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- PDB-9evk: Crystal Structure of human Collagen Hydroxylysine Galactosyltrans... -

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Basic information

Entry
Database: PDB / ID: 9evk
TitleCrystal Structure of human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1
ComponentsProcollagen galactosyltransferase 1
KeywordsTRANSFERASE / Collagen Biosynthesis / Extracellular Matrix / Post-translational modifications / Glycosyltransferase
Function / homology
Function and homology information


procollagen galactosyltransferase / procollagen galactosyltransferase activity / positive regulation of collagen fibril organization / Collagen biosynthesis and modifying enzymes / collagen fibril organization / endoplasmic reticulum lumen / membrane
Similarity search - Function
Glycosyl transferase family 2 / Glycosyl transferase, family 25 / Glycosyltransferase family 25 (LPS biosynthesis protein) / : / Endoplasmic reticulum targeting sequence. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
GALACTOSE-URIDINE-5'-DIPHOSPHATE / Procollagen galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDe Marco, M. / Scietti, L. / Rai, S.R. / Mattoteia, D. / Pinnola, A. / Forneris, F.
Funding support Italy, United States, Japan, 4items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 20075 Italy
Italian Association for Cancer ResearchBRIDGE 27004 Italy
The Giovanni Armenise-Harvard FoundationCDA 2013 United States
Mizutani Foundation for Glycoscience200039 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Molecular structure and enzymatic mechanism of the human collagen hydroxylysine galactosyltransferase GLT25D1/COLGALT1.
Authors: De Marco, M. / Rai, S.R. / Scietti, L. / Mattoteia, D. / Liberi, S. / Moroni, E. / Pinnola, A. / Vetrano, A. / Iacobucci, C. / Santambrogio, C. / Colombo, G. / Forneris, F.
History
DepositionMar 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Procollagen galactosyltransferase 1
B: Procollagen galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,01715
Polymers137,1782
Non-polymers1,83913
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SEC-SAXS indicates elongated dimeric assembly, light scattering, SEC-MALS indicates dimeric assembly, microscopy, Mass photometry indicates dimeric assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-93 kcal/mol
Surface area45130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.907, 221.907, 221.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Procollagen galactosyltransferase 1 / Collagen beta(1-O)galactosyltransferase 1 / ColGalT 1 / Glycosyltransferase 25 family member 1 / ...Collagen beta(1-O)galactosyltransferase 1 / ColGalT 1 / Glycosyltransferase 25 family member 1 / Hydroxylysine galactosyltransferase 1


Mass: 68589.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GS and C-terminal AAA are restriction scars. Residues not modeled are flexible
Source: (gene. exp.) Homo sapiens (human) / Gene: COLGALT1, GLT25D1, PSEC0241 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q8NBJ5, procollagen galactosyltransferase

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Non-polymers , 6 types, 22 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.32 Å3/Da / Density % sol: 0.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% poly-ethylene-glycol (PEG) MW 4000, 100 mM 2-(N-morpholino)ethanesulfonic acid (MES)/NaOH, 20% glycerol, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 3→49.62 Å / Num. obs: 35735 / % possible obs: 98.4 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.101 / Net I/σ(I): 6.2
Reflection shellResolution: 3→3.13 Å / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 1 / Num. unique obs: 4385 / CC1/2: 0.402 / Rpim(I) all: 0.811

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.62 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1771 4.96 %
Rwork0.1968 --
obs0.199 35727 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8503 0 105 9 8617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028855
X-RAY DIFFRACTIONf_angle_d0.64512029
X-RAY DIFFRACTIONf_dihedral_angle_d7.721197
X-RAY DIFFRACTIONf_chiral_restr0.0431284
X-RAY DIFFRACTIONf_plane_restr0.0051540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.38131730.31952631X-RAY DIFFRACTION100
3.08-3.170.32261260.30122617X-RAY DIFFRACTION100
3.17-3.270.3391140.28782634X-RAY DIFFRACTION100
3.28-3.390.33371330.28072628X-RAY DIFFRACTION100
3.39-3.530.31891330.25372668X-RAY DIFFRACTION100
3.53-3.690.27211470.22282627X-RAY DIFFRACTION100
3.69-3.880.26461420.20912559X-RAY DIFFRACTION97
3.88-4.120.22891410.19342627X-RAY DIFFRACTION98
4.13-4.440.23321240.17722613X-RAY DIFFRACTION98
4.45-4.890.2021330.15352631X-RAY DIFFRACTION99
4.89-5.60.17681410.17592650X-RAY DIFFRACTION99
5.6-7.050.25511350.19422587X-RAY DIFFRACTION97
7.05-49.620.1911290.14892484X-RAY DIFFRACTION89
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)
12.19150.1175-0.06652.82860.87582.1774-0.1513-0.0101-0.2415-0.30620.09550.2704-0.05620.08560.04270.75150.06550.06750.43560.00710.463564.850228.398355.4698
20.7398-0.8029-0.4291.4155-0.06621.04820.0599-0.05860.1425-0.36040.1686-0.51270.14770.5912-0.04561.03180.0750.18160.9034-0.11950.975989.487614.158537.5308
31.54430.07270.92991.6516-0.61451.33250.22740.4241-0.1978-1.00250.0107-0.65980.32540.5477-0.11711.20710.1990.35960.8472-0.08651.028286.89344.924124.1277
41.9765-0.5452-1.64851.71520.25983.14680.02520.77360.0288-1.1113-0.1122-0.28840.34490.5961-0.13941.55150.1410.35571.0909-0.05810.907186.92929.142516.7572
51.4354-0.0977-0.22031.24870.24481.9948-0.0272-0.30030.1183-0.00870.0162-0.0642-0.1820.19320.00950.67990.10750.01060.5734-0.00710.417868.215151.132988.2564
61.2228-0.38810.15111.86960.87772.1861-0.03210.03770.3804-0.0709-0.02930.2982-0.46650.01910.06940.97250.0860.08350.6283-0.01180.646146.120876.849101.4502
71.0074-0.40860.05112.39830.58641.6343-0.2021-0.43370.43510.49410.5567-0.2356-0.52310.5116-0.2991.29850.07360.09310.9129-0.23280.837153.022784.1541114.5251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 283 )
2X-RAY DIFFRACTION2chain 'A' and (resid 284 through 406 )
3X-RAY DIFFRACTION3chain 'A' and (resid 407 through 528 )
4X-RAY DIFFRACTION4chain 'A' and (resid 529 through 561 )
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 300 )
6X-RAY DIFFRACTION6chain 'B' and (resid 301 through 406 )
7X-RAY DIFFRACTION7chain 'B' and (resid 407 through 561 )

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