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

ID or keywords:

Entry

Database: PDB / ID: 9evj

Title

Crystal Structure of human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: complex with Mn2+ and UDP-Gal

Components

Procollagen galactosyltransferase 1

Keywords

TRANSFERASE / 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 / protein O-linked glycosylation / collagen fibril organization / endoplasmic reticulum lumen / membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

De Marco, M. / Scietti, L. / Rai, S.R. / Mattoteia, D. / Pinnola, A. / Forneris, F.

Funding support

Italy,

United States,

Japan, 5items

Organization	Grant number	Country
Italian Association for Cancer Research	MFAG 20075	Italy
Italian Association for Cancer Research	BRIDGE 27004	Italy
The Giovanni Armenise-Harvard Foundation	CDA 2013	United States
Mizutani Foundation for Glycoscience	200039	Japan
The Ehlers-Danlos Society		United States

Citation

Journal: 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

Deposition	Mar 30, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 9, 2025	Provider: repository / Type: Initial release
Revision 1.1	Apr 23, 2025	Group: Database references / Category: citation / citation_author 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9evj.cif.gz	459.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9evj.ent.gz	375.8 KB	Display	PDB format
PDBx/mmJSON format	9evj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9evj_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	9evj_full_validation.pdf.gz	2.4 MB	Display
Data in XML	9evj_validation.xml.gz	43.6 KB	Display
Data in CIF	9evj_validation.cif.gz	56.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ev/9evj ftp://data.pdbj.org/pub/pdb/validation_reports/ev/9evj	HTTPS FTP

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Related structure data

Related structure data	9evkC 9evlC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	SASBDB: SAS5562associated SAS data, (draft ID 5562)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (2) #108 - Dec 2008 Hsp90 similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (2) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Procollagen galactosyltransferase 1

B: Procollagen galactosyltransferase 1

hetero molecules

139 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS, SEC-SAXS confirms elongated dimeric assembly, light scattering, SEC-MALS confirms dimers, microscopy, Mass Photometry confirms dimers

Unit cell

Length a, b, c (Å)	220.855, 220.855, 220.855
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

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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 from recombinant expression vector - 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

#1: Protein

Procollagen galactosyltransferase 1 / Collagen beta(1-O)galactosyltransferase 1 / ColGalT 1 / Glycosyltransferase 25 family member 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 from recombinant expression vector - 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 , 8 types, 151 molecules

#2: Chemical	ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE Mass: 566.302 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₁₅H₂₄N₂O₁₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: 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
#5: 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
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.27 Å³/Da / Density % sol: 62 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2.7→49.38 Å / Num. obs: 49018 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.11 / R_pim(I) all: 0.058 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.7→2.79 Å / Redundancy: 5.2 % / R_merge(I) obs: 1.251 / Num. unique obs: 4444 / CC_1/2: 0.395 / R_pim(I) all: 0.92 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→49.38 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2225	2445	4.99 %
R_work	0.1855	-	-
obs	0.1873	49006	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.7→49.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8562	0	225	136	8923

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9017
X-RAY DIFFRACTION	f_angle_d	0.532	12253
X-RAY DIFFRACTION	f_dihedral_angle_d	11.927	3373
X-RAY DIFFRACTION	f_chiral_restr	0.041	1311
X-RAY DIFFRACTION	f_plane_restr	0.004	1564

