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Yorodumi- PDB-7zsc: Crystal structure of the heterodimeric human C-P4H-II with trunca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zsc | ||||||
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Title | Crystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281) | ||||||
Components |
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Keywords | HYDROLASE / Collagen synthesis / PDI / DSBH fold / thioredoxin / dioxygenase | ||||||
Function / homology | Function and homology information procollagen-proline 4-dioxygenase / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase ...procollagen-proline 4-dioxygenase / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / endoplasmic reticulum chaperone complex / Chylomicron assembly / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / L-ascorbic acid binding / cellular response to interleukin-7 / Interleukin-12 signaling / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / positive regulation of cell adhesion / protein-disulfide reductase activity / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / electron transfer activity / cytoskeleton / iron ion binding / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å | ||||||
Authors | Lebedev, A. / Koski, M.K. / Wierenga, R.K. / Murthy, A.V. / Sulu, R. | ||||||
Funding support | Finland, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Crystal structure of the collagen prolyl 4-hydroxylase (C-P4H) catalytic domain complexed with PDI: Toward a model of the C-P4H alpha 2 beta 2 tetramer. Authors: Murthy, A.V. / Sulu, R. / Lebedev, A. / Salo, A.M. / Korhonen, K. / Venkatesan, R. / Tu, H. / Bergmann, U. / Janis, J. / Laitaoja, M. / Ruddock, L.W. / Myllyharju, J. / Koski, M.K. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zsc.cif.gz | 567.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zsc.ent.gz | 474.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/7zsc ftp://data.pdbj.org/pub/pdb/validation_reports/zs/7zsc | HTTPS FTP |
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-Related structure data
Related structure data | 2jigS 4el1S 6i7sS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30290.197 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: P4HA2, UNQ290/PRO330 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: O15460, procollagen-proline 4-dioxygenase #2: Protein | Mass: 55495.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P07237, protein disulfide-isomerase #3: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.91 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% (w/v) PEG4000, 0.2 M lithium sulfate, 0.1 M MES, 3% methanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2018 / Details: Toroidal mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.85→46.69 Å / Num. obs: 20176 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 203 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Rrim(I) all: 0.071 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.85→3.99 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.862 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1969 / Rpim(I) all: 0.873 / Rrim(I) all: 2.058 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JIG,4EL1,6I7S Resolution: 3.85→46.69 Å / Cor.coef. Fo:Fc: 0.587 / Cor.coef. Fo:Fc free: 0.604 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.751
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Displacement parameters | Biso mean: 73.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.76 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.85→46.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.85→3.88 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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