8K0F | pdb_00008k0f

Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, in its apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8K0F

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Literature

The structural basis for the collagen processing by human P3H1/CRTAP/PPIB ternary complex.

Li, W.Peng, J.Yao, D.Rao, B.Xia, Y.Wang, Q.Li, S.Cao, M.Shen, Y.Ma, P.Liao, R.Qin, A.Zhao, J.Cao, Y.

(2024) Nat Commun 15: 7844-7844

  • DOI: https://doi.org/10.1038/s41467-024-52321-6
  • Primary Citation Related Structures: 
    8K0E, 8K0F, 8K0I, 8K0M, 8K17, 8KC9

  • PubMed Abstract: 

    Collagen posttranslational processing is crucial for its proper assembly and function. Disruption of collagen processing leads to tissue development and structure disorders like osteogenesis imperfecta (OI). OI-related collagen processing machinery includes prolyl 3-hydroxylase 1 (P3H1), peptidyl-prolyl cis-trans isomerase B (PPIB), and cartilage-associated protein (CRTAP), with their structural organization and mechanism unclear. We determine cryo-EM structures of the P3H1/CRTAP/PPIB complex. The active sites of P3H1 and PPIB form a face-to-face bifunctional reaction center, indicating a coupled modification mechanism. The structure of the P3H1/CRTAP/PPIB/collagen peptide complex reveals multiple binding sites, suggesting a substrate interacting zone. Unexpectedly, a dual-ternary complex is observed, and the balance between ternary and dual-ternary states can be altered by mutations in the P3H1/PPIB active site and the addition of PPIB inhibitors. These findings provide insights into the structural basis of collagen processing by P3H1/CRTAP/PPIB and the molecular pathology of collagen-related disorders.


  • Organizational Affiliation
    • Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 163.85 kDa 
  • Atom Count: 9,595 
  • Modeled Residue Count: 1,182 
  • Deposited Residue Count: 1,434 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prolyl 3-hydroxylase 1736Homo sapiensMutation(s): 0 
Gene Names: P3H1GROS1LEPRE1PSEC0109
EC: 1.14.11.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q32P28 (Homo sapiens)
Explore Q32P28 
Go to UniProtKB:  Q32P28
PHAROS:  Q32P28
GTEx:  ENSG00000117385 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32P28
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q32P28-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cartilage-associated protein442Homo sapiensMutation(s): 0 
Gene Names: CRTAPCASP
UniProt & NIH Common Fund Data Resources
Find proteins for O75718 (Homo sapiens)
Explore O75718 
Go to UniProtKB:  O75718
PHAROS:  O75718
GTEx:  ENSG00000170275 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75718
Glycosylation
Glycosylation Sites: 2Go to GlyGen: O75718-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase B256Homo sapiensMutation(s): 0 
Gene Names: PPIBCYPB
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P23284 (Homo sapiens)
Explore P23284 
Go to UniProtKB:  P23284
PHAROS:  P23284
GTEx:  ENSG00000166794 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23284
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82072468
National Natural Science Foundation of China (NSFC)China82272519

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary