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- PDB-7zsc: Crystal structure of the heterodimeric human C-P4H-II with trunca... -

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Basic information

Entry
Database: PDB / ID: 7zsc
TitleCrystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281)
Components
  • Prolyl 4-hydroxylase subunit alpha-2
  • Protein disulfide-isomerase
KeywordsHYDROLASE / Collagen synthesis / PDI / DSBH fold / thioredoxin / dioxygenase
Function / homology
Function and homology information


procollagen-proline 4-dioxygenase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / insulin processing / VLDL assembly / thiol oxidase activity / procollagen-proline 4-dioxygenase activity / LDL remodeling / protein disulfide-isomerase ...procollagen-proline 4-dioxygenase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / insulin processing / VLDL assembly / thiol oxidase activity / procollagen-proline 4-dioxygenase activity / LDL remodeling / protein disulfide-isomerase / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Chylomicron assembly / interleukin-23-mediated signaling pathway / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / L-ascorbic acid binding / cellular response to interleukin-7 / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of T cell migration / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of cell adhesion / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / electron transfer activity / iron ion binding / endoplasmic reticulum lumen / protein heterodimerization activity / 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
Prolyl 4-hydroxylase alpha-subunit, N-terminal / Prolyl 4-Hydroxylase alpha-subunit, N-terminal region / Prolyl 4-hydroxylase peptide-substrate-binding domain / Prolyl 4-hydroxylase / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / 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, N-terminal / Prolyl 4-Hydroxylase alpha-subunit, N-terminal region / Prolyl 4-hydroxylase peptide-substrate-binding domain / Prolyl 4-hydroxylase / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / 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. / q2cbj1_9rhob like domain / Endoplasmic reticulum targeting sequence. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / TPR repeat region circular profile. / TPR repeat profile. / Thioredoxin domain profile. / Thioredoxin domain / Tetratricopeptide repeat / Glutaredoxin / Glutaredoxin / Tetratricopeptide-like helical domain superfamily / Thioredoxin-like superfamily / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Prolyl 4-hydroxylase subunit alpha-2 / Protein disulfide-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsLebedev, A. / Koski, M.K. / Wierenga, R.K. / Murthy, A.V. / Sulu, R.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: 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
DepositionMay 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl 4-hydroxylase subunit alpha-2
B: Prolyl 4-hydroxylase subunit alpha-2
C: Protein disulfide-isomerase
D: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,7646
Polymers171,5724
Non-polymers1922
Water00
1
A: Prolyl 4-hydroxylase subunit alpha-2
C: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8823
Polymers85,7862
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-37 kcal/mol
Surface area33990 Å2
MethodPISA
2
B: Prolyl 4-hydroxylase subunit alpha-2
D: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8823
Polymers85,7862
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-36 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)252.879, 252.879, 89.4
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Prolyl 4-hydroxylase subunit alpha-2 / 4-PH alpha-2 / Procollagen-proline / 2-oxoglutarate-4-dioxygenase subunit alpha-2


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 Protein disulfide-isomerase / PDI / Cellular thyroid hormone-binding protein / Prolyl 4-hydroxylase subunit beta / p55


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 ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2018 / Details: Toroidal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JIG,4EL1,6I7S

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 1992 -RANDOM
Rwork0.2438 ---
obs0.2472 20135 99.7 %-
Displacement parametersBiso mean: 73.21 Å2
Baniso -1Baniso -2Baniso -3
1-48.6191 Å20 Å20 Å2
2--48.6191 Å20 Å2
3----97.2383 Å2
Refine analyzeLuzzati coordinate error obs: 0.76 Å
Refinement stepCycle: LAST / Resolution: 3.85→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11081 0 10 0 11091
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811371HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9815369HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3976SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1944HARMONIC5
X-RAY DIFFRACTIONt_it11363HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1422SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7439SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.8
LS refinement shellResolution: 3.85→3.88 Å
RfactorNum. reflection% reflection
Rfree0.2853 40 -
Rwork0.2705 --
obs0.2719 403 95.6 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6756-2.4005-1.97883.2772-2.39341.99170.2268-0.3086-0.1818-0.3086-0.04540.5235-0.18180.5235-0.1814-0.15860.23590.0556-0.080.2076-0.304-80.5238175.3818-21.8543
24.0075-1.425-2.61876.45790.08282.94730.29470.47180.50510.4718-0.3332-0.12960.5051-0.12960.0384-0.1723-0.0760.1823-0.4356-0.0702-0.304-102.9814169.30146.1508
38.4424-0.0733-1.14428.1885-3.8398.31550.0731-0.2845-0.7435-0.2845-0.46250.1992-0.74350.19920.38950.17230.0760.05560.43560.20760.304-55.1482192.7021-39.957
49.0202-0.4069-2.827.6107-0.93648.31550.0335-0.03350.1992-0.03350.24390.74350.19920.7435-0.27740.3537-0.02870.05560.25430.20760.304-72.9639220.9624-39.1227
55.7951.45520.987610.8359-0.86198.31550.0420.2124-0.74350.2124-0.26040.1992-0.74350.19920.21840.31990.12440.0747-0.17470.17460.304-82.3048210.2567-11.256
64.22410.44481.06535.63093.97575.52240.22210.75550.1550.7555-0.02180.71790.1550.7179-0.20020.4356-0.076-0.09120.17230.12290.0193-70.8624187.183710.008
79.5482-0.7117-3.97577.08271.06538.31550.3058-0.1426-0.1992-0.1426-0.4241-0.7435-0.1992-0.74350.11840.3976-0.05410.20760.2103-0.05560.304-132.9837170.599124.7902
85.7951.4552-1.504310.8359-0.54098.3155-0.27760.23810.63180.23810.0962-0.26370.6318-0.26370.18140.26910.0201-0.0130.3388-0.1830.304-133.6389203.618223.8463
910.8359-1.45521.8165.7950.33555.34210.0293-0.2131-0.1992-0.2131-0.5735-0.7435-0.1992-0.74350.54420.03140.25310.2076-0.1235-0.05560.304-119.9839199.3406-4.0679
100.5908-1.04853.97577.0159-1.06538.31550.1496-0.3086-0.0908-0.3086-0.1225-0.6809-0.0908-0.6809-0.0270.08570.2261-0.05220.17550.14540.304-117.4561174.0815-25.3357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|284 - A|601 }
2X-RAY DIFFRACTION2{B|284 - B|601}
3X-RAY DIFFRACTION3{C|21 - C|134}
4X-RAY DIFFRACTION4{C|135 - C|235}
5X-RAY DIFFRACTION5{C|236 - C|354}
6X-RAY DIFFRACTION6{C|355 - C|476}
7X-RAY DIFFRACTION7{D|21 - D|134}
8X-RAY DIFFRACTION8{D|135 - D|235}
9X-RAY DIFFRACTION9{D|236 - D|354}
10X-RAY DIFFRACTION10{D|355 - D|478}

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