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8k0i

Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, in its dual-ternary state

Method: ELECTRON MICROSCOPY Dmax: 167.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Prolyl 3-hydroxylase 1

Homo sapiens

UniProt Q32P28

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–736 Chain a； UniProt 1–736 Not recorded Cartilage-associated protein × 2 （O75718） Peptidyl-prolyl cis-trans isomerase B × 2 （P23284） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.62 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8K0I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8K0E Human collagen prolyl processing enzyme complex, P3H1/CRTAP heterodimer Deposited 2023-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–736（736 aa）
Not recorded FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.65 Å
8K0F Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, in its apo state Deposited 2023-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–736（736 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8K0M Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to 2-oxoglutarate Deposited 2023-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–736（736 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
8K17 Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to collagen alpha-1(I) chain Deposited 2023-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–736（736 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
8KC9 Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to cyclosporin A Deposited 2023-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–736（736 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name P3H1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–736； UniProt 1–736 Author chain a； PDBConstruct 1–736； UniProt 1–736

Cartilage-associated protein

Homo sapiens

UniProt O75718

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain B； UniProt 1–401 Chain b； UniProt 1–401 Not recorded Prolyl 3-hydroxylase 1 × 2 （Q32P28） Peptidyl-prolyl cis-trans isomerase B × 2 （P23284） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.62 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8K0I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8K0E Human collagen prolyl processing enzyme complex, P3H1/CRTAP heterodimer Deposited 2023-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–401（401 aa）
Not recorded FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.65 Å
8K0F Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, in its apo state Deposited 2023-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–401（401 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8K0M Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to 2-oxoglutarate Deposited 2023-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–401（401 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
8K17 Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to collagen alpha-1(I) chain Deposited 2023-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–401（401 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
8KC9 Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to cyclosporin A Deposited 2023-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–401（401 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRTAP_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–401； UniProt 1–401 Author chain b； PDBConstruct 1–401； UniProt 1–401

Peptidyl-prolyl cis-trans isomerase B

Homo sapiens

UniProt P23284

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain C； UniProt 1–216 Chain c； UniProt 1–216 Not recorded Prolyl 3-hydroxylase 1 × 2 （Q32P28） Cartilage-associated protein × 2 （O75718） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.62 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8K0I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CYN CYCLOPHILIN B COMPLEXED WITH [D-(CHOLINYLESTER)SER8]-CYCLOSPORIN Deposited 1995-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 31–208（178 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.85 Å
3ICH Crystal structure of cyclophilin B at 1.2 A resolution Deposited 2009-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 34–216（183 aa） Fragment：UNP residues 34-216
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；25% w/v PEG 1500, 0.1M MMT buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.20 Å R-free 0.162
3ICI Crystal structure of cyclophilin B in complex with calmegin fragment Deposited 2009-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 34–216（183 aa） Fragment：UNP residues 34-216
Not recorded ZN ZINC ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；22% w/v PEG 8000, 10mM ZnCl2, 0.1M Tris buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.239
3ICI Crystal structure of cyclophilin B in complex with calmegin fragment Deposited 2009-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 34–216（183 aa） Fragment：UNP residues 34-216
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；22% w/v PEG 8000, 10mM ZnCl2, 0.1M Tris buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.239
8K0F Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, in its apo state Deposited 2023-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–216（216 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8K0M Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to 2-oxoglutarate Deposited 2023-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–216（216 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
8K17 Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to collagen alpha-1(I) chain Deposited 2023-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–216（216 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
8KC9 Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to cyclosporin A Deposited 2023-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–216（216 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PPIB_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–216； UniProt 1–216 Author chain c； PDBConstruct 1–216； UniProt 1–216

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8k0i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8k0i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8k0i
Deposition date deposition_date2023-07-09
Structure title titleHuman collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, in its dual-ternary state
Keywords keywordscomplex, hydroxylase, collagen, ER protein, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.17 Å
Radius of gyration Rg (electron density) rg_electron49.25 Å
Forward intensity I(0) i0689480000.00
Molecular weight molecular_weight217640.0 kDa
Excluded volume excluded_volume272280 ų
Envelope volume envelope_volume419060 ų
Hydration-shell volume shell_volume73765 ų
Envelope diameter envelope_diameter180.3 Å
Shell Rg shell_rg50.81 Å
Envelope Rg envelope_rg47.57 Å
Shape Rg shape_rg49.28 Å
Total Rg total_rg49.20 Å
Total atoms total_atoms15356
Residues n_residues1882
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax167.7 Å
Rg (real space) rg_real49.25 Å
Rg uncertainty (real space) rg_real_error1.88 Å
I(0) (real space) i0_real6.8950e+08
I(0) uncertainty (real space) i0_real_error1.5330e+07
Rg (reciprocal space) rg_reciprocal49.17 Å
I(0) (reciprocal space) i0_reciprocal689400000.0000
Solution quality estimate total_estimate0.6728
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.4 Å
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.392
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51570000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 0.087; Positv: 1.000; Valcen: 0.995; Smooth: 0.891
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)