[English] 日本語
Yorodumi
- PDB-6fzw: Crystal structure of the metalloproteinase enhancer PCPE-1 bound ... -

+
Open data


ID or keywords:

Loading...

-
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 / Collagen chain trimerization / negative regulation of neuron migration / endochondral bone morphogenesis ...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 / Collagen chain trimerization / negative regulation of neuron migration / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / Extracellular matrix organization / negative regulation of immune response / layer formation in cerebral cortex / basement membrane organization / peptidase activator activity / Collagen biosynthesis and modifying enzymes / peptide cross-linking / Signaling by PDGF / tissue homeostasis / NCAM1 interactions / response to angiotensin / digestive tract development / collagen fibril organization / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / Scavenging by Class A Receptors / MET activates PTK2 signaling / Syndecan interactions / positive regulation of Rho protein signal transduction / skin development / 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 / transforming growth factor beta receptor signaling pathway / response to cytokine / cell-matrix adhesion / integrin-mediated signaling pathway / cellular response to amino acid stimulus / lung development / neuron migration / 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 / protease binding / fibroblast proliferation / collagen-containing extracellular matrix / 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 / 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 / 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more