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- PDB-8uf4: Crystal structure of wildtype dystroglycan proteolytic domain (ju... -

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Basic information

Entry
Database: PDB / ID: 8uf4
TitleCrystal structure of wildtype dystroglycan proteolytic domain (juxtamembrane domain)
Components
  • Beta-dystroglycan
  • a-dystroglycan
KeywordsCELL ADHESION / SEA domain / mechanoreceptor
Function / homology
Function and homology information


Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / muscle attachment / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / regulation of embryonic cell shape / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / O-linked glycosylation ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / muscle attachment / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / regulation of embryonic cell shape / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / O-linked glycosylation / contractile ring / regulation of gastrulation / calcium-dependent cell-matrix adhesion / morphogenesis of an epithelial sheet / dystrophin-associated glycoprotein complex / microtubule anchoring / laminin-1 binding / response to denervation involved in regulation of muscle adaptation / positive regulation of myelination / basement membrane organization / photoreceptor ribbon synapse / nerve development / dystroglycan binding / cellular response to cholesterol / Formation of the dystrophin-glycoprotein complex (DGC) / vinculin binding / regulation of epithelial to mesenchymal transition / EGR2 and SOX10-mediated initiation of Schwann cell myelination / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / skeletal muscle tissue regeneration / costamere / commissural neuron axon guidance / node of Ranvier / angiogenesis involved in wound healing / axon regeneration / structural constituent of muscle / positive regulation of cell-matrix adhesion / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / response to muscle activity / epithelial tube branching involved in lung morphogenesis / regulation of synapse organization / alpha-actinin binding / membrane protein ectodomain proteolysis / basement membrane / positive regulation of oligodendrocyte differentiation / Non-integrin membrane-ECM interactions / postsynaptic cytosol / plasma membrane raft / ECM proteoglycans / negative regulation of MAPK cascade / heart morphogenesis / laminin binding / tubulin binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / SH2 domain binding / nuclear periphery / axon guidance / negative regulation of cell migration / morphogenesis of an epithelium / GABA-ergic synapse / filopodium / adherens junction / sarcolemma / regulation of synaptic plasticity / response to peptide hormone / Golgi lumen / Regulation of expression of SLITs and ROBOs / cellular response to mechanical stimulus / protein transport / lamellipodium / actin binding / virus receptor activity / : / basolateral plasma membrane / postsynaptic membrane / cytoskeleton / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / calcium ion binding / protein-containing complex binding / glutamatergic synapse / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Cadherin-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsAnderson, M.J.M. / Shi, K. / Hayward, A.N. / Uhlens, C. / Evans III, R.L. / Grant, E. / Greenberg, L. / Aihara, H. / Gordon, W.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM119483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM118047 United States
CitationJournal: Structure / Year: 2024
Title: Molecular basis of proteolytic cleavage regulation by the extracellular matrix receptor dystroglycan.
Authors: Anderson, M.J.M. / Hayward, A.N. / Smiley, A.T. / Shi, K. / Pawlak, M.R. / Aird, E.J. / Grant, E. / Greenberg, L. / Aihara, H. / Evans 3rd, R.L. / Ulens, C. / Gordon, W.R.
History
DepositionOct 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: a-dystroglycan
B: Beta-dystroglycan
C: a-dystroglycan
D: Beta-dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0187
Polymers57,9074
Non-polymers1113
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-30 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.945, 86.577, 128.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 494 or resid 496 through 499...
d_2ens_1(chain "C" and (resid 494 through 499 or (resid 500...
d_1ens_2(chain "B" and (resid 654 through 679 or (resid 680...
d_2ens_2(chain "D" and (resid 654 through 679 or (resid 680...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNASNASNAA4944
d_12ens_1ARGARGPHEPHEAA496 - 5236 - 33
d_13ens_1HISHISTHRTHRAA526 - 53136 - 41
d_14ens_1LEULEULEULEUAA534 - 54044 - 50
d_15ens_1LYSLYSASPASPAA549 - 58159 - 91
d_16ens_1LEULEUVALVALAA585 - 61395 - 123
d_17ens_1ASPASPILEILEAA615 - 650125 - 160
d_21ens_1ASNASNPHEPHECC494 - 5234 - 33
d_22ens_1HISHISTHRTHRCC526 - 53136 - 41
d_23ens_1LEULEULEULEUCC534 - 54044 - 50
d_24ens_1LYSLYSASPASPCC549 - 58159 - 91
d_25ens_1LEULEUVALVALCC585 - 61395 - 123
d_26ens_1ASPASPILEILECC615 - 650125 - 160
d_11ens_2SERSERPROPROBB654 - 7201 - 67
d_21ens_2SERSERPROPRODD654 - 7201 - 67

