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

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Basic information

Entry
Database: PDB / ID: 9c3c
TitleCryo-EM structure of native dystrophin-glycoprotein complex (DGC)
Components
  • Alpha-dystroglycan
  • Alpha-sarcoglycan
  • Beta-dystroglycan
  • Beta-sarcoglycan
  • Dystrobrevin
  • Dystrophin
  • Gamma-sarcoglycan
  • Sarcoglycan delta
  • Sarcospan
KeywordsMEMBRANE PROTEIN / beta-helix / sarcolemma / glycosylation / muscular dystrophy
Function / homology
Function and homology information


sarcoglycan complex / dystroglycan complex / nerve maturation / muscle attachment / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / contractile ring / coronary vasculature morphogenesis / regulation of gastrulation / microtubule anchoring ...sarcoglycan complex / dystroglycan complex / nerve maturation / muscle attachment / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / contractile ring / coronary vasculature morphogenesis / regulation of gastrulation / microtubule anchoring / morphogenesis of an epithelial sheet / dystrophin-associated glycoprotein complex / laminin-1 binding / basement membrane organization / regulation of epithelial to mesenchymal transition / dystroglycan binding / photoreceptor ribbon synapse / vinculin binding / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / node of Ranvier / commissural neuron axon guidance / protein-containing complex localization / cardiac muscle cell contraction / cardiac muscle cell development / cardiac muscle tissue development / response to muscle activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / structural constituent of muscle / muscle organ development / epithelial tube branching involved in lung morphogenesis / heart contraction / regulation of synapse organization / alpha-actinin binding / membrane protein ectodomain proteolysis / cellular response to organic cyclic compound / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of MAPK cascade / calcium ion homeostasis / heart morphogenesis / GABA-ergic synapse / tubulin binding / SH2 domain binding / negative regulation of cell migration / filopodium / sarcoplasmic reticulum / calcium-mediated signaling / regulation of synaptic plasticity / sarcolemma / cell-cell junction / protein transport / lamellipodium / virus receptor activity / actin binding / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLiu, S. / Su, T. / Xia, X. / Zhou, Z.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
CitationJournal: To Be Published
Title: Native DGC Structure Rationalizes Muscular Dystrophy-Causing Mutations
Authors: Liu, S. / Su, T. / Xia, X. / Zhou, Z.H.
History
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-dystroglycan
B: Beta-dystroglycan
D: Dystrophin
a: Alpha-sarcoglycan
b: Beta-sarcoglycan
d: Sarcoglycan delta
g: Gamma-sarcoglycan
n: Sarcospan
V: Dystrobrevin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)769,84519
Polymers764,8729
Non-polymers4,97310
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 9 types, 9 molecules ABDabdgnV

#1: Protein Alpha-dystroglycan / Beta-DG


Mass: 67623.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q28685
#2: Protein Beta-dystroglycan / Beta-DG


Mass: 15714.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q28685
#3: Protein Dystrophin


Mass: 427942.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: Protein Alpha-sarcoglycan / Alpha-SG / 50 kDa dystrophin-associated glycoprotein / 50DAG / Adhalin / Dystroglycan-2


Mass: 35969.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q28686
#5: Protein Beta-sarcoglycan / Beta-SG


Mass: 34768.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q28635
#6: Protein Sarcoglycan delta


Mass: 32142.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGL0
#7: Protein Gamma-sarcoglycan


Mass: 32005.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q28646
#8: Protein Sarcospan


Mass: 26058.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P82352
#9: Protein Dystrobrevin


Mass: 92647.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Sugars , 3 types, 10 molecules

#10: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 7 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#11: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#12: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: dystrophin-glycoprotein complex (DGC) / Type: COMPLEX / Entity ID: #1, #3, #5, #8-#9 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
Details: 150 mM NaCl, 0.1% digitonin, 50 mM Tris-HCl, pH 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Detector modeFilm or detector model
1150SUPER-RESOLUTIONGATAN K2 SUMMIT (4k x 4k)
2150GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
8UCSF ChimeraXmodel fitting
9Cootmodel fitting
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
15PHENIXmodel refinement
Image processingDetails: both K2 and K3 detector were used for this reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134481 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319856
ELECTRON MICROSCOPYf_angle_d0.64626949
ELECTRON MICROSCOPYf_dihedral_angle_d5.0392811
ELECTRON MICROSCOPYf_chiral_restr0.053180
ELECTRON MICROSCOPYf_plane_restr0.0053418

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