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

ID or keywords:

Entry

Database: PDB / ID: 9evl

Title

Crystal Structure of human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Hg2+ soak for experimental phasing

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 /

SAD / Resolution: 2.8 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
Other private		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 / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9evl.cif.gz	451.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9evl.ent.gz	371.9 KB	Display	PDB format
PDBx/mmJSON format	9evl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9evl_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	9evl_full_validation.pdf.gz	2 MB	Display
Data in XML	9evl_validation.xml.gz	41.7 KB	Display
Data in CIF	9evl_validation.cif.gz	53.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ev/9evl ftp://data.pdbj.org/pub/pdb/validation_reports/ev/9evl	HTTPS FTP

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Related structure data

Related structure data	9evjC 9evkC 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	#108 - Dec 2008 Hsp90 similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (2) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #224 - Aug 2018 Legumain similarity (1) #225 - Sep 2018 Phytase similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #58 - Oct 2004 G Proteins similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#108 - Dec 2008
Hsp90
similarity (1)
#156 - Dec 2012
ABO Blood Type Glycosyltransferases
similarity (2)
#110 - Feb 2009
Auxin and TIR1 Ubiquitin Ligase
similarity (1)
#254 - Feb 2021
Cellulose Synthase
similarity (1)
#147 - Mar 2012
Rhodopsin
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#224 - Aug 2018
Legumain
similarity (1)
#225 - Sep 2018
Phytase
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#27 - Mar 2002
Bacteriorhodopsin
similarity (1)
#49 - Jan 2004
Carbonic Anhydrase
similarity (1)
#58 - Oct 2004
G Proteins
similarity (1)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Procollagen galactosyltransferase 1

B: Procollagen galactosyltransferase 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering, SEC-MALS confirms dimers in solution, microscopy, mass photometry confirms dimers, SAXS, SEC-SAXS confirms elongated dimers

Unit cell

Length a, b, c (Å)	220.187, 220.187, 220.187
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 introduced by recombinant expression vector 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 introduced by recombinant expression vector
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, 26 molecules

#2: Chemical	ChemComp-HG / MERCURY (II) ION Mass: 200.590 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Hg
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: 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
#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-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.24 Å³/Da / Density % sol: 62.07 %
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

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.7749 Å / Relative weight: 1
Reflection	Resolution: 2.8→49.24 Å / Num. obs: 84831 / % possible obs: 100 % / Redundancy: 23.2 % / CC_1/2: 0.998 / R_merge(I) obs: 0.169 / R_pim(I) all: 0.051 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.8→2.91 Å / Redundancy: 23.3 % / R_merge(I) obs: 3.609 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4551 / CC_1/2: 0.599 / R_pim(I) all: 1.093 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
XDS		data reduction
Aimless		data scaling
HKL2Map		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.8→49.24 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2389	4203	4.95 %
R_work	0.2021	-	-
obs	0.204	84831	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→49.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8503	0	114	4	8621

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8837
X-RAY DIFFRACTION	f_angle_d	0.564	12003
X-RAY DIFFRACTION	f_dihedral_angle_d	12.355	3325
X-RAY DIFFRACTION	f_chiral_restr	0.042	1282
X-RAY DIFFRACTION	f_plane_restr	0.005	1536

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 (%)
2.8-2.83	0.3483	114	0.358	2737	X-RAY DIFFRACTION	100
2.83-2.87	0.3544	128	0.3303	2675	X-RAY DIFFRACTION	100
2.87-2.9	0.3643	162	0.3409	2683	X-RAY DIFFRACTION	100
2.9-2.94	0.4515	122	0.4312	2713	X-RAY DIFFRACTION	100
2.94-2.98	0.4304	114	0.3869	2668	X-RAY DIFFRACTION	100
2.98-3.02	0.3929	144	0.3444	2753	X-RAY DIFFRACTION	100
3.02-3.06	0.3466	116	0.3043	2646	X-RAY DIFFRACTION	100
3.06-3.11	0.2818	112	0.2834	2720	X-RAY DIFFRACTION	100
3.11-3.15	0.2983	152	0.2722	2726	X-RAY DIFFRACTION	100
3.15-3.2	0.287	104	0.2602	2644	X-RAY DIFFRACTION	100
3.21-3.26	0.3025	112	0.2675	2748	X-RAY DIFFRACTION	100
3.26-3.32	0.2858	174	0.2549	2641	X-RAY DIFFRACTION	100
3.32-3.38	0.2698	140	0.2545	2721	X-RAY DIFFRACTION	100
3.38-3.45	0.3237	160	0.2487	2654	X-RAY DIFFRACTION	100
3.45-3.53	0.3063	150	0.2458	2669	X-RAY DIFFRACTION	100
3.53-3.61	0.2587	190	0.2211	2682	X-RAY DIFFRACTION	100
3.61-3.7	0.2358	138	0.2108	2650	X-RAY DIFFRACTION	100
3.7-3.8	0.251	122	0.195	2733	X-RAY DIFFRACTION	100
3.8-3.91	0.3097	154	0.1835	2671	X-RAY DIFFRACTION	100
3.91-4.04	0.2713	148	0.1727	2676	X-RAY DIFFRACTION	100
4.04-4.18	0.2215	168	0.199	2652	X-RAY DIFFRACTION	100
4.18-4.35	0.216	150	0.1793	2671	X-RAY DIFFRACTION	100
4.35-4.55	0.1723	110	0.1621	2728	X-RAY DIFFRACTION	100
4.55-4.79	0.2036	138	0.157	2690	X-RAY DIFFRACTION	100
4.79-5.09	0.2072	176	0.1622	2675	X-RAY DIFFRACTION	100
5.09-5.48	0.2057	148	0.1908	2649	X-RAY DIFFRACTION	100
5.48-6.03	0.226	156	0.208	2679	X-RAY DIFFRACTION	100
6.03-6.89	0.2929	116	0.1901	2708	X-RAY DIFFRACTION	100
6.9-8.68	0.2085	118	0.1724	2732	X-RAY DIFFRACTION	100
8.69-49.24	0.1757	167	0.1627	2634	X-RAY DIFFRACTION	99

