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- PDB-9en2: Crystal structure of the metalloproteinase enhancer PCPE-1 comple... -

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Basic information

Entry
Database: PDB / ID: 9en2
TitleCrystal structure of the metalloproteinase enhancer PCPE-1 complexed with nanobodies VHH-H4 and VHH-I5
Components
  • Procollagen C-endopeptidase enhancer 1
  • VHH-H4
  • VHH-I5
KeywordsCELL ADHESION / COLLAGEN / STRUCTURAL PROTEIN / EXTRACELLULAR MATRIX / FIBROSIS / NANOBODIES
Function / homology
Function and homology information


Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen biosynthesis and modifying enzymes / peptidase activator activity / collagen binding / heparin binding / collagen-containing extracellular matrix / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Procollagen C-endopeptidase enhancer, NTR domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Netrin domain ...Procollagen C-endopeptidase enhancer, NTR domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / CUB domain / 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
Similarity search - Domain/homology
Procollagen C-endopeptidase enhancer 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLagoutte, P. / Gueguen-Chaignon, V. / Bourhis, J.-M. / Vadon-Le Goff, S.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE14-0033 France
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Mono- and bi-specific nanobodies targeting the CUB domains of PCPE-1 reduce the proteolytic processing of fibrillar procollagens.
Authors: Lagoutte, P. / Bourhis, J.M. / Mariano, N. / Gueguen-Chaignon, V. / Vandroux, D. / Moali, C. / Vadon-Le Goff, S.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Procollagen C-endopeptidase enhancer 1
B: VHH-H4
C: VHH-I5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9397
Polymers64,6753
Non-polymers2644
Water6,575365
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-30 kcal/mol
Surface area22050 Å2
Unit cell
Length a, b, c (Å)54.830, 95.945, 110.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Procollagen C-endopeptidase enhancer 1 / Procollagen COOH-terminal proteinase enhancer 1 / PCPE-1 / Procollagen C-proteinase enhancer 1 / ...Procollagen COOH-terminal proteinase enhancer 1 / PCPE-1 / Procollagen C-proteinase enhancer 1 / Type 1 procollagen C-proteinase enhancer protein / Type I procollagen COOH-terminal proteinase enhancer


Mass: 32437.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCOLCE, PCPE1 / Production host: Homo sapiens (human) / Strain (production host): 293-F / References: UniProt: Q15113

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Antibody , 2 types, 2 molecules BC

#2: Antibody VHH-H4


Mass: 16608.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody VHH-I5


Mass: 15628.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 369 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / pH: 6.5
Details: 10% PEG 8000, 50 mM L-argininamide dihydrochloride, 50 mM spermine, 50 mM sodium cacodylate pH 6.5, 50 mM potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.977794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977794 Å / Relative weight: 1
ReflectionResolution: 2.2→49 Å / Num. obs: 30184 / % possible obs: 99.5 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.063 / Rrim(I) all: 0.107 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.033 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 28630 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDS20210322data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.24216 --
Rwork0.2083 --
obs-28630 99.82 %
Refinement stepCycle: LAST / Resolution: 2.2→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 14 365 4023

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