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.294630294807, 0.955291864733, -0.0247071357539), (0.955480996401, -0.294918615832, -0.00889244354304), (-0.015781473252, -0.0209872154257, -0.999655181495)7.87663248496, -10.2318232472, -23.0431314254
2given(0.234662453626, 0.97168626849, -0.0275559156165), (0.971558493001, -0.235368736651, -0.0259933161673), (-0.0317431494382, -0.0206725284999, -0.999282251933)7.56471016559, -10.7903468338, -23.088647026

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Components

#1: Protein a-dystroglycan


Mass: 18549.994 Da / Num. of mol.: 2 / Fragment: residues 491-653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAG1 / Plasmid: pTD68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q14118
#2: Protein Beta-dystroglycan / Beta-DG


Mass: 10403.554 Da / Num. of mol.: 2 / Fragment: residues 654-748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAG1 / Plasmid: pTD68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q14118
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 0.1 M Tris, 0.2 M lithium sulfate, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.43→51.43 Å / Num. obs: 19288 / % possible obs: 98.92 % / Redundancy: 7.2 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.09652 / Rpim(I) all: 0.03876 / Rrim(I) all: 0.1043 / Net I/σ(I): 10.62
Reflection shellResolution: 2.432→2.519 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.799 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 12051 / CC1/2: 0.656 / CC star: 0.89 / Rpim(I) all: 0.7412 / Rrim(I) all: 1.952 / % possible all: 94.33

