PDB-6x5h: Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP

ID or keywords:

Entry

Database: PDB / ID: 6x5h

Title

Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP

Components

Alpha-(1,6)-fucosyltransferase

Keywords

TRANSFERASE / Glycosyl transferase / Fucosyl transferase / GT-B fold / Inverting

Function / homology

Function and homology information

glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / N-glycan fucosylation / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / L-fucose catabolic process / N-glycan processing ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Kadirvelraj, R. / Wood, Z.A.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Characterizing human alpha-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases.
Authors: Boruah, B.M. / Kadirvelraj, R. / Liu, L. / Ramiah, A. / Li, C. / Zong, G. / Bosman, G.P. / Yang, J.Y. / Wang, L.X. / Boons, G.J. / Wood, Z.A. / Moremen, K.W.

History

Deposition	May 26, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 7, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 21, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Dec 23, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6x5h.cif.gz	784.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6x5h.ent.gz	647.2 KB	Display	PDB format
PDBx/mmJSON format	6x5h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6x5h_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	6x5h_full_validation.pdf.gz	1.5 MB	Display
Data in XML	6x5h_validation.xml.gz	76.9 KB	Display
Data in CIF	6x5h_validation.cif.gz	112 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x5/6x5h ftp://data.pdbj.org/pub/pdb/validation_reports/x5/6x5h	HTTPS FTP

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Related structure data

Related structure data	6x5rC 6x5sC 6x5tC 6x5uC 2de0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vle-d 6vlf-d 6tkv-1 6vld-2 6x5u-1 6x5t-2 6x5t-3 6x5t-1 6x5u-4 3ua5-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#88 - Apr 2007 Clathrin similarity (1)

Deposited unit

A: Alpha-(1,6)-fucosyltransferase

B: Alpha-(1,6)-fucosyltransferase

C: Alpha-(1,6)-fucosyltransferase

D: Alpha-(1,6)-fucosyltransferase

hetero molecules

250 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Alpha-(1,6)-fucosyltransferase

hetero molecules

D: Alpha-(1,6)-fucosyltransferase

hetero molecules

defined by author&software
Evidence: light scattering
125 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alpha-(1,6)-fucosyltransferase

C: Alpha-(1,6)-fucosyltransferase

hetero molecules

defined by author&software
125 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	173.490, 173.490, 207.420
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Alpha-(1,6)-fucosyltransferase / Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6- ...Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6-fucosyltransferase / GDP-fucose--glycoprotein fucosyltransferase / Glycoprotein 6-alpha-L-fucosyltransferase Mass: 61845.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FUT8 / Cell (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₁₀H₁₅N₅O₁₁P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1299 / Source method: isolated from a natural source / Formula: H₂O
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: 3.75 Å³/Da / Density % sol: 67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6 M Ammonium sulfate, 0.6 M L-proline, 100 mM Hepes pH 7.5 Temp details: Room temperature

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 21, 2017
Radiation	Monochromator: Si (111) Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.25→86.75 Å / Num. obs: 165616 / % possible obs: 99.2 % / Redundancy: 5.1 % / B_iso Wilson estimate: 31.7 Å² / CC_1/2: 0.995 / R_rim(I) all: 0.158 / Net I/σ(I): 10.44
Reflection shell	Resolution: 2.25→2.31 Å / Redundancy: 4.1 % / Num. unique obs: 11970 / CC_1/2: 0.556 / R_rim(I) all: 1.1 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2DE0

2de0

Resolution: 2.25→86.745 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.202	8312	5.02 %	Random selection
R_work	0.1706	-	-	-
obs	0.1721	165569	99.17 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.25→86.745 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14933	0	148	1301	16382

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15554
X-RAY DIFFRACTION	f_angle_d	0.918	21100
X-RAY DIFFRACTION	f_dihedral_angle_d	10.945	9293
X-RAY DIFFRACTION	f_chiral_restr	0.053	2233
X-RAY DIFFRACTION	f_plane_restr	0.006	2701

