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- PDB-6te3: Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Co... -

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Basic information

Entry
Database: PDB / ID: 6te3
TitleCrystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP
ComponentsProcollagen-lysine,2-oxoglutarate 5-dioxygenase 3
KeywordsTRANSFERASE / Collagen / lysyl hydroxylase / hydroxylysine / galactosyltransferase / glucosyltransferase
Function / homology
Function and homology information


procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen-lysine 5-dioxygenase / procollagen galactosyltransferase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase activity / basement membrane assembly / epidermis morphogenesis ...procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen-lysine 5-dioxygenase / procollagen galactosyltransferase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase activity / basement membrane assembly / epidermis morphogenesis / Collagen biosynthesis and modifying enzymes / collagen metabolic process / endothelial cell morphogenesis / protein O-linked glycosylation / collagen fibril organization / L-ascorbic acid binding / neural tube development / small molecule binding / lung morphogenesis / rough endoplasmic reticulum / trans-Golgi network / vasodilation / intracellular protein localization / : / in utero embryonic development / iron ion binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome / metal ion binding
Similarity search - Function
Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / PLOD GT domain / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Oxoglutarate/iron-dependent dioxygenase ...Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / PLOD GT domain / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Nucleotide-diphospho-sugar transferases / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChiapparino, A. / De Giorgi, F. / Scietti, L. / Faravelli, S. / Roscioli, T. / Forneris, F.
Funding support Italy, 4items
OrganizationGrant numberCountry
European CommissionMSCA-IF 745934 - COTETHERS
Italian Association for Cancer Research20075 Italy
Other privateThe Giovanni Armenise-Harvard Foundation CDA 2013 Italy
Italian Ministry of EducationDipartimenti di Eccellenza Program 2018-2022 Italy
CitationJournal: Int J Mol Sci / Year: 2023
Title: Identification of Regulatory Molecular 'Hot Spots' for LH/PLOD Collagen Glycosyltransferase Activity
Authors: Mattoteia, D. / Chiapparino, A. / Fumagalli, M. / De Marco, M. / De Giorgi, F. / Negro, L. / Pinnola, A. / Faravelli, S. / Roscioli, T. / Scietti, L. / Forneris, F.
History
DepositionNov 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,01910
Polymers82,7841
Non-polymers1,2359
Water2,792155
1
A: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
hetero molecules

A: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,03820
Polymers165,5692
Non-polymers2,46918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area5610 Å2
ΔGint-37 kcal/mol
Surface area58070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.995, 100.035, 225.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

21A-990-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 / Lysyl hydroxylase 3 / LH3


Mass: 82784.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLOD3 / Plasmid: pUPE.106.08 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: O60568, procollagen-lysine 5-dioxygenase, procollagen galactosyltransferase, procollagen glucosyltransferase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 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.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 5 types, 162 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.8
Details: 600 mM sodium formate, 12% PGA-LM, 100 mM HEPES/NaOH, 500 mM FeCl2, 500 mM MnCl2, 1 mM UDP
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.3→48.84 Å / Num. obs: 48288 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 26.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.086 / Net I/σ(I): 8.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.476 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4455 / CC1/2: 0.512 / Rpim(I) all: 1.107 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
STARANISOdata scaling
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FXM

6fxm


Resolution: 2.3→48.84 Å / SU ML: 0.2684 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0174
RfactorNum. reflection% reflection
Rfree0.2458 1642 5.36 %
Rwork0.1943 --
obs0.197 30657 62.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5611 0 73 155 5839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365880
X-RAY DIFFRACTIONf_angle_d0.61797986
X-RAY DIFFRACTIONf_chiral_restr0.044835
X-RAY DIFFRACTIONf_plane_restr0.00481044
X-RAY DIFFRACTIONf_dihedral_angle_d16.49363483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.2931260.2538745X-RAY DIFFRACTION19.14
2.37-2.440.3214600.2564945X-RAY DIFFRACTION24.88
2.44-2.530.2887670.27751145X-RAY DIFFRACTION30.2
2.53-2.630.3356680.27371453X-RAY DIFFRACTION37.52
2.63-2.750.3311960.27231806X-RAY DIFFRACTION46.95
2.75-2.90.3307970.25542182X-RAY DIFFRACTION56.08
2.9-3.080.34811620.24452530X-RAY DIFFRACTION66.39
3.08-3.320.25361830.23372989X-RAY DIFFRACTION77.56
3.32-3.650.2571860.19223428X-RAY DIFFRACTION88.75
3.65-4.180.2172290.17173843X-RAY DIFFRACTION99.37
4.18-5.260.20622230.14493917X-RAY DIFFRACTION99.95
5.26-48.830.2142450.17564032X-RAY DIFFRACTION99.6
Refinement TLS params.

Method: refined / 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)
10.0640347933886-0.01341964761090.04839448037290.017257553043-0.001913211035470.0418357318165-0.1450575670340.174836256439-0.0162599906414-0.0979410390569-0.0165139225259-0.0981579515044-0.1948090138650.0400427730682-0.009883267212620.296348275493-0.0064802219570.02651550480980.155122372664-0.00299061995640.1441919115270.558247889330.7938796554146.76437515
20.1243821180570.0535879442465-0.04428079915880.07573380707820.09106677985560.2279319305230.03316810797760.127780066325-0.0678225429384-0.126004776142-0.0699750157385-0.0629381471679-0.188282503885-0.3237951765280.02404242434280.04163558016190.130078585709-0.07622578570610.244910052756-0.03998219256380.12929535509858.758346759622.074348559148.691726727
30.09280813811840.0723939374092-0.1111867248930.113796576552-0.1368540621770.1766321529370.111811293978-0.0512359453390.07776480309780.178681503616-0.0625745607608-0.0661689759436-0.08866841471970.0497696055820.0125086571820.129091731411-0.0536158338504-0.07534058519030.12743688204-0.003258733583920.195145409176.585039599741.6954233042188.340857329
40.04555444224720.04962015380730.0207439606370.08870718414970.05574873527090.0989871270002-0.004005877956-0.02482967681970.007101949583620.06206972401160.0198920065925-0.01401845731980.0734516641137-0.0679544009590.0179493988690.131296932544-0.00414288548681-0.01148884637080.09561592503230.01976588418670.17402970827368.725562858830.4075572636180.705674049
51.50312562884-0.570291907442-0.05494284591690.8711280230540.3963654053130.627294069691-0.0304336801521-0.139040234892-0.04223357840250.08920810961990.01291022553240.0670566014724-0.01444282669140.0745041876455-0.01890381651090.29448419966-0.0936038258263-0.000451984668920.1710644187810.04669579343320.074506374949177.173207667319.8352311726216.434961151
60.0597503246392-0.0534287450044-0.04900079689640.07573758833710.02224871990840.0442994999574-0.09484358965660.06374241668710.03294753216970.126799824446-0.01170744913390.02162192086080.001141540614630.0417006454735-0.01203417986490.303075677592-0.0565210503149-0.04412070704510.2019934045220.05216804173640.13648015558478.514602147716.0007316274223.675207955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 277 )
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 392 )
4X-RAY DIFFRACTION4chain 'A' and (resid 393 through 527 )
5X-RAY DIFFRACTION5chain 'A' and (resid 528 through 607 )
6X-RAY DIFFRACTION6chain 'A' and (resid 608 through 738 )

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