SASDFW4

Conformation of R8-15 human dystrophin fragment

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2019-12-06T13:07:15.624532+01:00

SEC-SAXS was performed at 15°C using the following parameters: Column: BioSEC5-500Å (4.6 mm id * 300 mm); Flow rate: 0.2 mL/min; Sample injection concentration: 4 mg/mL; Injection volume: 60μL. The data were collected through the SEC peak of the protein as a series of 38 x 1.5 second exposures. The experimental molecular weight was determined from the volume of correlation, Vc.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Conformation of R8-15 human dystrophin fragment

Concentration— – — Buffer / pHNaP 10 mM, NaCl 500 mM, EDTA 1 mM, Glycerol 2% / 7.5
Experimental temperature15.0 Facility / beamlineSOLEIL / SWING
Wavelength0.1033 nmExposure1.5 s × 38

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Human dystrophin central domain R8-15 fragment
View sequence
MSYYHHHHHHDYDIPTTENLYFQGAMDPEFDCGSRKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTTNYQWLCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISEVLDSLENLMRHSEDNPNQIRILAQTLTDGGVMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHLIQESLTFIDKQLAAYIADKVDAAQMPQEAQKIQSDLTSHEISLEEMKKHNQGKEAAQRVLSQIDVAQKKLQDVSMKFRLFQKPANFELRLQESKMILDEVKMHLPALETKSVEQEVVQSQLNHCVNLYKSLSEVKSEVEMVIKTGRQIVQKKQTENPKELDERVTALKLHYNELGAKVTERKQQLEKCLKLSRKMRKEMNVLTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVLGKKETLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHITKWIIQADTLLDESEKKKPQQKEDVLKRLKAELNDIRPKVDSTRDQAANLMANRGDHCRKLVEPQISELNHRFAAISHRIKTGKASIPLKELEQFNSDIQKLLEPLEAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRITDERKREEIKIKQQLLQTKHNALKDLRSQRRKKALEISHQWYQYKRQADDLLKCLDDIEKKLASLPEPRDERKIKEIDRELQKKKEELNAVRRQAEGLSEDGAAMAVEPTQIQLSKRWREIESKFAQFRRLNFAQ
protein—P115321156–1973monomerMolecule count 1100.208 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11081[3]0.0062195710557–0.614504068039 1/AHas uncertainty columnMissing 016sasbdb/entries/w4/sasdfw4/source/SASDFW4.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)36.0—Å
i0Guinier0.0327—arbitrary
i0P(r)0.03204—arbitrary
mwExperimental88.0—kDa
rgGuinier10.06—Å
rgP(r)9.93—Å

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

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3. Source Fits and Models Source Fits & Models

Fit 1 · CRYSOL

χ²: 1.819CorMap p: 0.0Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—atomicCustom in-house —96.13—Model Image
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4. Source File Index Source Files

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5. Experiment Description and Publication Experiment & Publication

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6. Complete Source Record Complete Source Record

The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.

Open the original SASBDB entry

Buffer and Sample Properties

Buffer nameNaP 10 mM, NaCl 500 mM, EDTA 1 mM, Glycerol 2%Buffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2015-09-23Storage / measurement temperature— / 15.0
Exposure time1.5Frames38
Wavelength0.1033Sample-to-detector distance1.8
SourceX-ray synchrotronDetectorAVIEX PCCD170170
Facility / beamlineSOLEIL / SWING · Saint-Aubin, France
q range0.062 – 6.145Sample volume / flow rate— / —

Original SASBDB Plots

Experimental I(q)
Experimental I(q)
Experimental I(q), log-log
Experimental I(q), log-log
Guinier plot
Guinier plot
Kratky plot
Kratky plot
P(r) plot
P(r) plot

