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

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Basic information

Entry
Database: PDB / ID: 6fzw
TitleCrystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (long)
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 / transforming growth factor beta1 production / Crosslinking of collagen fibrils / collagen biosynthetic process / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding ...collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / Crosslinking of collagen fibrils / collagen biosynthetic process / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / basement membrane organization / Extracellular matrix organization / layer formation in cerebral cortex / Collagen biosynthesis and modifying enzymes / peptidase activator activity / peptide cross-linking / tissue homeostasis / Signaling by PDGF / negative regulation of immune response / NCAM1 interactions / digestive tract development / response to angiotensin / collagen fibril organization / Scavenging by Class A Receptors / extracellular matrix structural constituent / skin development / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / positive regulation of Rho protein signal transduction / SMAD binding / Collagen degradation / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / supramolecular fiber organization / collagen binding / extracellular matrix organization / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / response to cytokine / integrin-mediated signaling pathway / cellular response to amino acid stimulus / neuron migration / lung development / wound healing / response to radiation / multicellular organism growth / cerebral cortex development / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / heparin binding / heart development / fibroblast proliferation / collagen-containing extracellular matrix / in utero embryonic development / protease binding / 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 / 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 ...Procollagen C-endopeptidase enhancer, NTR domain / Jelly Rolls - #1000 / 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 / Netrin C-terminal Domain / Netrin module, non-TIMP type / CUB domain / UNC-6/NTR/C345C module / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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: 2.78 Å
AuthorsHohenester, E. / Pulido, D.
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 11, 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

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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)125,45812
Polymers124,6914
Non-polymers7688
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-113 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.880, 143.650, 156.710
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: 31997.879 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 / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7

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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: 4.01 Å3/Da / Density % sol: 69.34 %
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 ammonium citrate, 18% 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: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.78→68.8 Å / Num. obs: 46452 / % possible obs: 91.4 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.1
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.634 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FZV

6fzv


Resolution: 2.78→68.787 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.3
RfactorNum. reflection% reflection
Rfree0.2712 2249 4.86 %
Rwork0.2474 --
obs0.2486 46312 90.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.78→68.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6868 0 44 0 6912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047086
X-RAY DIFFRACTIONf_angle_d0.7149580
X-RAY DIFFRACTIONf_dihedral_angle_d12.8942570
X-RAY DIFFRACTIONf_chiral_restr0.031014
X-RAY DIFFRACTIONf_plane_restr0.0031258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7801-2.84060.41561460.39652742X-RAY DIFFRACTION93
2.8406-2.90670.41621540.37492815X-RAY DIFFRACTION94
2.9067-2.97940.37851420.34872832X-RAY DIFFRACTION94
2.9794-3.05990.43221320.34452832X-RAY DIFFRACTION94
3.0599-3.14990.32521440.33172780X-RAY DIFFRACTION93
3.1499-3.25160.32151300.2942812X-RAY DIFFRACTION93
3.2516-3.36780.32051410.29392813X-RAY DIFFRACTION93
3.3678-3.50270.30751570.30182767X-RAY DIFFRACTION92
3.5027-3.66210.30971350.27312820X-RAY DIFFRACTION92
3.6621-3.85510.26731440.24272752X-RAY DIFFRACTION91
3.8551-4.09660.26161350.25042763X-RAY DIFFRACTION90
4.0966-4.41290.25811280.23082671X-RAY DIFFRACTION88
4.4129-4.85690.21831290.20562671X-RAY DIFFRACTION87
4.8569-5.55940.24091500.21242660X-RAY DIFFRACTION86
5.5594-7.00320.25881390.23312627X-RAY DIFFRACTION85
7.0032-68.80840.23411430.20882706X-RAY DIFFRACTION83
Refinement TLS params.Method: refined / Origin x: 6.9696 Å / Origin y: -21.6768 Å / Origin z: 4.1677 Å
111213212223313233
T0.7817 Å2-0.0631 Å20.0444 Å2-0.7479 Å2-0.0272 Å2--0.8055 Å2
L1.2323 °20.1027 °20.2955 °2-0.816 °2-0.048 °2--0.494 °2
S-0.0322 Å °-0.0402 Å °0.115 Å °0.0251 Å °0.0002 Å °-0.0442 Å °-0.1081 Å °-0.0593 Å °0 Å °
Refinement TLS groupSelection details: all

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