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	2.4755	-0.2707	-0.2389	2.8274	0.9575	3.3517	-0.2927	-0.4629	0.0035	0.2558	0.1686	0.0972	-0.5319	0.222	0.1314	0.8258	0.1548	0.0062	0.5549	0.0348	0.4071	44.9806	56.196	81.9793
2	1.2339	-0.7807	-1.0909	2.9302	2.5442	2.445	-0.0305	0.0533	-0.1553	0.0232	-0.4799	0.9237	-0.0363	-0.7899	0.4371	1.0618	0.1984	0.1087	1.1837	-0.0743	0.8617	22.5494	66.6544	98.294
3	1.99	1.8612	0.6322	6.0552	-0.9077	2.8951	-0.3819	0.7921	1.2797	-0.3239	0.1911	0.8633	-0.9174	-1.2906	0.2758	1.5389	0.5226	-0.0761	1.9886	0.0873	1.5887	4.3009	92.5196	93.9402
4	2.6034	0.6305	0.3705	2.6295	-0.4436	3.4515	0.2742	-0.4855	0.6129	0.1734	-0.2419	0.6481	-0.9793	-0.5288	-0.0493	1.2358	0.312	0.2253	1.1153	-0.1349	0.8036	22.82	86.6247	105.0549
5	1.7906	-1.9024	0.1783	5.6636	0.7301	0.9105	-0.1466	0.1989	0.4546	-0.2958	-0.1604	1.3116	-1.1012	-0.2194	0.295	1.7545	0.3461	0.1106	1.0568	-0.111	1.1303	22.5229	94.0341	100.6088
6	1.894	-0.1701	0.0152	2.0919	0.3875	2.0755	-0.1246	-0.2037	-0.4731	0.1841	0.0884	0.0497	0.2184	0.1195	0.012	0.6565	0.0447	0.1403	0.4255	0.0669	0.5816	47.5177	23.5157	64.2842
7	4.4982	-0.4115	-2.5497	2.9796	-0.5979	7.4492	-0.5289	0.9333	-0.55	-0.5227	0.0646	-0.1654	0.7461	-0.9999	0.444	0.9855	-0.0285	-0.0436	0.7113	-0.1146	0.7551	34.7845	19.3381	45.6642
8	2.9025	0.2486	0.1747	3.6265	-0.5224	1.9674	-0.0847	0.1569	-0.1294	-0.4263	0.233	0.8899	-0.1835	-0.3996	-0.0331	0.7242	-0.0173	0.1099	0.5742	0.0439	0.8213	29.9135	24.3829	61.2734
9	2.6367	-1.8643	-0.5507	1.3218	0.7066	2.8081	0.0691	0.1994	-0.396	-0.563	-0.0605	-0.419	0.3346	0.1059	0.0724	0.9072	-0.0391	0.1559	0.5783	-0.0609	0.8523	49.5095	12.2356	49.0791
10	1.3095	-0.0731	-1.2064	1.1035	2.0085	5.0944	-0.2692	0.3993	-0.0779	-0.2977	0.2338	0.0764	0.1896	0.6602	-0.0266	1.2837	0.1453	0.2057	0.9255	-0.0066	1.0097	67.3154	6.8782	29.762
11	2.8966	0.6564	-0.5001	2.7783	-0.9443	4.3528	-0.285	0.6652	-0.822	-0.3359	-0.2286	0.7828	1.2153	-0.1834	0.4076	1.4849	0.0292	0.2343	0.8451	-0.1847	1.3263	53.7138	-4.9817	33.1341
12	2.6126	0.0936	-0.5906	3.7258	0.4701	5.0569	-0.1785	1.0634	-0.7953	-1.3376	-0.0915	0.5324	1.2541	0.0772	0.2801	1.9028	0.1945	0.1881	1.2635	-0.224	1.1347	63.7017	-5.849	19.9902
13	1.1795	-1.3038	-0.6294	5.8673	4.8263	7.7468	-0.2496	1.237	-0.7785	-0.6235	-0.4421	1.0529	0.8514	0.2353	0.6976	1.5531	0.0201	-0.0027	1.2235	-0.3655	1.2728	54.1753	-3.6591	21.3744

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 44 through 300 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 301 through 373 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 374 through 407 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 408 through 528 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 529 through 561 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 42 through 190 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 191 through 236 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 237 through 283 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 284 through 318 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 319 through 426 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 427 through 497 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 498 through 528 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 529 through 561 )

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