Integrin beta4, fragment of the cytoplasmic region that includes the final part of the connecting segment and the third and fourth FnIII domains (FnIII-3,4). Point mutant A1468R
Data type: SASBDB experimental dataStatus: PublishedCurve type: MergedLast updated: 2023-06-21T07:56:39.492710+02:00
Synchrotron SAXS data from solutions of a fragment of the cytoplasmic region of the human integrin Beta4 subunit. This fragment includes the final part of a region named the "connecting segment" the third and fourth fibronectin type III domains (FnIII-3,4). The protein contains the point mutation A1468R. Samples at different solute concentration in the range 1.5 – 11.9 mg/ml were obtained by 2-fold serial dilution and were measured.
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1. Samples, Components and Experimental Conditions Sample & Experiment
Sample 1 · Integrin beta4, fragment of the cytoplasmic region that includes the final part of the connecting segment and the third and fourth FnIII domains (FnIII-3,4). Point mutant A1468R
Concentration
1.5 – 11.9
Buffer / pH
20 mM Sodium Phosphate 150 mM NaCl 5% glycerol 3 mM DTT / 7.5
5. Experiment Description and Publication Experiment & Publication
Original Experiment Description
Synchrotron SAXS data from solutions of the integrin beta4 fragment (point mutant A1468R) in 20 mM sodium phosphate 150 mM NaCl 5% glycerol 3 mM DTT, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.5 and 11.9 mg/ml were measured at 10°C. 30 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.
Related Publication
Title
Integrin α6β4 Recognition of a Linear Motif of Bullous Pemphigoid Antigen BP230 Controls Its Recruitment to Hemidesmosomes.
Authors
Manso JA, Gómez-Hernández M, Carabias A, Alonso-García N, García-Rubio I, Kreft M, Sonnenberg A, de Pereda JM
DOI / PMID
10.1016/j.str.2019.03.016 / 31006587
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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.
20 mM Sodium Phosphate 150 mM NaCl 5% glycerol 3 mM DTT
experiment.sample.buffer.concentration_unit
mM
experiment.sample.buffer.comment
null
experiment.sample.buffer.additive
150 mM NaCl, 5% glycerol, 3 mM DTT
experiment.sample.buffer.concentration
20.0
experiment.sample.buffer.pka
null
experiment.sample.buffer.ph
7.5
experiment.sample.buffer.deuteration
null
experiment.sample.purity_method
null
experiment.sample.name
Integrin beta4, fragment of the cytoplasmic region that includes the final part of the connecting segment and the third and fourth FnIII domains (FnIII-3,4). Point mutant A1468R
Synchrotron SAXS data from solutions of a fragment of the cytoplasmic region of the human integrin Beta4 subunit. This fragment includes the final part of a region named the "connecting segment" the third and fourth fibronectin type III domains (FnIII-3,4). The protein contains the point mutation A1468R. Samples at different solute concentration in the range 1.5 – 11.9 mg/ml were obtained by 2-fold serial dilution and were measured.
experiment_description
Synchrotron SAXS data from solutions of the integrin beta4 fragment (point mutant A1468R) in 20 mM sodium phosphate 150 mM NaCl 5% glycerol 3 mM DTT, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.5 and 11.9 mg/ml were measured at 10°C. 30 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.
