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- PDB-1fbm: ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1fbm
TitleASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN IN COMPLEX WITH ALL-TRANS RETINOL
ComponentsPROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
KeywordsCELL ADHESION / EXTRACELLULAR MATRIX PROTEIN / ASSEMBLY DOMAIN / CARTILAGE / OLIGOMERIC MATRIX PROTEIN / GLYCOPROTEIN / RETINOL-COMPLEX
Function / homology
Function and homology information


cartilage homeostasis / Integrin cell surface interactions / tendon development / negative regulation of hemostasis / ECM proteoglycans / musculoskeletal movement / vascular associated smooth muscle contraction / vascular associated smooth muscle cell development / bone growth / chondrocyte development ...cartilage homeostasis / Integrin cell surface interactions / tendon development / negative regulation of hemostasis / ECM proteoglycans / musculoskeletal movement / vascular associated smooth muscle contraction / vascular associated smooth muscle cell development / bone growth / chondrocyte development / BMP binding / chondrocyte proliferation / endochondral bone growth / growth plate cartilage development / vitamin D binding / positive regulation of chondrocyte proliferation / muscle cell development / regulation of bone mineralization / heparan sulfate proteoglycan binding / collagen fibril organization / bone morphogenesis / cartilage development / limb development / proteoglycan binding / neuromuscular process / artery morphogenesis / skin development / extracellular matrix structural constituent / bone mineralization / fibronectin binding / response to unfolded protein / protein secretion / BMP signaling pathway / collagen binding / ossification / skeletal system development / protein homooligomerization / multicellular organism growth / protein processing / platelet aggregation / cellular senescence / blood coagulation / integrin binding / heparin binding / regulation of gene expression / collagen-containing extracellular matrix / protease binding / apoptotic process / calcium ion binding / negative regulation of 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 / Concanavalin A-like lectin/glucanase domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RETINOL / Cartilage oligomeric matrix protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsGuo, Y. / Bozic, D. / Malashkevich, V.N. / Kammerer, R.A. / Schulthess, T.
Citation
Journal: EMBO J. / Year: 1998
Title: All-trans retinol, vitamin D and other hydrophobic compounds bind in the axial pore of the five-stranded coiled-coil domain of cartilage oligomeric matrix protein.
Authors: Guo, Y. / Bozic, D. / Malashkevich, V.N. / Kammerer, R.A. / Schulthess, T.
#1: Journal: Proteins / Year: 1996
Title: Crystallization and Preliminary Crystallographic Study of the Pentamerizing Domain from Cartilage Oligomeric Matrix Protein: a Five-stranded Alpha-helical Bundle.
Authors: Efimov, V.P. / Engel, J. / Malashkevich, V.N.
#2: Journal: Science / Year: 1996
Title: The Crystal Structure of a Five-stranded Coiled Coil in COMP: a Prototype Ion Channel?
Authors: Malashkevich, V.N. / Kammerer, R.A. / Efimov, V.P. / Schulthess, T. / Engel, J.
History
DepositionJul 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.5Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
B: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
C: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
D: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
E: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7826
Polymers26,4965
Non-polymers2861
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-120 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.470, 49.470, 54.980
Angle α, β, γ (deg.)90.00, 103.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN) / COMP


Mass: 5299.129 Da / Num. of mol.: 5 / Fragment: ASSEMBLY DOMAIN
Source method: isolated from a genetically manipulated source
Details: PENTAMERIC COILED-COIL / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: CARTILAGE / Plasmid: PET-3B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P35444
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 35.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: COMPcc (16 mg/ml) in 20 mM sodium phosphate, 200 mM NaCl (pH 7.5) precipitant: 7-8% PEG 8000, 50 mM sodium cacodylate (pH 6.0), 50 mM sodium acetate, 50 mM calcium acetate , VAPOR DIFFUSION, ...Details: COMPcc (16 mg/ml) in 20 mM sodium phosphate, 200 mM NaCl (pH 7.5) precipitant: 7-8% PEG 8000, 50 mM sodium cacodylate (pH 6.0), 50 mM sodium acetate, 50 mM calcium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 20.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
27-8 %PEG80001reservoir
350 mMsodium cacodylate1reservoir
450 mMsodium acetate1reservoir
550 mMcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→3 Å / Num. all: 5464 / Num. obs: 5464 / % possible obs: 86 % / Redundancy: 3.71 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.132
Reflection shellResolution: 2.7→3 Å / Num. unique all: 5464 / % possible all: 87.6
Reflection
*PLUS
Num. measured all: 20313
Reflection shell
*PLUS
% possible obs: 87.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
AMoREphasing
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.7→3 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.195 --
all0.195 5464 -
Rfree-0 -
obs-5464 87.6 %
Refinement stepCycle: LAST / Resolution: 2.7→3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 21 152 2003
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d18.68
X-RAY DIFFRACTIONx_improper_angle_d1.1
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.68
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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