8KC9 | pdb_00008kc9

Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to cyclosporin A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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 of Related Structures:  
    8K0I, 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
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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
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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

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DSN-MLE-MLE-MVA-BMT-ABA-SAR-MLE-VAL-MLE-ALAD [auth E]11Tolypocladium inflatumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
D [auth E]L-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
D [auth E]L-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
D [auth E]L-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
D [auth E]L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
D [auth E]PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 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