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 (%)
2.2503-2.2758	0.3241	261	0.2855	4929	X-RAY DIFFRACTION	94
2.2758-2.3026	0.2964	273	0.241	5235	X-RAY DIFFRACTION	100
2.3026-2.3307	0.276	284	0.2211	5314	X-RAY DIFFRACTION	100
2.3307-2.3602	0.2711	269	0.2268	5241	X-RAY DIFFRACTION	100
2.3602-2.3913	0.2584	285	0.2206	5260	X-RAY DIFFRACTION	100
2.3913-2.424	0.2508	282	0.2074	5287	X-RAY DIFFRACTION	100
2.424-2.4587	0.2643	273	0.2151	5267	X-RAY DIFFRACTION	100
2.4587-2.4954	0.2655	281	0.2079	5267	X-RAY DIFFRACTION	100
2.4954-2.5344	0.2389	283	0.1977	5226	X-RAY DIFFRACTION	100
2.5344-2.5759	0.2284	277	0.1958	5274	X-RAY DIFFRACTION	100
2.5759-2.6203	0.2439	283	0.1966	5241	X-RAY DIFFRACTION	100
2.6203-2.668	0.2647	280	0.2019	5327	X-RAY DIFFRACTION	100
2.668-2.7193	0.2214	267	0.1878	5216	X-RAY DIFFRACTION	100
2.7193-2.7748	0.2132	278	0.1824	5276	X-RAY DIFFRACTION	100
2.7748-2.8351	0.2337	278	0.1802	5265	X-RAY DIFFRACTION	100
2.8351-2.9011	0.2279	281	0.1798	5263	X-RAY DIFFRACTION	100
2.9011-2.9737	0.21	269	0.1751	5258	X-RAY DIFFRACTION	100
2.9737-3.0541	0.2245	275	0.1783	5253	X-RAY DIFFRACTION	99
3.0541-3.1439	0.2116	277	0.1813	5279	X-RAY DIFFRACTION	99
3.1439-3.2454	0.2321	280	0.1794	5226	X-RAY DIFFRACTION	99
3.2454-3.3614	0.2008	276	0.1682	5267	X-RAY DIFFRACTION	99
3.3614-3.496	0.195	278	0.1642	5227	X-RAY DIFFRACTION	99
3.496-3.6551	0.1893	276	0.1475	5282	X-RAY DIFFRACTION	99
3.6551-3.8478	0.1734	275	0.1446	5250	X-RAY DIFFRACTION	99
3.8478-4.0889	0.1582	284	0.137	5223	X-RAY DIFFRACTION	99
4.0889-4.4046	0.1604	282	0.1288	5190	X-RAY DIFFRACTION	99
4.4046-4.8478	0.14	276	0.1241	5249	X-RAY DIFFRACTION	98
4.8478-5.5492	0.1623	275	0.1506	5228	X-RAY DIFFRACTION	99
5.5492-6.9909	0.1921	283	0.1743	5211	X-RAY DIFFRACTION	98
6.9909-86.745	0.1734	271	0.1765	5226	X-RAY DIFFRACTION	97