Downloadable Files

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All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json:156 field values
Field pathRaw value
codeSASDFW4
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleHow the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids.
project.publication.titleHow the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids.
project.publication.author_listMias-Lucquin D, Dos Santos Morais R, Chéron A, Lagarrigue M, Winder SJ, Chenuel T, Pérez J, Appavou MS, Martel A, Alviset G, Le Rumeur E, Combet S, Hubert JF, Delalande O
project.publication.journalJ Struct Biol
project.publication.doi10.1016/j.jsb.2019.107411
project.publication.pmid31689503
project.publication.published_date2019 Nov 2
project.statusreleased
project.submitted_date2019-03-30
project.released_date2019-11-14
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDFW4.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDFW4.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFW4_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFW4_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFW4_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFW4_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDFW4.sascif
experiment.instrument.detector.typeCCD
experiment.instrument.detector.nameAVIEX PCCD170170
experiment.instrument.detector.resolutionnull
experiment.instrument.nameSOLEIL
experiment.instrument.citySaint-Aubin
experiment.instrument.countryFrance
experiment.instrument.beamline_nameSWING
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameHuman dystrophin central domain R8-15 fragment
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMSYYHHHHHHDYDIPTTENLYFQGAMDPEFDCGSRKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTTNYQWLCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISEVLDSLENLMRHSEDNPNQIRILAQTLTDGGVMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHLIQESLTFIDKQLAAYIADKVDAAQMPQEAQKIQSDLTSHEISLEEMKKHNQGKEAAQRVLSQIDVAQKKLQDVSMKFRLFQKPANFELRLQESKMILDEVKMHLPALETKSVEQEVVQSQLNHCVNLYKSLSEVKSEVEMVIKTGRQIVQKKQTENPKELDERVTALKLHYNELGAKVTERKQQLEKCLKLSRKMRKEMNVLTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVLGKKETLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHITKWIIQADTLLDESEKKKPQQKEDVLKRLKAELNDIRPKVDSTRDQAANLMANRGDHCRKLVEPQISELNHRFAAISHRIKTGKASIPLKELEQFNSDIQKLLEPLEAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRITDERKREEIKIKQQLLQTKHNALKDLRSQRRKKALEISHQWYQYKRQADDLLKCLDDIEKKLASLPEPRDERKIKEIDRELQKKKEELNAVRRQAEGLSEDGAAMAVEPTQIQLSKRWREIESKFAQFRRLNFAQ
experiment.sample.molecule[0].organismnull
experiment.sample.molecule[0].uniprot_codeP11532
experiment.sample.molecule[0].uniprot_range_first1156
experiment.sample.molecule[0].uniprot_range_last1973
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMLWWEEVEDCYEREDVQKKTFTKWVNAQFSKFGKQHIENLFSDLQDGRRLLDLLEGLTGQ KLPKEKGSTRVHALNNVNKALRVLQNNNVDLVNIGSTDIVDGNHKLTLGLIWNIILHWQV KNVMKNIMAGLQQTNSEKILLSWVRQSTRNYPQVNVINFTTSWSDGLALNALIHSHRPDL FDWNSVVCQQSATQRLEHAFNIARYQLGIEKLLDPEDVDTTYPDKKSILMYITSLFQVLP QQVSIEAIQEVEMLPRPPKVTKEEHFQLHHQMHYSQQITVSLAQGYERTSSPKPRFKSYA YTQAAYVTTSDPTRSPFPSQHLEAPEDKSFGSSLMESEVNLDRYQTALEEVLSWLLSAED TLQAQGEISNDVEVVKDQFHTHEGYMMDLTAHQGRVGNILQLGSKLIGTGKLSEDEETEV QEQMNLLNSRWECLRVASMEKQSNLHRVLMDLQNQKLKELNDWLTKTEERTRKMEEEPLG PDLEDLKRQVQQHKVLQEDLEQEQVRVNSLTHMVVVVDESSGDHATAALEEQLKVLGDRW ANICRWTEDRWVLLQDILLKWQRLTEEQCLFSAWLSEKEDAVNKIHTTGFKDQNEMLSSL QKLAVLKADLEKKKQSMGKLYSLKQDLLSTLKNKSVTQKTEAWLDNFARCWDNLVQKLEK STAQISQAVTTTQPSLTQTTVMETVTTVTTREQILVKHAQEELPPPPPQKKRQITVDSEI RKRLDVDITELHSWITRSEAVLQSPEFAIFRKEGNFSDLKEKVNAIEREKAEKFRKLQDA SRSAQALVEQMVNEGVNADSIKQASEQLNSRWIEFCQLLSERLNWLEYQNNIIAFYNQLQ QLEQMTTTAENWLKIQPTTPSEPTAIKSQLKICKDEVNRLSDLQPQIERLKIQSIALKEK GQGPMFLDADFVAFTNHFKQVFSDVQAREKELQTIFDTLPPMRYQETMSAIRTWVQQSET KLSIPQLSVTDYEIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQS EFEEIEGRWKKLSSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEVDVFLKEEWPALGD SEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAEPEFASRLETELKELNTQWDH MCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLERDFEYKTPDELQKAVEEM KRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTTNYQWLCTRLNGKCKT LEEVWACWHELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISEVLDSLENLMRHSEDNP NQIRILAQTLTDGGVMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLH LIQESLTFIDKQLAAYIADKVDAAQMPQEAQKIQSDLTSHEISLEEMKKHNQGKEAAQRV LSQIDVAQKKLQDVSMKFRLFQKPANFEQRLQESKMILDEVKMHLPALETKSVEQEVVQS QLNHCVNLYKSLSEVKSEVEMVIKTGRQIVQKKQTENPKELDERVTALKLHYNELGAKVT ERKQQLEKCLKLSRKMRKEMNVLTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKE IEKQKVHLKSITEVGEALKTVLGKKETLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKH METFDQNVDHITKWIIQADTLLDESEKKKPQQKEDVLKRLKAELNDIRPKVDSTRDQAAN