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- PDB-3v2n: COMPcc in complex with fatty acids -

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Basic information

Entry
Database: PDB / ID: 3v2n
TitleCOMPcc in complex with fatty acids
ComponentsCartilage Oligomerization matrix protein (coiled-coil domain)
KeywordsPROTEIN BINDING / coiled coil fatty acids / storage
Function / homology
Function and homology information


tendon development / negative regulation of hemostasis / cartilage homeostasis / musculoskeletal movement / vascular associated smooth muscle contraction / ECM proteoglycans / endochondral bone growth / chondrocyte development / vascular associated smooth muscle cell development / bone growth ...tendon development / negative regulation of hemostasis / cartilage homeostasis / musculoskeletal movement / vascular associated smooth muscle contraction / ECM proteoglycans / endochondral bone growth / chondrocyte development / vascular associated smooth muscle cell development / bone growth / BMP binding / chondrocyte proliferation / growth plate cartilage development / Integrin cell surface interactions / vitamin D binding / positive regulation of chondrocyte proliferation / muscle cell development / regulation of bone mineralization / bone morphogenesis / heparan sulfate proteoglycan binding / collagen fibril organization / cartilage development / limb development / proteoglycan binding / artery morphogenesis / extracellular matrix structural constituent / neuromuscular process / skin development / bone mineralization / fibronectin binding / response to unfolded protein / protein secretion / BMP signaling pathway / collagen binding / ossification / skeletal system development / protein homooligomerization / multicellular organism growth / platelet aggregation / protein processing / cellular senescence / blood coagulation / integrin binding / heparin binding / regulation of gene expression / protease binding / collagen-containing extracellular matrix / calcium ion binding / negative regulation of apoptotic process / apoptotic process / protein-containing complex / extracellular space / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain / Thrombospondin-5, coiled coil region / : / Cartilage oligomeric matrix protein / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain / Thrombospondin-5, coiled coil region / : / Cartilage oligomeric matrix protein / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Calcium-binding EGF domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand calcium-binding domain. / Concanavalin A-like lectin/glucanase domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MYRISTIC ACID / Cartilage oligomeric matrix protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStetefeld, J.
CitationJournal: Plos One / Year: 2012
Title: The pentameric channel of COMPcc in complex with different fatty acids.
Authors: MacFarlane, A.A. / Orriss, G. / Okun, N. / Meier, M. / Klonisch, T. / Khajehpour, M. / Stetefeld, J.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cartilage Oligomerization matrix protein (coiled-coil domain)
B: Cartilage Oligomerization matrix protein (coiled-coil domain)
C: Cartilage Oligomerization matrix protein (coiled-coil domain)
D: Cartilage Oligomerization matrix protein (coiled-coil domain)
E: Cartilage Oligomerization matrix protein (coiled-coil domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4396
Polymers26,2105
Non-polymers2281
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12200 Å2
ΔGint-114 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.356, 49.391, 54.820
Angle α, β, γ (deg.)90.000, 103.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Cartilage Oligomerization matrix protein (coiled-coil domain)


Mass: 5242.078 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: COMPcc / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9R0G6*PLUS
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.05 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.25 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 164578 / Num. obs: 17542 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.8 Å2

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Processing

Software
NameVersionClassificationNB
CNS1.3refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MZ9

1mz9


Resolution: 1.8→20.58 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1109552 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1533 8.7 %RANDOM
Rwork0.211 ---
obs-17542 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.8197 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 127.61 Å2 / Biso mean: 29.4906 Å2 / Biso min: 13.93 Å2
Baniso -1Baniso -2Baniso -3
1-9.99 Å20 Å21.93 Å2
2---10.12 Å2-0 Å2
3---0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.8→20.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 16 352 2178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d15.6
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 87 3 %
Rwork0.259 2819 -
all-2906 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6myr.parmyr.top

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