{
"code": "SASDDH8",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Integrin α6β4 Recognition of a Linear Motif of Bullous Pemphigoid Antigen BP230 Controls Its Recruitment to Hemidesmosomes.",
"publication": {
"title": "Integrin α6β4 Recognition of a Linear Motif of Bullous Pemphigoid Antigen BP230 Controls Its Recruitment to Hemidesmosomes.",
"author_list": "Manso JA, Gómez-Hernández M, Carabias A, Alonso-García N, García-Rubio I, Kreft M, Sonnenberg A, de Pereda JM",
"journal": "Structure",
"doi": "10.1016/j.str.2019.03.016",
"pmid": "31006587",
"published_date": "2019 Jun 4"
},
"status": "released",
"submitted_date": "2018-06-07",
"released_date": "2019-03-14"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDH8.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDH8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH8_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDH8_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDH8.sascif",
"experiment": {
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"name": "Pilatus 2M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": null,
"line_collimation": null,
"sample_path_length": null,
"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "Integrin beta-4 (1436-1666) A1468R",
"short_name": "B4 CS-FnIII-3,4",
"sequence": "GSHM LPRDY\r\nSTLTSVSSHDSRLTAGVPDTPTRLVFSRLGPTSLRVSWQEPRCERPLQGYSVEYQLLNGG\r\nELHRLNIPNPAQTSVVVEDLLPNHSYVFRVRAQSQEGWGREREGVITIESQVHPQSPLCP \r\nLPGSAFTLSTPSAPGPLVFTALSPDSLQLSWERPRRPNGDIVGYLVTCEMAQGGGPATAF\r\nRVDGDSPESRLTVPGLSENVPYKFKVQARTTEGFGPEREGIITIES",
"organism": "Homo sapiens",
"uniprot_code": "P16144",
"uniprot_range_first": 1436,
"uniprot_range_last": 1666,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAGPRPSPWARLLLAALISVSLSGTLANRCKKAPVKSCTECVRVDKDCAYCTDEMFRDRR\nCNTQAELLAAGCQRESIVVMESSFQITEETQIDTTLRRSQMSPQGLRVRLRPGEERHFEL\nEVFEPLESPVDLYILMDFSNSMSDDLDNLKKMGQNLARVLSQLTSDYTIGFGKFVDKVSV\nPQTDMRPEKLKEPWPNSDPPFSFKNVISLTEDVDEFRNKLQGERISGNLDAPEGGFDAIL\nQTAVCTRDIGWRPDSTHLLVFSTESAFHYEADGANVLAGIMSRNDERCHLDTTGTYTQYR\nTQDYPSVPTLVRLLAKHNIIPIFAVTNYSYSYYEKLHTYFPVSSLGVLQEDSSNIVELLE\nEAFNRIRSNLDIRALDSPRGLRTEVTSKMFQKTRTGSFHIRRGEVGIYQVQLRALEHVDG\nTHVCQLPEDQKGNIHLKPSFSDGLKMDAGIICDVCTCELQKEVRSARCSFNGDFVCGQCV\nCSEGWSGQTCNCSTGSLSDIQPCLREGEDKPCSGRGECQCGHCVCYGEGRYEGQFCEYDN\nFQCPRTSGFLCNDRGRCSMGQCVCEPGWTGPSCDCPLSNATCIDSNGGICNGRGHCECGR\nCHCHQQSLYTDTICEINYSAIHPGLCEDLRSCVQCQAWGTGEKKGRTCEECNFKVKMVDE\nLKRAEEVVVRCSFRDEDDDCTYSYTMEGDGAPGPNSTVLVHKKKDCPPGSFWWLIPLLLL\nLLPLLALLLLLCWKYCACCKACLALLPCCNRGHMVGFKEDHYMLRENLMASDHLDTPMLR\nSGNLKGRDVVRWKVTNNMQRPGFATHAASINPTELVPYGLSLRLARLCTENLLKPDTREC\nAQLRQEVEENLNEVYRQISGVHKLQQTKFRQQPNAGKKQDHTIVDTVLMAPRSAKPALLK\nLTEKQVEQRAFHDLKVAPGYYTLTADQDARGMVEFQEGVELVDVRVPLFIRPEDDDEKQL\nLVEAIDVPAGTATLGRRLVNITIIKEQARDVVSFEQPEFSVSRGDQVARIPVIRRVLDGG\nKSQVSYRTQDGTAQGNRDYIPVEGELLFQPGEAWKELQVKLLELQEVDSLLRGRQVRRFH\nVQLSNPKFGAHLGQPHSTTIIIRDPDELDRSFTSQMLSSQPPPHGDLGAPQNPNAKAAGS\nRKIHFNWLPPSGKPMGYRVKYWIQGDSESEAHLLDSKVPSVELTNLYPYCDYEMKVCAYG\nAQGEGPYSSLVSCRTHQEVPSEPGRLAFNVVSSTVTQLSWAEPAETNGEITAYEVCYGLV\nNDDNRPIGPMKKVLVDNPKNRMLLIENLRESQPYRYTVKARNGAGWGPEREAIINLATQP\nKRPMSIPIIPDIPIVDAQSGEDYDSFLMYSDDVLRSPSGSQRPSVSDDTGCGWKFEPLLG\nEELDLRRVTWRLPPELIPRLSASSGRSSDAEAPHGPPDDGGAGGKGGSLPRSATPGPPGE\nHLVNGRMDFAFPGSTNSLHRMTTTSAAAYGTHLSPHVPHRVLSTSSTLTRDYNSLTRSEH\nSHSTTLPRDYSTLTSVSSHDSRLTAGVPDTPTRLVFSALGPTSLRVSWQEPRCERPLQGY\nSVEYQLLNGGELHRLNIPNPAQTSVVVEDLLPNHSYVFRVRAQSQEGWGREREGVITIES\nQVHPQSPLCPLPGSAFTLSTPSAPGPLVFTALSPDSLQLSWERPRRPNGDIVGYLVTCEM\nAQGGGPATAFRVDGDSPESRLTVPGLSENVPYKFKVQARTTEGFGPEREGIITIESQDGG\nPFPQLGSRAGLFQHPLQSEYSSITTTHTSATEPFLVDGLTLGAQHLEAGGSLTRHVTQEF\nVSRTLTTSGTLSTHMDQQFFQT",
