFLLAAF DPEGHGKISV FAVKMALATL CGGKIMDKLR YIFSMISDSS G VMVYGRYD QFLREVLKLP TAVFEGPSFG YTEQSARSCF SQQKKVTLNG FLDTLMSDPP PQCLVWLPLL HRLANVENVF HP VECSYCH SESMMGFRYR CQQCHNYQLC QDCFWRGHAG GSHSNQHQMK EYTSWKSPAK KLTNALSKSL SCASSREPLH PMF PDQPEK PLNLAHIVPP RPVTSMNDTL FSHSVPSSGS PFITRRLPEG ISAASPVAEE HSLIKLYVNQ LDHGARSPPK DSEV EQNKM LARAAPAFLK GKGIQYSLNV ADRLADEHVL IGLYVNMLRN NPSCMLESSN RLDEEHRLIA RYAARLAAES SSSQP TQQR SAPDISFTID ANKQQRQLIA ELENKNREIL QEIQRLRLEH EQASQPAPEK AQQNPTLLAE LRLLRQRKDE LEQRMS ALQ ESRRELMVQL EGLMKLLKEE ELKQGTQGAS SPRSSPSHTI SRPIPMPIRS ASACSTPTHT PQDSLTGVGG DVQEAFA QS SRRNLRNDLL VAADSITNTM SSLVKELNSE VGSETESNVD SEFTRTQFED LVPSPTSEKA FLAQIQARKP GYIHSGAT T STVRSDMVTE DGDSYVRPED ENYDSDSVRQ LENELKMEEY LKQKLQDEAY QLHVSTETRL KHPCPVTETK WHVLFWVFV FFGGLLSLAL QIYFWGLF

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
Details: 150 mM NaCl, 0.1% digitonin, 50 mM Tris-HCl, pH 7.4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Detailsboth K2 and K3 detector were used for this reconstruction
Startup modelType of model: INSILICO MODEL / In silico model: Ab-Initio Reconstruction via CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 134481
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9c3c:
Cryo-EM structure of native dystrophin-glycoprotein complex (DGC)

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