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→51.43 Å / SU ML: 0.2826 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8395
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 862 5.17 %
Rwork0.2246 15803 -
obs0.2272 16665 85.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.99 Å2
Refinement stepCycle: LAST / Resolution: 2.43→51.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 3 105 3702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793677
X-RAY DIFFRACTIONf_angle_d1.00344976
X-RAY DIFFRACTIONf_chiral_restr0.0603547
X-RAY DIFFRACTIONf_plane_restr0.0107649
X-RAY DIFFRACTIONf_dihedral_angle_d5.1216481
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.0234464384
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.632993192083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.580.3073640.29491281X-RAY DIFFRACTION42.31
2.58-2.780.37251190.29612197X-RAY DIFFRACTION72.28
2.78-3.060.34781580.28282961X-RAY DIFFRACTION97.74
3.06-3.510.27621670.25793059X-RAY DIFFRACTION99.72
3.51-4.420.25581840.19793054X-RAY DIFFRACTION99.57
4.42-51.430.23651700.18493251X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.970996934183.05054358603-2.8733610477.28433694529-3.142624152257.11643837372-0.8216339240340.165754206077-0.881651100714-0.6745907960060.00129501740604-0.5134545200721.002826397890.7255500629360.801546082420.4961350842790.09779834032370.1366859394110.4563273326260.156917265860.32738971290719.0983449967-0.0816248725714-43.3897915452
23.38087797267-0.38192571045-1.835930979223.55098097471-0.7165074376453.26345670607-0.309400256404-0.0588544801025-0.280464745463-0.0452818328379-0.4013033312590.07916395299120.417031197540.09209685080550.2422881210880.3260823058260.07032378279720.04135735069280.48080714977-0.08373869906360.1241755973413.931679197251.18719477825-22.1605109789
30.6924262753010.279474424845-0.4982741126141.156514799570.6771153220251.10025590115-0.2298341883980.3107485162360.438272077095-0.158770739299-0.151719761792-0.7619109004870.1393506362280.7944813635920.208023349420.3132555058510.2077359174580.06811738680210.5558894865070.2644395086040.43980302022819.90518489043.72228031306-36.661101749
41.595540145482.166907002451.253246309482.956821377811.599972210241.714787123980.0519136367540.6665391480890.970408657071-0.634728852056-0.3101266699661.22297134759-0.556505376492-0.5494007627240.4571776426890.4985622908980.400530794737-0.05908086123131.071906902880.1021553300520.907943821512-1.5267849524915.4164142913-29.7892764383
52.81646747838-1.138961183720.1332084305131.090568454020.963489179812.04271056912-0.05335010640830.03652726788660.301556126012-0.040862834289-0.1566797046430.00767284301974-0.593392295994-0.90565109680.1537567950530.2971583674620.11195407636-0.05849047198580.47378399365-0.002433718382320.243050873157.04148728247.33042684719-31.3201384542
66.317886661274.03174168916-7.811456013643.95695603707-4.422006638479.91992794714-0.336012488583-0.10774155595-0.586871121395-0.561985451926-0.4487253973220.05442214094080.64500779513-0.4139792800940.5731215241440.2702351108190.0851349952177-0.01718863447110.521751727501-0.01265256149080.3867896815453.758729553040.257104134033-33.4936821895
70.736942994872-0.5041885238011.074351319492.51802821766-2.31447588885.33479064203-0.04657865781860.403640810805-0.178612452003-0.3379990178150.01933005436510.521366129950.384742704119-0.268802920870.06863376529310.688016263125-0.408723928080.1771828421160.912098471107-0.3633338906640.598055940432-8.80752474014-2.88235714407-11.7822787618
82.153051695380.305788781001-0.06979103427521.31250579473-0.6542600841922.259170393180.215905239558-0.1051175627020.460948667495-0.0846556212705-0.3282522024750.582428681865-0.625828666882-1.07896374059-0.1516936156120.335024935310.1971258390690.01955730037790.453522870989-0.1419271426220.514101515334-0.33689483209613.7666092291-10.7104829838
93.33815967896-0.661139161847-0.6217730273676.90433776910.2942942601465.398641458860.194747407589-0.3139675345650.436091411863-0.00414444330405-0.569435027121-0.197679602753-0.242127390121-0.1995035909290.2517317906190.207745657063-0.1247600972460.06562416712970.601925939647-0.1832523000160.30437070378-0.2008713314287.21111209529-10.4545752564
