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- PDB-2v53: Crystal structure of a SPARC-collagen complex -

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Basic information

Entry
Database: PDB / ID: 2v53
TitleCrystal structure of a SPARC-collagen complex
Components
  • COLLAGEN ALPHA-1(III) CHAIN
  • SPARC
KeywordsCELL ADHESION / GLYCOSYLATED PROTEIN / GLYCOPROTEIN / IONIC CHANNEL / ION TRANSPORT / COPPER / CALCIUM / SECRETED / COLLAGEN / TRANSPORT / BASEMENT MEMBRANE / EXTRACELLULAR MATRIX
Function / homology
Function and homology information


collagen type III trimer / semicircular canal morphogenesis / aorta smooth muscle tissue morphogenesis / Scavenging by Class H Receptors / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / negative regulation of neuron migration ...collagen type III trimer / semicircular canal morphogenesis / aorta smooth muscle tissue morphogenesis / Scavenging by Class H Receptors / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / negative regulation of neuron migration / endochondral bone morphogenesis / platelet-derived growth factor binding / Extracellular matrix organization / negative regulation of immune response / layer formation in cerebral cortex / basement membrane organization / Collagen biosynthesis and modifying enzymes / peptide cross-linking / Signaling by PDGF / platelet alpha granule / platelet alpha granule membrane / tissue homeostasis / response to angiotensin / NCAM1 interactions / regulation of cell morphogenesis / extracellular matrix binding / collagen fibril organization / digestive tract development / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / MET activates PTK2 signaling / Scavenging by Class A Receptors / skin development / Syndecan interactions / regulation of synapse organization / positive regulation of Rho protein signal transduction / SMAD binding / negative regulation of endothelial cell proliferation / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / chondrocyte differentiation / Integrin cell surface interactions / Nuclear signaling by ERBB4 / supramolecular fiber organization / collagen binding / response to cytokine / endocytic vesicle lumen / positive regulation of endothelial cell migration / transforming growth factor beta receptor signaling pathway / negative regulation of angiogenesis / platelet alpha granule lumen / cell-matrix adhesion / integrin-mediated signaling pathway / cellular response to amino acid stimulus / lung development / wound healing / response to radiation / cerebral cortex development / platelet activation / multicellular organism growth / nuclear matrix / neuron migration / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / Platelet degranulation / heart development / protease binding / fibroblast proliferation / : / in utero embryonic development / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / calcium ion binding / cell surface / extracellular space / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
SPARC / Osteonectin-like, conserved site / SPARC/Testican, calcium-binding domain / Osteonectin domain signature 1. / Osteonectin domain signature 2. / Secreted protein acidic and rich in cysteine Ca binding region / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like ...SPARC / Osteonectin-like, conserved site / SPARC/Testican, calcium-binding domain / Osteonectin domain signature 1. / Osteonectin domain signature 2. / Secreted protein acidic and rich in cysteine Ca binding region / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / von Willebrand factor type C domain / Kazal type serine protease inhibitors / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Wheat Germ Agglutinin (Isolectin 2); domain 1 / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Collagen alpha-1(III) chain / SPARC
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHohenester, E. / Sasaki, T. / Giudici, C. / Farndale, R.W. / Bachinger, H.P.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural Basis of Sequence-Specific Collagen Recognition by Sparc.
Authors: Hohenester, E. / Sasaki, T. / Giudici, C. / Farndale, R.W. / Bachinger, H.P.
#1: Journal: Embo J. / Year: 1998
Title: Crystal Structure and Mapping by Site-Directed Mutagenesis of the Collagen-Binding Epitope of an Activated Form of Bm-40,Sparc,Osteonectin
Authors: Sasaki, T. / Hohenester, E. / Gohring, W. / Timpl, R.
History
DepositionOct 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / 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.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPARC
B: COLLAGEN ALPHA-1(III) CHAIN
C: COLLAGEN ALPHA-1(III) CHAIN
D: COLLAGEN ALPHA-1(III) CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3967
Polymers35,8354
Non-polymers5613
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-58.6 kcal/mol
Surface area21580 Å2
MethodPQS
Unit cell
Length a, b, c (Å)89.790, 89.790, 127.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein SPARC / SECRETED PROTEIN ACIDIC AND RICH IN CYSTEINE / OSTEONECTIN / ON / BASEMENT-MEMBRANE PROTEIN 40 / BM-40


