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- PDB-2ka3: Structure of EMILIN-1 C1Q-like domain -

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Basic information

Entry
Database: PDB / ID: 2ka3
TitleStructure of EMILIN-1 C1Q-like domain
ComponentsEMILIN-1
KeywordsSTRUCTURAL PROTEIN / EMILIN-1 / C1Q-like domain / Homotrimeric protein complex / Beta-sandwich / Cell adhesion / extracellular matrix
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 alpha4-beta1 complex / integrin binding involved in cell-matrix adhesion / elastic fiber assembly / positive regulation of defense response to bacterium / negative regulation of vascular endothelial growth factor signaling pathway ...EMILIN complex / negative regulation of collagen fibril organization / negative regulation of macrophage migration / extracellular matrix constituent conferring elasticity / negative regulation of cell activation / integrin alpha4-beta1 complex / integrin binding involved in cell-matrix adhesion / elastic fiber assembly / positive regulation of defense response to bacterium / negative regulation of vascular endothelial growth factor signaling pathway / 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 SMAD protein signal transduction / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of blood coagulation / negative regulation of angiogenesis / cell-matrix adhesion / negative regulation of cell migration / 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 / collagen-containing extracellular matrix / 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 / Collagen triple helix repeat ...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, restrained energy minimization
AuthorsVerdone, G. / Corazza, A. / Colebrooke, S.A. / Cicero, D.O. / Eliseo, T. / Boyd, J. / Doliana, R. / Fogolari, F. / Viglino, P. / Colombatti, A. ...Verdone, G. / Corazza, A. / Colebrooke, S.A. / Cicero, D.O. / Eliseo, T. / Boyd, J. / Doliana, R. / Fogolari, F. / Viglino, P. / Colombatti, A. / Campbell, I.D. / Esposito, G.
Citation
Journal: J.Biomol.Nmr / Year: 2009
Title: NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1
Authors: Verdone, G. / Corazza, A. / Colebrooke, S.A. / Cicero, D. / Eliseo, T. / Boyd, J. / Doliana, R. / Fogolari, F. / Viglino, P. / Colombatti, A. / Campbell, I.D. / Esposito, G.
#1: Journal: J.Biol.Chem. / Year: 2008
Title: The solution structure of EMILIN1 globular C1q domain reveals a disordered insertion necessary for interaction with the alpha4beta1 integrin
Authors: Verdone, G. / Doliana, R. / Corazza, A. / Colebrooke, S.A. / Spessotto, P. / Bot, S. / Bucciotti, F. / Capuano, A. / Silvestri, A. / Viglino, P. / Campbell, I.D. / Colombatti, A. / Esposito, G.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 2000
Title: Self-assembly and supramolecular organization of EMILIN
Authors: Mongiat, M. / Mungiguerra, G. / Bot, S. / Mucignat, M.T. / Giacomello, E. / Doliana, R. / Colombatti, A.
History
DepositionOct 30, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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 #1closest to the average

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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, UNP residues 867-1016
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EM1, EMILIN1 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Variant (production host): M15 cells / 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
10.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, 95% H2O/5% D2O95% H2O/5% D2O
21.0mM [U-100% 15N; 70% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, 95% H2O/5% D2O95% H2O/5% D2O
31.0mM [U-100% 13C; U-100% 15N] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, 95% H2O/5% D2O95% H2O/5% D2O
40.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, in polyacrylamide gel (Acrylamide:bisacrylamide=4%:3%), 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMC1q[U-100% 13C; U-100% 15N; 80% 2H]1
20 mMphosphate buffer1
100 mMsodium chloride1
0.02 w/vNaN31
1.0 mMC1q[U-100% 15N; 70% 2H]2
20 mMphosphate buffer2
100 mMsodium chloride2
0.02 w/vNaN32
1.0 mMC1q[U-100% 13C; U-100% 15N]3
20 mMphosphate buffer3
100 mMsodium chloride3
0.02 w/vNaN33
0.6 mMC1q[U-100% 13C; U-100% 15N; 80% 2H]4
20 mMphosphate buffer4
100 mMsodium chloride4
0.02 w/vNaN34
Sample conditionsIonic strength: 0.15 / pH: 7.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
GE OMEGAGEOMEGA6002
GE OMEGAGEOMEGA7503
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Bruker Biospincollection
Felix2.3Accelrys Software Inc.data analysis
XEASY1.2Bartels et al.data analysis
Sparky3.106Goddarddata analysis
X-PLOR2.9.9Brungerrefinement
NAMD2.6b2Schulten et al.refinement
RefinementMethod: simulated annealing, restrained energy minimization / 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. The structures were further refined in order to improve the quality of backbone geometry. For this purpose 2,000 steps of restrained energy minimization were performed using the program NAMD (Kale et al. 1999). The forcefield used is CHARMM v.27b (MacKerell et al. 1998) with the CMAP correction (MacKerell et al., 2004). Since the program does not readily incorporate RDC derived restraints, the z co-ordinates of the backbone amide N and H atoms were restrained at their starting values. Only NOE derived restraints and chemical-shift-derived dihedral angle restraints (with unequivocal secondary structure definition) were imposed.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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