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- PDB-5ms9: Solution structure of Human Fibrillin-1 EGF2-EGF3-Hybrid1-cbEGF1 ... -

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Basic information

Entry
Database: PDB / ID: 5ms9
TitleSolution structure of Human Fibrillin-1 EGF2-EGF3-Hybrid1-cbEGF1 four domain fragment
ComponentsFibrillin-1
KeywordsSTRUCTURAL PROTEIN / fibrillin EGF hybrid Extracellular
Function / homology
Function and homology information


post-embryonic eye morphogenesis / extracellular matrix constituent conferring elasticity / sequestering of BMP in extracellular matrix / sequestering of TGFbeta in extracellular matrix / microfibril / embryonic eye morphogenesis / negative regulation of osteoclast development / Elastic fibre formation / metanephros development / camera-type eye development ...post-embryonic eye morphogenesis / extracellular matrix constituent conferring elasticity / sequestering of BMP in extracellular matrix / sequestering of TGFbeta in extracellular matrix / microfibril / embryonic eye morphogenesis / negative regulation of osteoclast development / Elastic fibre formation / metanephros development / camera-type eye development / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / extracellular matrix structural constituent / cell adhesion mediated by integrin / lung alveolus development / negative regulation of osteoclast differentiation / TGF-beta receptor signaling activates SMADs / basement membrane / anatomical structure morphogenesis / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / Degradation of the extracellular matrix / extracellular matrix / skeletal system development / Post-translational protein phosphorylation / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / heparin binding / heart development / gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / calcium ion binding / protein-containing complex binding / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Fibrillin 1, unique N-terminal domain / : / Fibrillin 1 unique N-terminal domain / Fibrillin, first EGF domain / TB domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / EGF domain / EGF domain ...Fibrillin 1, unique N-terminal domain / : / Fibrillin 1 unique N-terminal domain / Fibrillin, first EGF domain / TB domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / EGF domain / EGF domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRobertson, I.B. / Redfield, C. / Handford, P.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M009831/1 United Kingdom
Citation
Journal: Structure / Year: 2017
Title: The N-Terminal Region of Fibrillin-1 Mediates a Bipartite Interaction with LTBP1.
Authors: Robertson, I.B. / Dias, H.F. / Osuch, I.H. / Lowe, E.D. / Jensen, S.A. / Redfield, C. / Handford, P.A.
#1: Journal: Biomol NMR Assign / Year: 2014
Title: 1H, 13C and 15N resonance assignments for the fibrillin-1 EGF2-EGF3-hybrid1-cbEGF1 four-domain fragment.
Authors: Robertson, I.B. / Osuch, I. / Yadin, D.A. / Handford, P.A. / Jensen, S.A. / Redfield, C.
History
DepositionJan 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibrillin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9112
Polymers18,8711
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11700 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Fibrillin-1


Mass: 18870.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBN1, FBN / Production host: Escherichia coli (E. coli) / References: UniProt: P35555
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
122isotropic13D 1H-15N NOESY
133isotropic13D 1H-13C NOESY
143isotropic23D 1H-13C NOESY aromatic
153isotropic43D 1H-13C NOESY
173isotropic13D 1H-15N NOESY
162isotropic5IPAP
184anisotropic5IPAP
195anisotropic5IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM fibrillin-1 e2cb1, 5 mM CALCIUM ION, 100% D2OUnlabelled100% D2O
solution21 mM [U-15N] fibrillin-1 e2cb1, 5 mM CALCIUM ION, 95% H2O/5% D2ON1595% H2O/5% D2O
solution31 mM [U-13C; U-15N] fibrillin-1 e2cb1, 5 mM CALCIUM ION, 95% H2O/5% D2On15-c1395% H2O/5% D2O
bicelle41 mM [U-15N] fibrillin-1 e2cb1, 5 mM CALCIUM ION, 4 % bicelles, 90% H2O/10% D2Obicelles90% H2O/10% D2O
gel solution51 mM [U-15N] fibrillin-1 e2cb1, 5 mM CALCIUM ION, 2.2 % peg-hexanol solution, 90% H2O/10% D2Opeg-hexanol liquid crystal90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMfibrillin-1 e2cb1natural abundance1
5 mMCALCIUM IONnatural abundance1
1 mMfibrillin-1 e2cb1[U-15N]2
5 mMCALCIUM IONnatural abundance2
1 mMfibrillin-1 e2cb1[U-13C; U-15N]3
5 mMCALCIUM IONnatural abundance3
1 mMfibrillin-1 e2cb1[U-15N]4
5 mMCALCIUM IONnatural abundance4
4 %bicellesnatural abundance4
1 mMfibrillin-1 e2cb1[U-15N]5
5 mMCALCIUM IONnatural abundance5
2.2 %peg-hexanol solutionnatural abundance5
Sample conditionsIonic strength: 15 mM / Label: ph 5.4 / pH: 5.4 / Pressure: 1 atm / Temperature: 268 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built OMEGAHome-builtOMEGA9501
Home-built OMEGAHome-builtOMEGA7502
Home-built OMEGAHome-builtOMEGA6005
Bruker AVANCEBrukerAVANCE5004

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
Refinement
MethodSoftware ordinal
simulated annealing1
simulated annealing2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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