Mass: 26633.367 Da / Num. of mol.: 1 / Fragment: FS AND EC DOMAINS, RESIDUES 70-212,221-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P09486
#2: Protein/peptide COLLAGEN ALPHA-1(III) CHAIN


Mass: 3067.350 Da / Num. of mol.: 3 / Fragment: RESIDUES 564-584 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02461
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Nonpolymer details4-HYDROXYPROLINE (HYP): 2R,4R-HYDROXYPROLINE N-ACETYLGLUCOSAMINE (NAG): A401 IS N-LINKED TO ...4-HYDROXYPROLINE (HYP): 2R,4R-HYDROXYPROLINE N-ACETYLGLUCOSAMINE (NAG): A401 IS N-LINKED TO ASPARAGINE A99, A402 IS 1-4 LINKED TO A401
Sequence detailsREGARDING CHAIN A: VECTOR-DERIVED APLA AT N-TERMINUS, 196-203 DELETED REGARDING CHAINS B, C AND D: ...REGARDING CHAIN A: VECTOR-DERIVED APLA AT N-TERMINUS, 196-203 DELETED REGARDING CHAINS B, C AND D: PEPTIDE CORRESPONDS TO 564-584 OF HUMAN COLLAGEN ALPHA1(III) CHAIN, FLANKED BY GPOGPO AT N-TERMINUS AND GPOGAO AT C-TERMINUS (O IS 4-HYDROXYPROLINE)

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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: 3.98 Å3/Da / Density % sol: 68.84 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.97976
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 9046 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 74.08 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 7.4 / % possible all: 100

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
autoSHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NUB

1nub


Resolution: 3.2→19.842 Å / SU ML: 0.58 / σ(F): 1.37 / Phase error: 32.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3202 950 10.53 %
Rwork0.2536 --
obs0.2609 9019 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.822 Å2 / ksol: 0.253 e/Å3
Displacement parametersBiso mean: 87.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.4895 Å20 Å2-0 Å2
2--2.4895 Å20 Å2
3----10.7831 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 34 0 2300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d02392
X-RAY DIFFRACTIONf_angle_d1.413275
X-RAY DIFFRACTIONf_dihedral_angle_d23.5859
X-RAY DIFFRACTIONf_chiral_restr0.07355
X-RAY DIFFRACTIONf_plane_restr0433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.36810.40581120.30941134X-RAY DIFFRACTION100
3.3681-3.57790.38421370.27571111X-RAY DIFFRACTION100
3.5779-3.85230.33561300.28421151X-RAY DIFFRACTION100
3.8523-4.23660.30921330.25661146X-RAY DIFFRACTION100
4.2366-4.84180.3031420.21871132X-RAY DIFFRACTION100
4.8418-6.07110.33711460.24241159X-RAY DIFFRACTION100
6.0711-19.84220.26941500.22291236X-RAY DIFFRACTION100
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)
10.34770.36640.12030.08970.01810.13060.81260.05550.564-1.4577-0.0712-1.5319-0.70071.36290.00191.6696-0.00070.57170.64920.14161.009511.2295-0.578441.1595
24.5242-1.451-3.42922.18850.87472.46640.1266-0.8493-0.2257-2.23871.30841.46520.48530.07920.33030.9646-0.0532-0.30340.29140.17810.74611.208514.992752.4997
30.3610.17850.72342.5222-0.78580.9679-0.12450.29190.3433-0.37910.14680.0317-0.4203-0.2269-00.7424-0.08490.06430.34080.13230.66814.535134.818845.7834
41.05610.07110.641-0.3754-0.28581.19130.21480.48720.30980.3994-0.4553-0.22170.39360.0857-0.00011.01910.0640.1750.6426-0.16780.526824.262916.119554.1475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 54:85 OR RESSEQ 105:114)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 86:104 OR RESSEQ 115:135 OR RESSEQ 401:402)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 136:187 OR RESSEQ 206:285 OR RESSEQ 301)
4X-RAY DIFFRACTION4CHAIN B OR CHAIN C OR CHAIN D OR CHAIN Z

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