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	1.2798	0.2451	-0.3434	0.479	-0.0375	0.6172	-0.0883	-0.0223	0.0409	-0.0071	0.0411	0.0351	-0.0166	0.045	0.0429	0.2466	0.0046	-0.0203	0.2342	-0.0426	0.2278	137.1757	16.895	-10.0262
2	2.8538	0.6892	-1.5202	1.3002	-0.1987	2.1679	-0.0993	0.1578	-0.1339	-0.0329	0.0294	0.0451	0.0218	-0.1054	0.0792	0.2276	-0.0439	-0.0083	0.2269	-0.076	0.1951	129.3001	2.3021	-21.2761
3	0.6555	0.0203	-0.1423	0.6221	0.1008	0.6097	-0.063	-0.0915	-0.0445	0.063	0.0292	0.0151	0.0608	0.0368	0.0309	0.2407	0.0129	0.0071	0.2634	-0.0289	0.2617	135.829	6.537	-7.8094
4	5.3018	-1.0645	-1.7244	2.181	-0.041	2.8117	-0.0724	0.0324	0.0837	-0.1768	-0.0607	-0.3641	0.0005	0.2796	0.1332	0.3289	-0.0679	-0.0647	0.2516	0.0759	0.3734	197.2043	58.6279	-57.8703
5	8.1446	3.9785	-3.0269	4.531	-3.3402	3.1181	0.3551	0.0008	0.8263	0.5042	-0.0882	0.781	-0.381	-0.1545	-0.1983	0.2279	0.046	-0.0639	0.2612	-0.054	0.2477	164.1202	49.7361	-43.9047
6	2.2503	0.3122	0.5438	0.769	0.0669	1.3104	0.0091	-0.156	-0.0004	0.0024	-0.0503	0.0474	0.105	-0.1098	0.0482	0.2729	-0.0434	-0.0234	0.2627	0.0104	0.2497	163.9091	26.8345	-37.5217
7	1.4114	0.6509	0.132	1.6924	0.3455	1.1202	-0.0404	0.0034	0.0251	-0.1538	-0.0107	0.0848	0.1461	-0.0359	0.0478	0.2243	-0.0231	-0.0659	0.269	-0.0067	0.2183	162.9236	31.1779	-48.0035
8	3.5283	0.6949	-0.4304	2.1629	-1.5536	1.4126	0.1059	-0.1708	-0.0194	-0.0011	-0.2105	-0.086	-0.1328	0.054	0.096	0.2108	-0.0461	-0.0883	0.2511	0.0453	0.1808	185.5648	36.4642	-33.2702
9	1.558	0.9284	-0.4898	2.088	-1.4983	1.8951	-0.0198	-0.1297	-0.0158	0.0466	-0.0805	-0.0881	-0.0246	0.1002	0.1119	0.202	-0.012	-0.0492	0.252	0.0161	0.2057	191.5319	38.9827	-34.3255
10	1.5018	0.1377	-0.2035	0.9172	-0.257	0.8974	-0.0687	0.1889	-0.0148	-0.2319	0.0133	-0.0483	0.0883	0.0356	0.0521	0.3085	-0.024	-0.0338	0.2339	0.0239	0.2394	180.4562	38.4319	-57.4282
11	7.7494	-3.4222	-0.4942	4.0697	0.0722	2.0093	-0.0585	0.3942	0.0742	-0.3245	-0.0892	-0.3271	0.0894	0.0246	0.1394	0.3088	-0.0895	-0.0203	0.2095	0.0429	0.2354	192.3713	50.6734	-64.0417
12	1.4174	-0.9992	0.1378	3.1399	0.121	0.7092	0.0257	0.4458	0.5657	-0.4967	-0.1466	-0.2658	-0.2686	-0.1131	-0.0137	0.569	0.0225	-0.1048	0.4466	0.3108	0.646	185.7738	92.1408	-72.1337
13	1.2683	-0.4073	0.3845	2.5747	-0.9392	2.5995	0.0397	0.7367	0.2543	-0.8905	-0.0412	-0.2612	-0.0621	-0.0043	0.0533	0.7435	0.0301	0.0452	0.6373	0.1832	0.3836	193.6119	70.5465	-84.7522
14	1.1628	-0.6448	0.3546	2.0048	-0.7671	1.3461	-0.0413	0.0878	0.2793	-0.1314	-0.047	-0.1669	-0.2091	0.0921	0.0982	0.3583	-0.0467	-0.0452	0.2802	0.1306	0.4748	196.57	76.7435	-59.8017
15	1.8318	0.704	-0.6053	1.2148	-0.078	1.0341	-0.0062	-0.2303	-0.2079	0.1584	-0.0127	0.2122	0.0402	-0.15	-0.026	0.2748	-0.0215	0.0829	0.3194	0.0602	0.33	210.6011	98.3555	-25.3097
16	3.7834	-0.2147	1.8412	1.1096	1.5863	3.6273	-0.2321	-0.3871	-0.5336	0.3976	0.4132	0.3348	0.6232	-0.2523	-0.0931	0.4855	-0.0802	0.2958	0.7872	0.1445	0.7933	185.2514	82.9639	-12.0426
17	2.438	0.9619	0.0722	1.7917	0.221	1.0456	-0.2034	0.1657	-0.5525	-0.042	0.1431	0.3122	0.3627	-0.5591	-0.0788	0.3356	-0.1724	0.133	0.5516	0.0512	0.6934	190.2928	84.1039	-27.3168
18	3.4351	1.0727	-1.3011	1.5354	-0.5749	3.0061	0.1569	-0.7231	-0.2407	0.5308	-0.236	0.1141	0.0469	0.2197	0.0916	0.4424	-0.0201	0.0911	0.5465	0.0822	0.3347	214.1339	95.267	-6.1256
19	1.8548	-0.4195	-0.873	1.0997	0.6112	2.5048	-0.116	-0.2867	-0.1729	0.2081	0.053	0.1567	0.3006	-0.0837	0.0932	0.2748	-0.0385	0.0818	0.2974	0.0835	0.4021	211.024	87.4242	-23.3422
20	3.8413	-0.0671	-0.7924	0.0454	-0.3212	1.1713	0.1622	0.0574	-0.1972	-0.052	-0.0043	0.2387	0.1086	-0.3581	-0.1292	0.288	-0.0831	0.066	0.3926	0.0161	0.5168	203.2962	89.2455	-35.849

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 108 through 339 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 340 through 412 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 413 through 574 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 108 through 172 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 173 through 199 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 200 through 267 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 268 through 339 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 340 through 378 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 379 through 458 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 459 through 574 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 108 through 172 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 173 through 378 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 379 through 469 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 470 through 574 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 108 through 237 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 238 through 267 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 268 through 339 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 340 through 427 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 428 through 548 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 549 through 574 )

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