"mw": 25.691,
"total_mw": 25.691,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Sodium Phosphate 150 mM NaCl 5% glycerol 3 mM DTT",
"concentration_unit": "mM",
"comment": null,
"additive": "150 mM NaCl, 5% glycerol, 3 mM DTT",
"concentration": 20.0,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Integrin beta4, fragment of the cytoplasmic region that includes the final part of the connecting segment and the third and fourth FnIII domains (FnIII-3,4). Point mutant A1468R",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "USAL",
"address": "Salamanca, Spain",
"full_name": "La Universidad de Salamanca",
"webpage": "http://www.usal.es"
}
],
"contributor_name": "Jose M",
"contributor_surname": "de Pereda",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2013-11-26",
"storage_temperature": null,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 30,
"wavelength": 0.124,
"sample_detector_distance": 3.1,
"concentration_min": 1.5,
"concentration_max": 11.9,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.056,
"s_max": 4.45,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDH8_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.003,
"p_value": 0.665832,
"fit_residual_plot": "SASDDH8_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDH8_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/EOM_B460_A1468R_logFile_002_1.log",
"software_version": "2.1",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "Synchrotron SAXS data from solutions of a fragment of the cytoplasmic region of the human integrin Beta4 subunit. This fragment includes the final part of a region named the \"connecting segment\" the third and fourth fibronectin type III domains (FnIII-3,4). The protein contains the point mutation A1468R. Samples at different solute concentration in the range 1.5 – 11.9 mg/ml were obtained by 2-fold serial dilution and were measured.",
"experiment_description": "Synchrotron SAXS data from solutions of the integrin beta4 fragment (point mutant A1468R) in 20 mM sodium phosphate 150 mM NaCl 5% glycerol 3 mM DTT, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.5 and 11.9 mg/ml were measured at 10°C. 30 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 22.43,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 23.5,
"porod_mw_error": null,
"pddf_i0": 0.01641,
"pddf_i0_error": null,
"guinier_i0": 0.0162,
"guinier_i0_error": null,
"pddf_rg": 2.971,
"pddf_rg_error": null,
"guinier_rg": 2.781,
"guinier_rg_error": null,
"pddf_dmax": 10.9,
"pddf_dmax_error": null,
"porod_volume": 35.3,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 157,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDH8_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
