PDB-7xjv: Crystal Structure of Alpha-1,3-mannosyltransferase MNT2 from Sacc...

ID or keywords:

Entry

Database: PDB / ID: 7xjv

Title

Crystal Structure of Alpha-1,3-mannosyltransferase MNT2 from Saccharomyces cerevisiae, Mn/GDP-mannose form

Components

Alpha-1,3-mannosyltransferase MNT2

Keywords

TRANSFERASE / Mannosyltransferase

Function / homology

Function and homology information

alpha-1,3-mannosyltransferase activity / protein O-linked glycosylation / fungal-type vacuole membrane / Transferases; Glycosyltransferases; Hexosyltransferases / cell periphery / Golgi membrane / Golgi apparatus
Similarity search - Function

Biological species

Saccharomyces cerevisiae W303 (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Hira, D. / Kadooka, C. / Oka, T.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal Structure of Alpha-1,3-mannosyltransferase MNT2 from Saccharomyces cerevisiae, Mn/GDP-mannose form
Authors: Hira, D. / Kadooka, C. / Oka, T.

History

Deposition	Apr 18, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Oct 30, 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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Validation report

Summary document	7xjv_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	7xjv_full_validation.pdf.gz	3.3 MB	Display
Data in XML	7xjv_validation.xml.gz	69.2 KB	Display
Data in CIF	7xjv_validation.cif.gz	91.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xj/7xjv ftp://data.pdbj.org/pub/pdb/validation_reports/xj/7xjv	HTTPS FTP

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Related structure data

Similar structure data	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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Alpha-1,3-mannosyltransferase MNT2

B: Alpha-1,3-mannosyltransferase MNT2

C: Alpha-1,3-mannosyltransferase MNT2

D: Alpha-1,3-mannosyltransferase MNT2

hetero molecules

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

1

A: Alpha-1,3-mannosyltransferase MNT2

hetero molecules

defined by author
Evidence: gel filtration
64.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alpha-1,3-mannosyltransferase MNT2

hetero molecules

defined by author
64.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Alpha-1,3-mannosyltransferase MNT2

hetero molecules

defined by author
64.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Alpha-1,3-mannosyltransferase MNT2

hetero molecules

defined by author
64.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	130.849, 131.189, 169.552
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

End auth comp-ID: ILE / End label comp-ID: ILE

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	CYS	CYS	A	A	4 - 518	34 - 548
2	1	1	CYS	CYS	B	B	4 - 518	34 - 548
3	2	2	TRP	TRP	A	A	5 - 518	35 - 548
4	2	2	TRP	TRP	C	C	5 - 518	35 - 548
5	3	3	CYS	CYS	A	A	4 - 518	34 - 548
6	3	3	CYS	CYS	D	D	4 - 518	34 - 548
7	4	4	TRP	TRP	B	B	5 - 518	35 - 548
8	4	4	TRP	TRP	C	C	5 - 518	35 - 548
9	5	5	CYS	CYS	B	B	4 - 518	34 - 548
10	5	5	CYS	CYS	D	D	4 - 518	34 - 548
11	6	6	TRP	TRP	C	C	5 - 518	35 - 548
12	6	6	TRP	TRP	D	D	5 - 518	35 - 548

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Alpha-1,3-mannosyltransferase MNT2 Mass: 63580.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: MNT2, YGL257C, NRD558 / Production host: Escherichia coli (E. coli) References: UniProt: P53059, Transferases; Glycosyltransferases; Hexosyltransferases

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Non-polymers , 5 types, 59 molecules

#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE Mass: 605.341 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₆H₂₅N₅O₁₆P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.05 Å³/Da / Density % sol: 59.63 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 20000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. obs: 139005 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC_1/2: 0.988 / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.8→2.97 Å / Num. unique obs: 22509 / CC_1/2: 0.947

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Predicted structure model by Alphafold

Resolution: 2.8→40.003 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.92 / WR_factor R_free: 0.274 / WR_factor R_work: 0.234 / SU B: 14.596 / SU ML: 0.281 / Average fsc free: 0.8968 / Average fsc work: 0.9092 / Cross valid method: FREE R-VALUE / ESU R: 5.551 / ESU R Free: 0.357
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2508	3516	4.854 %
R_work	0.2135	68918	-
all	0.215	-	-
obs	-	72434	99.916 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 71.951 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.681 Å²	0 Å²	0 Å²
2-	-	3.125 Å²	-0 Å²
3-	-	-	-5.807 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→40.003 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16882	0	267	29	17178

