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- PDB-2oii: Structure of EMILIN-1 C1q-like domain -

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Basic information

Entry
Database: PDB / ID: 2oii
TitleStructure of EMILIN-1 C1q-like domain
ComponentsEMILIN-1
KeywordsSTRUCTURAL PROTEIN / Emilin-1 / C1q-like domain / homotrimeric protein complex / beta-sandwich
Function / homology
Function and homology information


EMILIN complex / negative regulation of collagen fibril organization / negative regulation of macrophage migration / extracellular matrix constituent conferring elasticity / negative regulation of cell activation / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / elastic fiber assembly / negative regulation of vascular endothelial growth factor signaling pathway / positive regulation of defense response to bacterium ...EMILIN complex / negative regulation of collagen fibril organization / negative regulation of macrophage migration / extracellular matrix constituent conferring elasticity / negative regulation of cell activation / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / elastic fiber assembly / negative regulation of vascular endothelial growth factor signaling pathway / positive regulation of defense response to bacterium / negative regulation of collagen biosynthetic process / positive regulation of extracellular matrix assembly / collagen trimer / positive regulation of platelet aggregation / aortic valve morphogenesis / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / cell adhesion mediated by integrin / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of SMAD protein signal transduction / positive regulation of blood coagulation / negative regulation of angiogenesis / negative regulation of cell migration / cell-matrix adhesion / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / regulation of blood pressure / positive regulation of angiogenesis / cell migration / regulation of cell population proliferation / : / molecular adaptor activity / cell adhesion / positive regulation of apoptotic process / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
EMI domain / EMI domain / EMI domain profile. / : / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily ...EMI domain / EMI domain / EMI domain profile. / : / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVerdone, G. / Colebrooke, S.A. / Corazza, A. / Cicero, D.O. / Eliseo, T. / Viglino, P. / Campbell, I.D. / Colombatti, A. / Esposito, G.
Citation
Journal: To be Published
Title: The solution structure of the C-terminal domain of EMILIN-1
Authors: Verdone, G. / Colebrooke, S.A. / Corazza, A. / Cicero, D.O. / Eliseo, T. / Viglino, P. / Campbell, I.D. / Colombatti, A. / Esposito, G.
#1: Journal: J.Biomol.NMR / Year: 2004
Title: Sequence-specific backbone NMR assignments for the C-terminal globular domain of EMILIN-1
Authors: Verdone, G. / Colebrooke, S.A. / Boyd, J. / Viglino, P. / Corazza, A. / Doliana, R. / Mungiguerra, G. / Colombatti, A. / Esposito, G. / Campbell, I.D.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: Self-assembly and supramolecular organization of Emillin
Authors: Mongiat, M. / Mungiguerra, G. / Bot, S. / Mucignat, M.T. / Giacomello, E. / Doliana, R. / Colombatti, A.
History
DepositionJan 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EMILIN-1
B: EMILIN-1
C: EMILIN-1


Theoretical massNumber of molelcules
Total (without water)51,6823
Polymers51,6823
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein EMILIN-1 / Elastin microfibril interface-located protein 1 / Elastin microfibril interfacer 1


Mass: 17227.217 Da / Num. of mol.: 3 / Fragment: C-Terminal domain, C1q domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMILIN1, EMI / Cell line (production host): M15 cells / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6C2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-NOESY-HSQC
124IPAP 1H,15N-HSQC
134TROSY 1H-15N HSQC
1443D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM of C1q U-13C, U-15N and U-80% 2H, 20 mM Phosphate buffer, 100 mM NaCl, 0.02%(w/v)NaN3, 95% H2O, 5% D2O95% H2O/5% D2O
21 mM of C1q U-15N and U-70% 2H, 20 mM Phosphate buffer, 100 mM NaCl, 0.02%(w/v)NaN3, 95% H2O, 5% D2O95% H2O/5% D2O
31 mM of C1q U-13C, U-15N, 20 mM Phosphate buffer, 100 mM NaCl, 0.02%(w/v)NaN3, 95% H2O, 5% D2O95% H2O/5% D2O
40.6 mM of C1q U-13C, U-15N and U-80% 2H, 20 mM Phosphate buffer, 100 mM NaCl, 0.02%(w/v)NaN3 in polyacrylamide gel (acrylamide:bisacrylamide = 4%:3%), 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 20 mM Phosphate buffer, 100 mM NaCl / pH: 7.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
GE OMEGAGEOMEGA6002
GE OMEGAGEOMEGA7503
Bruker AVANCEBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
Felix2.3Accelrysdata analysis
XEASY1.2Bartels, C. et al.data analysis
Sparky3.106Goddard, T.D. et al.data analysis
X-PLOR2.9.9Nilges, M.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was obtained as the refinement of the homology model of emilin trimer C1q-domain based on the chain A of ACRP-30 crystal structure. The quaternary structure of C1q-domain ...Details: The structure was obtained as the refinement of the homology model of emilin trimer C1q-domain based on the chain A of ACRP-30 crystal structure. The quaternary structure of C1q-domain homology model was built with a three-fold simmetry axis. The region between Tyr927 and Gly945 was not modelled and was not included in the refinement. Dihedral angles (obtained with TALOS), RDC values, NOE constraints were used in the refinement procedure.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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