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- EMDB-36774: Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB ... -

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Basic information

Entry
Database: EMDB / ID: EMD-36774
TitleHuman collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to 2-oxoglutarate
Map data
Sample
  • Complex: A protein modification complex bound with co-substrate
    • Protein or peptide: Prolyl 3-hydroxylase 1
    • Protein or peptide: Cartilage-associated protein
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FE (III) ION
  • Ligand: 2-OXOGLUTARIC ACID
Keywordscomplex / hydroxylase / collagen / ER protein / CYTOSOLIC 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 / L-ascorbic acid binding / collagen fibril organization / RNA polymerase binding / cyclosporin A binding / regulation of protein secretion / protein peptidyl-prolyl isomerization / smooth endoplasmic reticulum / chaperone-mediated protein folding / neutrophil chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / bone development / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 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, 2 items
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 9, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36774.png

Downloads & links

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Map

FileDownload / File: emd_36774.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-4.4531655 - 7.587138
Average (Standard dev.)0.0025036489 (±0.15111823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 246.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36774_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36774_half_map_2.map
Projections & Slices
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Sample components

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Entire : A protein modification complex bound with co-substrate

EntireName: A protein modification complex bound with co-substrate
Components
  • Complex: A protein modification complex bound with co-substrate
    • Protein or peptide: Prolyl 3-hydroxylase 1
    • Protein or peptide: Cartilage-associated protein
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FE (III) ION
  • Ligand: 2-OXOGLUTARIC ACID

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Supramolecule #1: A protein modification complex bound with co-substrate

SupramoleculeName: A protein modification complex bound with co-substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prolyl 3-hydroxylase 1

MacromoleculeName: Prolyl 3-hydroxylase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: procollagen-proline 3-dioxygenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.485727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVRALKLLT TLLAVVAAAS QAEVESEAGW GMVTPDLLFA EGTAAYARGD WPGVVLSMER ALRSRAALRA LRLRCRTQCA ADFPWELDP DWSPSPAQAS GAAALRDLSF FGGLLRRAAC LRRCLGPPAA HSLSEEMELE FRKRSPYNYL QVAYFKINKL E KAVAAAHT ...String:
MAVRALKLLT TLLAVVAAAS QAEVESEAGW GMVTPDLLFA EGTAAYARGD WPGVVLSMER ALRSRAALRA LRLRCRTQCA ADFPWELDP DWSPSPAQAS GAAALRDLSF FGGLLRRAAC LRRCLGPPAA HSLSEEMELE FRKRSPYNYL QVAYFKINKL E KAVAAAHT FFVGNPEHME MQQNLDYYQT MSGVKEADFK DLETQPHMQE FRLGVRLYSE EQPQEAVPHL EAALQEYFVA YE ECRALCE GPYDYDGYNY LEYNADLFQA ITDHYIQVLN CKQNCVTELA SHPSREKPFE DFLPSHYNYL QFAYYNIGNY TQA VECAKT YLLFFPNDEV MNQNLAYYAA MLGEEHTRSI GPRESAKEYR QRSLLEKELL FFAYDVFGIP FVDPDSWTPE EVIP KRLQE KQKSERETAV RISQEIGNLM KEIETLVEEK TKESLDVSRL TREGGPLLYE GISLTMNSKL LNGSQRVVMD GVISD HECQ ELQRLTNVAA TSGDGYRGQT SPHTPNEKFY GVTVFKALKL GQEGKVPLQS AHLYYNVTEK VRRIMESYFR LDTPLY FSY SHLVCRTAIE EVQAERKDDS HPVHVDNCIL NAETLVCVKE PPAYTFRDYS AILYLNGDFD GGNFYFTELD AKTVTAE VQ PQCGRAVGFS SGTENPHGVK AVTRGQRCAI ALWFTLDPRH SERDRVQADD LVKMLFSPEE MDLSQEQPLD AQQGPPEP A QESLSGSESK PKDEL

UniProtKB: Prolyl 3-hydroxylase 1

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Macromolecule #2: Cartilage-associated protein

MacromoleculeName: Cartilage-associated protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.749184 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPGRRGAAA LLALLCVACA LRAGRAQYER YSFRSFPRDE LMPLESAYRH ALDKYSGEHW AESVGYLEIS LRLHRLLRDS EAFCHRNCS AAPQPEPAAG LASYPELRLF GGLLRRAHCL KRCKQGLPAF RQSQPSREVL ADFQRREPYK FLQFAYFKAN N LPKAIAAA ...String:
MEPGRRGAAA LLALLCVACA LRAGRAQYER YSFRSFPRDE LMPLESAYRH ALDKYSGEHW AESVGYLEIS LRLHRLLRDS EAFCHRNCS AAPQPEPAAG LASYPELRLF GGLLRRAHCL KRCKQGLPAF RQSQPSREVL ADFQRREPYK FLQFAYFKAN N LPKAIAAA HTFLLKHPDD EMMKRNMAYY KSLPGAEDYI KDLETKSYES LFIRAVRAYN GENWRTSITD MELALPDFFK AF YECLAAC EGSREIKDFK DFYLSIADHY VEVLECKIQC EENLTPVIGG YPVEKFVATM YHYLQFAYYK LNDLKNAAPC AVS YLLFDQ NDKVMQQNLV YYQYHRDTWG LSDEHFQPRP EAVQFFNVTT LQKELYDFAK ENIMDDDEGE VVEYVDDLLE LEET SAAAL EVLFQGPSAW SHPQFEKGGG SGGGSGGSAW SHPQFEK

UniProtKB: Cartilage-associated protein

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Macromolecule #3: Peptidyl-prolyl cis-trans isomerase B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.669605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLRLSERNMK VLLAAALIAG SVFFLLLPGP SAADEKKKGP KVTVKVYFDL RIGDEDVGRV IFGLFGKTVP KTVDNFVALA TGEKGFGYK NSKFHRVIKD FMIQGGDFTR GDGTGGKSIY GERFPDENFK LKHYGPGWVS MANAGKDTNG SQFFITTVKT A WLDGKHVV ...String:
MLRLSERNMK VLLAAALIAG SVFFLLLPGP SAADEKKKGP KVTVKVYFDL RIGDEDVGRV IFGLFGKTVP KTVDNFVALA TGEKGFGYK NSKFHRVIKD FMIQGGDFTR GDGTGGKSIY GERFPDENFK LKHYGPGWVS MANAGKDTNG SQFFITTVKT A WLDGKHVV FGKVLEGMEV VRKVESTKTD SRDKPLKDVI IADCGKIEVE KPFAIAKEAA AENLYFQGDY KDHDGDYKDH DI DYKDDDD KHHHHHHHH

UniProtKB: Peptidyl-prolyl cis-trans isomerase B

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #6: 2-OXOGLUTARIC ACID

MacromoleculeName: 2-OXOGLUTARIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: AKG
Molecular weightTheoretical: 146.098 Da
Chemical component information

ChemComp-AKG:
2-OXOGLUTARIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 699771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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