LMANRGDHCRKLVEPQISELNHRFAAISHRIKTGKASIPLKELEQFNSDIQKLLEPLEAE IQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRITDERKREEIKIKQQLLQTKHNA LKDLRSQRRKKALEISHQWYQYKRQADDLLKCLDDIEKKLASLPEPRDERKIKEIDRELQ KKKEELNAVRRQAEGLSEDGAAMAVEPTQIQLSKRWREIESKFAQFRRLNFAQIHTVREE TMMVMTEDMPLEISYVPSTYLTEITHVSQALLEVEQLLNAPDLCAKDFEDLFKQEESLKN IKDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFD RSVEKWRRFHYDIKIFNQWLTEAEQFLRKTQIPENWEHAKYKWYLKELQDGIGQRQTVVR TLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQKNILSEFQRDL NEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQGILKQLNETGGPVLVS APISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKDLGQLEKKLEDLEEQLNHL LLWLSPIRNQLEIYNQPNQEGPFDVKETEIAVQAKQPDVEEILSKGQHLYKEKPATQPVK RKLEDLSSEWKAVNRLLQELRAKQPDLAPGLTTIGASPTQTVTLVTQPVVTKETAISKLE MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM EQLNNSFPSSRGRNTPGKPMREDTM
experiment.sample.molecule[0].mw100.208
experiment.sample.molecule[0].total_mw100.208
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.nameNaP 10 mM, NaCl 500 mM, EDTA 1 mM, Glycerol 2%
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameConformation of R8-15 human dystrophin fragment
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressFrance
experiment.contributor[0].affiliation[0].full_nameUniversity of Lorraine
experiment.contributor[0].affiliation[0].webpagehttp://welcome.univ-lorraine.fr/
experiment.contributor[0].contributor_nameRaphael
experiment.contributor[0].contributor_surnameDos Santos Morais
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-09-23
experiment.storage_temperaturenull
experiment.cell_temperature15.0
experiment.exposure_time1.5
experiment.number_of_frames38
experiment.wavelength0.1033
experiment.sample_detector_distance1.8
experiment.concentration_minnull
experiment.concentration_maxnull
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.062
experiment.s_max6.145
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDFW4_fit1_model1_img.png
fits[0].models[0].softwareCustom in-house
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_versionnull
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDFW4_fit1_model1.pdb
fits[0].models[0].model_mw96.13
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user427
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/R8-15_fixed_fit_img.png
fits[0].softwareCRYSOL
fits[0].chi_square_value1.819
fits[0].p_value0.0
fits[0].fit_residual_plotnull
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDFW4_fit1.fit
fits[0].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/R8-15.HM.realigned_1_324_AAfittedww.log
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version4.6
i0_calibration_standardnull
descriptionSEC-SAXS was performed at 15°C using the following parameters: Column: BioSEC5-500Å (4.6 mm id * 300 mm); Flow rate: 0.2 mL/min; Sample injection concentration: 4 mg/mL; Injection volume: 60μL. The data were collected through the SEC peak of the protein as a series of 38 x 1.5 second exposures. The experimental molecular weight was determined from the volume of correlation, Vc.
experiment_descriptionSynchrotron SAXS data from solutions of the R8-15 human dystrophin fragment in NaP 10 mM, NaCl 500 mM, EDTA 1 mM, glycerol 2%, pH 7.5 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the SWING beam line at SOLEIL (Saint-Aubin, France) using a CCD AVIEX PCCD170170 detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[]
intensity_unitarbitrary
experimental_mw88.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i00.03204
pddf_i0_errornull
guinier_i00.0327
guinier_i0_errornull
pddf_rg9.93
pddf_rg_errornull
guinier_rg10.06
guinier_rg_errornull
pddf_dmax36.0
pddf_dmax_errornull
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manifest.json:36 field values
Field pathRaw value
codeSASDFW4
statussuccess
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View the complete summary.json source
{
  "code": "SASDFW4",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "How the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids.",
    "publication": {
      "title": "How the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids.",
      "author_list": "Mias-Lucquin D, Dos Santos Morais R, Chéron A, Lagarrigue M, Winder SJ, Chenuel T, Pérez J, Appavou MS, Martel A, Alviset G, Le Rumeur E, Combet S, Hubert JF, Delalande O",
      "journal": "J Struct Biol",
      "doi": "10.1016/j.jsb.2019.107411",
      "pmid": "31689503",
      "published_date": "2019 Nov 2"
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    "status": "released",
    "submitted_date": "2019-03-30",
    "released_date": "2019-11-14"
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View the complete manifest.json source
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