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	17631
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	16277
X-RAY DIFFRACTION	r_angle_refined_deg	1.204	1.634	23817
X-RAY DIFFRACTION	r_angle_other_deg	1.061	1.58	37585
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.745	5	2032
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.078	23.678	938
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.45	15	3066
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.609	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.04	0.2	2244
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	19494
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4163
X-RAY DIFFRACTION	r_nbd_refined	0.171	0.2	3390
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.162	0.2	15357
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	8417
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	7671
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	334
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.07	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.156	0.2	33
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	113
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.089	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	2.765	7.539	8155
X-RAY DIFFRACTION	r_mcbond_other	2.765	7.538	8154
X-RAY DIFFRACTION	r_mcangle_it	4.566	11.303	10178
X-RAY DIFFRACTION	r_mcangle_other	4.566	11.304	10179
X-RAY DIFFRACTION	r_scbond_it	2.81	7.777	9476
X-RAY DIFFRACTION	r_scbond_other	2.81	7.777	9477
X-RAY DIFFRACTION	r_scangle_it	4.616	11.534	13639
X-RAY DIFFRACTION	r_scangle_other	4.615	11.534	13640
X-RAY DIFFRACTION	r_lrange_it	7.224	85.838	19401
X-RAY DIFFRACTION	r_lrange_other	7.224	85.837	19401
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.087	0.05	17332
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.089	0.05	17256
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.093	0.05	17117
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.096	0.05	17357
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.094	0.05	17237
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.101	0.05	17124

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08687	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08687	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08927	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.08927	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09347	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.09347	0.0501
4	7	B	X-RAY DIFFRACTION	Local ncs	0.09551	0.0501
4	8	C	X-RAY DIFFRACTION	Local ncs	0.09551	0.0501
5	9	B	X-RAY DIFFRACTION	Local ncs	0.09375	0.0501
5	10	D	X-RAY DIFFRACTION	Local ncs	0.09375	0.0501
6	11	C	X-RAY DIFFRACTION	Local ncs	0.10101	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.10101	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.8-2.872	0.317	278	0.312	4980	0.313	5264	0.841	0.849	99.886	0.3
2.872-2.951	0.357	276	0.298	4860	0.301	5141	0.844	0.856	99.9027	0.286
2.951-3.036	0.317	235	0.282	4751	0.284	4986	0.862	0.861	100	0.271
3.036-3.129	0.314	218	0.271	4668	0.272	4888	0.847	0.875	99.9591	0.261
3.129-3.231	0.307	259	0.262	4419	0.264	4678	0.86	0.883	100	0.253
3.231-3.343	0.286	199	0.26	4399	0.261	4598	0.897	0.899	100	0.251
3.343-3.468	0.263	196	0.252	4217	0.252	4413	0.907	0.9	100	0.247
3.468-3.609	0.278	198	0.247	4043	0.248	4243	0.88	0.892	99.9529	0.247
3.609-3.768	0.253	202	0.224	3907	0.225	4109	0.914	0.931	100	0.228
3.768-3.95	0.233	189	0.214	3729	0.215	3918	0.936	0.936	100	0.224
3.95-4.162	0.24	171	0.198	3519	0.2	3690	0.924	0.938	100	0.213
4.162-4.411	0.237	203	0.178	3354	0.181	3559	0.939	0.956	99.9438	0.198
4.411-4.711	0.204	150	0.175	3195	0.177	3346	0.952	0.957	99.9701	0.202
4.711-5.083	0.23	116	0.166	2992	0.168	3109	0.936	0.959	99.9678	0.197
5.083-5.559	0.185	126	0.166	2753	0.167	2879	0.961	0.966	100	0.198
5.559-6.2	0.27	115	0.206	2527	0.209	2642	0.922	0.943	100	0.24
6.2-7.131	0.295	124	0.224	2229	0.228	2353	0.912	0.933	100	0.266
7.131-8.665	0.237	101	0.209	1909	0.21	2011	0.92	0.941	99.9503	0.262
8.665-11.977	0.182	96	0.161	1501	0.163	1599	0.963	0.97	99.8749	0.219
11.977-40.003	0.252	58	0.244	947	0.244	1005	0.934	0.941	100	0.307

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