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- PDB-2m74: 1H, 13C and 15N assignments of the four N-terminal domains of hum... -

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Basic information

Entry
Database: PDB / ID: 2m74
Title1H, 13C and 15N assignments of the four N-terminal domains of human fibrillin-1
ComponentsFibrillin-1
KeywordsSTRUCTURAL PROTEIN
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 / Laminin / Coagulation Factor Xa inhibitory site / Laminin / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsYadin, D.A. / Robertson, I.B. / Jensen, S.A. / Handford, P.A. / Redfield, C.
CitationJournal: Structure / Year: 2013
Title: Structure of the Fibrillin-1 N-Terminal Domains Suggests that Heparan Sulfate Regulates the Early Stages of Microfibril Assembly.
Authors: Yadin, D.A. / Robertson, I.B. / McNaught-Davis, J. / Evans, P. / Stoddart, D. / Handford, P.A. / Jensen, S.A. / Redfield, C.
History
DepositionApr 17, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibrillin-1


Theoretical massNumber of molelcules
Total (without water)14,1201
Polymers14,1201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fibrillin-1


Mass: 14120.085 Da / Num. of mol.: 1
Fragment: FUN-EGF3 region of fibrillin-1, UNP residues 45-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Cells were also transformed with the pREP4 plasmid, enabling inducible expression
Gene: FBN, FBN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P35555

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Chemical shift assignments for the FUN-EGF3 recombinant fragment of human fibrillin-1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1422D 1H-1H TOCSY
1522D DQF-COSY
1622D 1H-1H NOESY
1733D HNCA
1833D (H)CC(CO)NH
1933D HNCO
11033D HN(CA)CO
11142D 1H-13C HSQC aliphatic
11243D (H)CCH-TOCSY
11343D 1H-13C NOESY aliphatic
11442D 1H-13C HSQC aromatic
11513D 1H-15N HSQC-NOESY-HSQC
11612D 1H-15N HMQC-J
21752D 1H-15N IPAP-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 15N] FUN-EGF3, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-99% 15N] FUN-EGF3, 100% D2O100% D2O
31.5 mM [U-99% 13C; U-99% 15N] FUN-EGF3, 95% H2O/5% D2O95% H2O/5% D2O
41.5 mM [U-99% 13C; U-99% 15N] FUN-EGF3, 100% D2O100% D2O
50.5 mM [U-99% 13C; U-99% 15N] FUN-EGF3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMFUN-EGF3-1[U-99% 15N]1
0.5 mMFUN-EGF3-2[U-99% 15N]2
1.5 mMFUN-EGF3-3[U-99% 13C; U-99% 15N]3
1.5 mMFUN-EGF3-4[U-99% 13C; U-99% 15N]4
0.5 mMFUN-EGF3-5[U-99% 13C; U-99% 15N]5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 5.40 1 atm298 K
20 5.40 1 atm308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
home built home built using GE Omega softwareHome-builthome built using GE Omega software7501
home built home built using GE Omega softwareHome-builthome built using GE Omega software6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeJune 2006 Sun SolarisDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpN_Analysis2.1.5CCPNpeak picking
CcpN_Analysis2.1.5CCPNchemical shift assignment
X-PLOR3.8Brungerstructure solution
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Clorerefinement
TALOS+3.3Cornilescu, Delaglio and Baxdata analysis
Felix2.3Accelrys Software Inc.data analysis
X-PLORrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: An ensemble of 100 structures was generated. Floating chirality of prochiral groups was used for stereospecific assignment., An initial ensemble of 200 structures was using simulated ...Details: An ensemble of 100 structures was generated. Floating chirality of prochiral groups was used for stereospecific assignment., An initial ensemble of 200 structures was using simulated annealing from an extended template using NOE-derived distance restraints with stereospecific assignments. Coordinates of the 10 lowest-energy structures were then used as templates for refinement calculations, including the 'Rama' and 'HBDB' database potentials. The resulting 10 lowest-energy structures were then refined further using RDCs. Separate alignment tensors were used for the two halves of the molecule ('ne1' and 'e2e3'). Alignment tensor parameters were estimated using partially refined structures. The 20 lowest-structures from the final ensemble of 200 structures were selected as the representative structure ensemble.
NMR constraintsNOE constraints total: 2599 / NOE intraresidue total count: 890 / NOE long range total count: 632 / NOE medium range total count: 231 / NOE sequential total count: 571 / Hydrogen bond constraints total count: 30 / Protein chi angle constraints total count: 10 / Protein other angle constraints total count: 2 / Protein phi angle constraints total count: 73 / Protein psi angle constraints total count: 64
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.06 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 4.785 ° / Maximum upper distance constraint violation: 0.44 Å
Torsion angle constraint violation method: Xplor-NIH simulation tools
NMR ensemble rmsDistance rms dev: 0.024 Å / Distance rms dev error: 0.001 Å

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