101.414974726870.473413312427-0.9632475537252.27290152383-1.432430674223.87892249768-0.0210954252635-0.205734350202-0.08024692953860.244767121678-0.3739522084940.3686976111020.299541763254-0.412738250908-0.4564811905430.465069505479-0.2495943797990.2031903404940.829009585301-0.2590552978030.378031965188-4.892357184470.903757242002-5.58640108145
115.390904865743.223231464240.9175692908735.00780204762-1.387204224991.671318151420.236551946701-0.6921686627180.3419673747880.904791904183-0.73548451920.311110066154-0.178858251364-0.107162102863-0.2582636275890.714187744161-0.4972237491680.10379047640.972280624501-0.1736296754910.379658475785-0.1749597545564.415918893295.80303126573
120.5876590552470.215558418913-0.4579321089560.639065820994-0.9856135287591.549150247110.136802790628-0.440494815006-0.01821134743940.323351318752-0.8024613373880.4560305508940.161249289235-0.594874215489-1.097710306890.449165412485-0.2891986230960.1909528063060.850179783542-0.3439742472120.526076821654-3.508302072218.510048009070.365481569028
131.33899755451-1.28628013999-2.76585539783.559138447942.283977084515.772510455-0.2017592432440.3734467728890.23281712126-0.335095853518-0.6571593857230.446987262416-1.06108599986-0.5722214401850.606487616651.49665862818-0.0752931629833-0.2640922263550.479744514418-0.02287912024670.45887581741512.85846740325.9138436623717.6274716561
142.554889275540.9674156373170.91055219270.925586530621.663719942183.45478126775-0.075267558541-0.5568437388930.4447125452030.760954841731-0.448894640313-0.163686326558-0.2385688933530.3208031388440.1444955133350.773608170673-0.149957759427-0.1239902249070.3105876495060.0294289762240.37831723659717.5902393971-1.08851001727.97277468805
150.499307720367-0.304389829040.2179953104370.4355585208480.02580658795672.569813613980.0611290032058-0.0038341355248-0.2455401438830.486384812568-0.4252792345970.009889781983010.827512993113-0.130997944848-0.1379885380590.595214549957-0.197356661953-0.03474745685050.172533393469-0.01731508343370.35406155598115.6510995489-11.1852906437-1.96811067767
166.71172155189-2.27646290734-1.356480367611.12010313198-0.9366943121687.73961859898-0.0252682207264-0.2262873732030.4436724300171.095996708380.256325384325-0.89808618033-0.06687111826760.469852840387-0.1710706558250.504184196957-0.100719025224-0.1089041567550.30247023412-0.05419143888630.28087434830715.1008019216-12.9221437912-12.7193895893
177.741929173551.641421866172.853043446844.16066673831-0.6329690602784.733110432050.2678677901840.450808913339-0.2535856072510.171878860414-0.6266712343550.7131882408780.72287001065-0.822196923310.3149773461570.423847222818-0.06809860977640.03036289073750.52324685646-0.2302495247950.3242188979347.27869082419-13.7341688498-21.3133755805
186.385064198981.34853562340.2351007540537.1936807986-0.3548588619944.550349921590.1823215128150.943835027079-0.641894602637-0.555872797976-0.246926746506-0.5549945209471.01044428807-0.01317169629570.08818316650660.492095345750.06129038281970.0008871484881080.450496824996-0.03458418083380.24805225984115.8469932624-15.5960398022-24.8445879072
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 491 through 504 )AA491 - 5041 - 14
22chain 'A' and (resid 505 through 517 )AA505 - 51715 - 27
33chain 'A' and (resid 518 through 539 )AA518 - 53928 - 49
44chain 'A' and (resid 540 through 551 )AA540 - 55150 - 59
55chain 'A' and (resid 552 through 585 )AA552 - 58560 - 93
66chain 'A' and (resid 586 through 596 )AA586 - 59694 - 104
77chain 'A' and (resid 597 through 606 )AA597 - 606105 - 114
88chain 'A' and (resid 607 through 637 )AA607 - 637115 - 145
99chain 'A' and (resid 638 through 652 )AA638 - 652146 - 160
1010chain 'B' and (resid 654 through 670 )BC654 - 6701 - 17
1111chain 'B' and (resid 671 through 689 )BC671 - 68918 - 36
1212chain 'B' and (resid 690 through 721 )BC690 - 72137 - 68
1313chain 'C' and (resid 493 through 504 )CD493 - 5041 - 11
1414chain 'C' and (resid 505 through 559 )CD505 - 55912 - 65
1515chain 'C' and (resid 560 through 637 )CD560 - 63766 - 143
1616chain 'C' and (resid 638 through 653 )CD638 - 653144 - 159
1717chain 'D' and (resid 654 through 681 )DE654 - 6811 - 28
1818chain 'D' and (resid 682 through 720 )DE682 - 72029 - 67

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