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- PDB-3fby: The crystal structure of the signature domain of cartilage oligom... -

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Basic information

Entry
Database: PDB / ID: 3fby
TitleThe crystal structure of the signature domain of cartilage oligomeric matrix protein.
ComponentsCartilage oligomeric matrix protein
KeywordsCELL ADHESION / COMP / cartilage oligomeric matrix protein / signature domain / E4T3C5 / Disease mutation / Dwarfism / EGF-like domain / Glycoprotein / Secreted
Function / homology
Function and homology information


tendon development / negative regulation of hemostasis / cartilage homeostasis / vascular associated smooth muscle contraction / chondrocyte development / vascular associated smooth muscle cell development / musculoskeletal movement / BMP binding / chondrocyte proliferation / growth plate cartilage development ...tendon development / negative regulation of hemostasis / cartilage homeostasis / vascular associated smooth muscle contraction / chondrocyte development / vascular associated smooth muscle cell development / musculoskeletal movement / BMP binding / chondrocyte proliferation / growth plate cartilage development / positive regulation of chondrocyte proliferation / regulation of bone mineralization / heparan sulfate proteoglycan binding / collagen fibril organization / limb development / proteoglycan binding / extracellular matrix structural constituent / artery morphogenesis / skin development / bone mineralization / protein secretion / ECM proteoglycans / response to unfolded protein / Integrin cell surface interactions / BMP signaling pathway / collagen binding / extracellular matrix / animal organ morphogenesis / skeletal system development / protein processing / multicellular organism growth / protein homooligomerization / platelet aggregation / cellular senescence / integrin binding / heparin binding / regulation of gene expression / protease binding / : / apoptotic process / calcium ion binding / negative regulation of apoptotic process / protein-containing complex / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
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/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 / Laminin / Laminin / 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. / Jelly Rolls - #200 / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Ribbon / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cartilage oligomeric matrix protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsTan, K. / Lawler, J.
CitationJournal: Faseb J. / Year: 2009
Title: The crystal structure of the signature domain of cartilage oligomeric matrix protein: implications for collagen, glycosaminoglycan and integrin binding.
Authors: Tan, K. / Duquette, M. / Joachimiak, A. / Lawler, J.
History
DepositionNov 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cartilage oligomeric matrix protein
B: Cartilage oligomeric matrix protein
C: Cartilage oligomeric matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,590104
Polymers183,8573
Non-polymers6,734101
Water1086
1
A: Cartilage oligomeric matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,71737
Polymers61,2861
Non-polymers2,43136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cartilage oligomeric matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,22733
Polymers61,2861
Non-polymers1,94132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cartilage oligomeric matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,64734
Polymers61,2861
Non-polymers2,36133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)192.242, 192.242, 145.681
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Cartilage oligomeric matrix protein / COMP


Mass: 61285.578 Da / Num. of mol.: 3 / Fragment: UNP residues 225-757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMP, COMP(cartilage oligomeric matrix protein) / Plasmid: pMT/BIP/V5-HIS A / Production host: Drosophila (fruit flies) / Strain (production host): Drosophila S2 cell / References: UniProt: P49747

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 104 molecules

#5: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 88 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM Ammonium Sulfate, 0.05M Bis-Tris, 30% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2008 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.15→39 Å / Num. all: 53862 / Num. obs: 53862 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 15.4
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5338 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREP(CCP4)phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UX6 AND 1YO8

1ux6

1yo8


Resolution: 3.15→39 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.884 / SU B: 35.467 / SU ML: 0.296 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 2735 5.1 %RANDOM
Rwork0.2023 ---
all0.2054 51068 --
obs0.2054 51068 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 3.15→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12483 0 288 6 12777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02112974
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.94817682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24651602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99125.649786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.007151950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.04515102
X-RAY DIFFRACTIONr_chiral_restr0.1190.21815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110566
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4931.57974
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.047212828
X-RAY DIFFRACTIONr_scbond_it1.70935000
X-RAY DIFFRACTIONr_scangle_it2.9494.54854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 187 -
Rwork0.313 3652 -
obs-3839 97.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.48920.3279-0.47511.3483-0.41721.1250.0315-0.01030.34590.20460.0633-0.038-0.1974-0.0814-0.09480.1128-0.01670.05590.0331-0.03250.3203-76.71650.986-3.726
22.296-0.2070.07931.1501-0.03241.72780.04750.1169-0.1761-0.0908-0.12140.37570.0827-0.61580.07390.09380.0048-0.06420.4715-0.09890.1498-29.1384.553.186
31.52650.1035-0.18762.8698-0.1081.10710.0376-0.2022-0.24780.4749-0.0369-0.50690.13750.2803-0.00070.1638-0.0043-0.11540.11380.01280.1944-14.27170.0998.397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A223 - 757
2X-RAY DIFFRACTION2B223 - 757
3X-RAY DIFFRACTION3C223 - 757

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