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- PDB-6fzv: Crystal structure of the metalloproteinase enhancer PCPE-1 bound ... -

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Basic information

Entry
Database: PDB / ID: 6fzv
TitleCrystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (short)
Components
  • Collagen alpha-1(III) chain
  • Procollagen C-endopeptidase enhancer 1
KeywordsSTRUCTURAL PROTEIN / COLLAGEN
Function / homology
Function and homology information


collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / Crosslinking of collagen fibrils / transforming growth factor beta1 production / collagen biosynthetic process / elastic fiber assembly / Collagen chain trimerization / endochondral bone morphogenesis / negative regulation of neuron migration ...collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / Crosslinking of collagen fibrils / transforming growth factor beta1 production / collagen biosynthetic process / elastic fiber assembly / Collagen chain trimerization / endochondral bone morphogenesis / negative regulation of neuron migration / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / 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 / tissue homeostasis / response to angiotensin / NCAM1 interactions / 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 / peptidase activator activity / Syndecan interactions / skin development / SMAD binding / positive regulation of Rho protein signal transduction / Collagen degradation / Non-integrin membrane-ECM interactions / chondrocyte differentiation / ECM proteoglycans / Integrin cell surface interactions / collagen binding / supramolecular fiber organization / response to cytokine / transforming growth factor beta receptor signaling pathway / lung development / cell-matrix adhesion / integrin-mediated signaling pathway / cellular response to amino acid stimulus / wound healing / response to radiation / cerebral cortex development / platelet activation / integrin binding / multicellular organism growth / neuron migration / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / heparin binding / : / heart development / protease binding / fibroblast proliferation / in utero embryonic development / endoplasmic reticulum lumen / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Procollagen C-endopeptidase enhancer, NTR domain / Jelly Rolls - #1000 / Spermadhesin, CUB domain / Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. ...Procollagen C-endopeptidase enhancer, NTR domain / Jelly Rolls - #1000 / Spermadhesin, CUB domain / Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Collagen alpha-1(III) chain / Procollagen C-endopeptidase enhancer 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPulido, D. / Hohenester, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101748/Z/13/Z United Kingdom
CitationJournal: Structure / Year: 2018
Title: Structural Basis for the Acceleration of Procollagen Processing by Procollagen C-Proteinase Enhancer-1.
Authors: Pulido, D. / Sharma, U. / Vadon-Le Goff, S. / Hussain, S.A. / Cordes, S. / Mariano, N. / Bettler, E. / Moali, C. / Aghajari, N. / Hohenester, E. / Hulmes, D.J.S.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight
Revision 1.4Oct 23, 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: Collagen alpha-1(III) chain
B: Collagen alpha-1(III) chain
C: Collagen alpha-1(III) chain
D: Procollagen C-endopeptidase enhancer 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,98214
Polymers115,1434
Non-polymers83910
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-98 kcal/mol
Surface area44230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.090, 144.120, 158.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Collagen alpha-1(III) chain


Mass: 28815.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL3A1 / Plasmid: pHLsec / Production host: Homo sapiens (human) / References: UniProt: P02461
#2: Protein Procollagen C-endopeptidase enhancer 1 / Procollagen COOH-terminal proteinase enhancer 1 / Procollagen C-proteinase enhancer 1 / Type 1 ...Procollagen COOH-terminal proteinase enhancer 1 / Procollagen C-proteinase enhancer 1 / Type 1 procollagen C-proteinase enhancer protein / Type I procollagen COOH-terminal proteinase enhancer


Mass: 28696.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCOLCE, PCPE1 / Plasmid: pCEP-Pu / Production host: Homo sapiens (human) / References: UniProt: Q15113
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
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: 4.43 Å3/Da / Density % sol: 72.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20 mg/ml protein in 20 mM HEPES pH 7.5, 180 mM NaCl, 2.5 mM calcium chloride; 0.2 M potassium citrate, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.7→79.4 Å / Num. obs: 56733 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.1
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.94 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.743 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AE2

4ae2


Resolution: 2.7→79.37 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.24
RfactorNum. reflection% reflection
Rfree0.258 2827 4.98 %
Rwork0.2259 --
obs0.2275 56733 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→79.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7361 0 46 0 7407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037593
X-RAY DIFFRACTIONf_angle_d0.73710270
X-RAY DIFFRACTIONf_dihedral_angle_d12.5472766
X-RAY DIFFRACTIONf_chiral_restr0.0311089
X-RAY DIFFRACTIONf_plane_restr0.0031351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74660.39671200.37132661X-RAY DIFFRACTION100
2.7466-2.79650.37441430.37032670X-RAY DIFFRACTION100
2.7965-2.85030.38421430.34522622X-RAY DIFFRACTION100
2.8503-2.90850.37141490.34072667X-RAY DIFFRACTION100
2.9085-2.97180.39961330.35782688X-RAY DIFFRACTION100
2.9718-3.04090.42181320.37822641X-RAY DIFFRACTION100
3.0409-3.11690.40351370.3412663X-RAY DIFFRACTION100
3.1169-3.20120.3561480.31092699X-RAY DIFFRACTION100
3.2012-3.29540.30041440.28972644X-RAY DIFFRACTION100
3.2954-3.40180.32441520.28772669X-RAY DIFFRACTION100
3.4018-3.52340.33521290.28632695X-RAY DIFFRACTION100
3.5234-3.66440.32231330.27312673X-RAY DIFFRACTION100
3.6644-3.83120.27511500.2442690X-RAY DIFFRACTION100
3.8312-4.03320.2571450.23642697X-RAY DIFFRACTION100
4.0332-4.28590.23261370.2152707X-RAY DIFFRACTION100
4.2859-4.61680.23111310.18722707X-RAY DIFFRACTION100
4.6168-5.08130.22021500.16782725X-RAY DIFFRACTION100
5.0813-5.81640.21291360.18942743X-RAY DIFFRACTION100
5.8164-7.32720.22471570.19792755X-RAY DIFFRACTION100
7.3272-79.40430.20111580.17742890X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.6785 Å / Origin y: -22.037 Å / Origin z: 6.6587 Å
111213212223313233
T0.7621 Å2-0.0262 Å20.0115 Å2-0.7076 Å2-0.0051 Å2--0.7701 Å2
L1.0891 °20.0478 °20.1261 °2-0.7837 °2-0.009 °2--0.329 °2
S-0.0528 Å °-0.0353 Å °0.0867 Å °0.0411 Å °0.0013 Å °0.0303 Å °-0.0408 Å °-0.0738 Å °0 Å °
Refinement TLS groupSelection details: all

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