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- PDB-8k17: Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB ... -

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Basic information

Entry
Database: PDB / ID: 8k17
TitleHuman collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to collagen alpha-1(I) chain
Components
  • Cartilage-associated protein
  • Peptidyl-prolyl cis-trans isomerase B
  • Prolyl 3-hydroxylase 1
  • synthetic substrate
KeywordsCYTOSOLIC PROTEIN / complex / hydroxylase / collagen / ER protein
Function / homology
Function and homology information


procollagen-proline 3-dioxygenase / procollagen-proline 3-dioxygenase activity / protein hydroxylation / negative regulation of post-translational protein modification / endoplasmic reticulum chaperone complex / positive regulation by host of viral genome replication / Collagen biosynthesis and modifying enzymes / collagen metabolic process / positive regulation by host of viral process / positive regulation of multicellular organism growth ...procollagen-proline 3-dioxygenase / procollagen-proline 3-dioxygenase activity / protein hydroxylation / negative regulation of post-translational protein modification / endoplasmic reticulum chaperone complex / positive regulation by host of viral genome replication / Collagen biosynthesis and modifying enzymes / collagen metabolic process / positive regulation by host of viral process / positive regulation of multicellular organism growth / collagen fibril organization / L-ascorbic acid binding / RNA polymerase binding / cyclosporin A binding / regulation of protein secretion / protein peptidyl-prolyl isomerization / smooth endoplasmic reticulum / chaperone-mediated protein folding / neutrophil chemotaxis / bone development / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of neuron projection development / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / melanosome / protein folding / spermatogenesis / protein stabilization / iron ion binding / negative regulation of cell population proliferation / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / focal adhesion / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular space / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Prolyl 3-hydroxylase / : / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Endoplasmic reticulum targeting sequence. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site ...Prolyl 3-hydroxylase / : / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Endoplasmic reticulum targeting sequence. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / Cartilage-associated protein / Peptidyl-prolyl cis-trans isomerase B / Prolyl 3-hydroxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLi, W. / Peng, J. / Yao, D. / Rao, B. / Xia, Y. / Wang, Q. / Li, S. / Cao, M. / Shen, Y. / Ma, P. ...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.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072468 China
National Natural Science Foundation of China (NSFC)82272519 China
CitationJournal: Nat Commun / Year: 2024
Title: The structural basis for the collagen processing by human P3H1/CRTAP/PPIB ternary complex.
Authors: Wenguo Li / Junjiang Peng / Deqiang Yao / Bing Rao / Ying Xia / Qian Wang / Shaobai Li / Mi Cao / Yafeng Shen / Peixiang Ma / Rijing Liao / An Qin / Jie Zhao / Yu Cao /
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 ...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.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 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: Prolyl 3-hydroxylase 1
B: Cartilage-associated protein
C: Peptidyl-prolyl cis-trans isomerase B
E: synthetic substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,8039
Polymers164,8634
Non-polymers9415
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Prolyl 3-hydroxylase 1 / Growth suppressor 1 / Leucine- and proline-enriched proteoglycan 1 / Leprecan-1


Mass: 83485.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P3H1, GROS1, LEPRE1, PSEC0109 / Production host: Homo sapiens (human)
References: UniProt: Q32P28, procollagen-proline 3-dioxygenase
#2: Protein Cartilage-associated protein


Mass: 50749.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRTAP, CASP / Production host: Homo sapiens (human) / References: UniProt: O75718
#3: Protein Peptidyl-prolyl cis-trans isomerase B / PPIase B / CYP-S1 / Cyclophilin B / Rotamase B / S-cyclophilin / SCYLP


Mass: 28669.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIB, CYPB / Production host: Homo sapiens (human) / References: UniProt: P23284, peptidylprolyl isomerase

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Protein/peptide / Sugars / Non-polymers , 3 types, 6 molecules E

#4: Protein/peptide synthetic substrate


Mass: 1958.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A protein modification complex with synthetic substrate
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1779834 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089987
ELECTRON MICROSCOPYf_angle_d0.71213504
ELECTRON MICROSCOPYf_dihedral_angle_d4.4911360
ELECTRON MICROSCOPYf_chiral_restr0.0491424
ELECTRON MICROSCOPYf_plane_restr0.0051771

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