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7-2.76	0.4403	118	0.3516	2709	X-RAY DIFFRACTION	99
2.76-2.81	0.3359	134	0.3237	2717	X-RAY DIFFRACTION	100
2.82-2.88	0.2839	133	0.2709	2719	X-RAY DIFFRACTION	100
2.88-2.95	0.3207	161	0.2582	2694	X-RAY DIFFRACTION	100
2.95-3.03	0.284	145	0.2463	2750	X-RAY DIFFRACTION	100
3.03-3.12	0.2408	147	0.2324	2713	X-RAY DIFFRACTION	100
3.12-3.22	0.3277	166	0.2329	2676	X-RAY DIFFRACTION	100
3.22-3.34	0.2526	136	0.2283	2743	X-RAY DIFFRACTION	100
3.34-3.47	0.295	154	0.2298	2733	X-RAY DIFFRACTION	100
3.47-3.63	0.2108	144	0.1804	2741	X-RAY DIFFRACTION	100
3.63-3.82	0.2315	157	0.173	2727	X-RAY DIFFRACTION	100
3.82-4.06	0.2001	139	0.1647	2729	X-RAY DIFFRACTION	100
4.06-4.37	0.1874	145	0.1572	2739	X-RAY DIFFRACTION	100
4.37-4.81	0.1751	141	0.1413	2776	X-RAY DIFFRACTION	100
4.81-5.51	0.1956	150	0.1561	2738	X-RAY DIFFRACTION	100
5.51-6.94	0.2051	123	0.1734	2816	X-RAY DIFFRACTION	100
6.94-49.38	0.1706	152	0.1495	2841	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.184	0.2262	-0.0447	3.5219	1.2325	2.2387	-0.1571	-0.2357	-0.3288	0.07	0.0715	0.1647	0.236	0.1806	0.0815	0.5602	0.082	0.1183	0.3176	0.0708	0.3331	68.1589	25.1511	60.7338
2	3.0113	-0.8618	-1.0242	3.427	0.9995	2.5082	-0.0483	0.5067	-0.2193	-0.9204	-0.0507	0.375	-0.3804	-0.2072	0.0656	0.8075	0.0354	-0.0364	0.3059	-0.007	0.4039	59.6916	32.7859	46.055
3	3.0115	-1.2327	-0.7701	4.5714	0.9659	2.6063	-0.0607	-0.2966	-0.1709	-0.8891	0.2685	0.0864	-0.2505	0.2392	-0.0318	0.7465	0.0077	0.0677	0.3684	0.0636	0.2885	67.3339	28.1652	45.2637
4	2.1855	-1.5228	-1.789	2.4099	2.3273	3.8204	-0.0413	-0.2609	-0.1015	-0.1107	0.2282	-0.4954	0.4045	0.814	-0.1572	0.6708	0.1582	0.1083	0.5674	0.0003	0.6305	87.5045	11.7033	43.6916
5	1.052	-0.3109	-0.4882	1.2294	0.2157	2.0161	-0.0667	0.2827	0.5105	-0.9927	0.2484	-1.0925	-0.1861	0.7897	-0.1262	1.2989	0.1464	0.6545	1.2766	0.0483	1.4161	105.3011	15.8011	17.459
6	2.4412	-0.1651	0.1008	2.4248	0.5849	3.3423	0.1856	0.4846	-0.2274	-1.0668	-0.0857	-0.5532	0.2736	0.756	-0.0754	1.0899	0.2389	0.2825	0.6529	-0.0584	0.7715	87.4277	5.5413	22.1591
7	2.3265	-0.9453	-0.7275	2.2091	2.4571	4.7944	-0.0135	0.4653	0.27	-1.2291	0.2469	-0.4756	-0.2069	1.0313	-0.4505	1.2675	0.2368	0.3081	0.7143	-0.0702	0.7125	87.3397	13.9287	23.8732
8	6.7222	-1.4897	-6.2369	2.0361	1.647	5.8859	0.1201	2.9503	-0.9988	-1.639	-0.3118	-0.9511	-0.5307	0.2474	0.2046	1.7005	-0.1789	0.4584	1.8923	-0.1166	1.7494	107.519	21.3016	19.1274
9	1.26	-0.2185	-0.4025	1.3991	0.0836	1.962	-0.0272	-0.3289	0.0968	0.1161	0.0569	-0.0728	-0.1192	0.2389	-0.0137	0.5003	0.0701	0.0225	0.4209	0.0023	0.2635	67.491	51.6161	88.7204
10	0.4287	-0.6162	-0.5466	2.3241	1.0639	2.1736	-0.1768	0.0901	-0.0155	0.4012	-0.0192	0.8308	-0.0652	-0.1395	0.0418	0.7295	0.1164	0.11	0.562	-0.0452	0.5053	43.698	68.5346	100.9146
11	2.2255	-0.7143	-0.1551	2.9243	1.0796	2.5674	-0.2707	-0.46	0.6018	0.4271	0.4588	-0.1376	-0.7828	0.4585	-0.1547	1.1469	0.0246	0.0495	0.6885	-0.2166	0.6348	51.4228	86.179	112.7096
12	6.1916	-1.6345	5.706	2.6435	-2.0248	7.6838	1.5377	-5.9486	-1.6407	0.9941	-2.8287	-1.5752	5.982	2.4265	1.2669	1.7853	0.2264	0.3263	1.799	0.3795	1.1686	59.9368	82.414	97.5593

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 44 through 190 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 191 through 276 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 277 through 300 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 301 through 373 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 374 through 406 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 407 through 540 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 541 through 571 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 572 through 580 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 42 through 318 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 319 through 373 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 374 through 560 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 561 through 562 )

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