PDB-5ggj: Crystal structure of N-terminal domain of human protein O-mannose...

ID or keywords:

Entry

Database: PDB / ID: 5ggj

Title

Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Man-alpha-pNP

Components

Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1

Keywords

SUGAR BINDING PROTEIN / glycosyltransferease / O-mannosylation / alpha-dystroglycan

Function / homology

Function and homology information

beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / protein O-linked glycosylation via N-acetyl-galactosamine / protein O-linked glycosylation via mannose / reactive gliosis / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.424 Å

Authors

Kuwabara, N. / Senda, T. / Kato, R.

Funding support

Japan, 2items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
Authors: Kuwabara, N. / Manya, H. / Yamada, T. / Tateno, H. / Kanagawa, M. / Kobayashi, K. / Akasaka-Manya, K. / Hirose, Y. / Mizuno, M. / Ikeguchi, M. / Toda, T. / Hirabayashi, J. / Senda, T. / Endo, T. / Kato, R.

History

Deposition	Jun 16, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 10, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 31, 2016	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ggj.cif.gz	149.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ggj.ent.gz	117.3 KB	Display	PDB format
PDBx/mmJSON format	5ggj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ggj_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5ggj_full_validation.pdf.gz	1 MB	Display
Data in XML	5ggj_validation.xml.gz	18.7 KB	Display
Data in CIF	5ggj_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggj ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggj	HTTPS FTP

-
Related structure data

Related structure data	5ggfC 5gggSC 5ggiC 5ggkC 5gglC 5ggnC 5ggoC 5ggpC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ggl-1 5xfc-1 5ggn-1 5ggk-1 5xfc-2 6vgv-d 3sub-1 5ggo-1 4qxk-d 4a60-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

-
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: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1

B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1

hetero molecules

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

1

A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1

hetero molecules

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

2

B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.490, 88.830, 53.533
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-612- HOH
2	1	A-618- HOH

#1: Protein

Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 / POMGnT1 / UDP-GlcNAc:alpha-D-mannoside beta-1 / 2-N-acetylglucosaminyltransferase I.2 / GnT I.2

Mass: 17623.020 Da / Num. of mol.: 2 / Fragment: UNP residues 92-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q8WZA1, Transferases; Glycosyltransferases; Hexosyltransferases

#2: Sugar

ChemComp-PNA / 4-nitrophenyl alpha-D-mannopyranoside / 4'-NITROPHENYL-ALPHA-D-MANNOPYRANOSIDE / 4-nitrophenyl alpha-D-mannoside / 4-nitrophenyl D-mannoside / 4-nitrophenyl mannoside

Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₁₂H₁₅NO₈

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.52 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: Tris-HCl, PEG-6000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.42→19.2 Å / Num. obs: 62431 / % possible obs: 99.4 % / Redundancy: 7 % / R_merge(I) obs: 0.077 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.42→1.43 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.98 / Mean I/σ(I) obs: 1 / % possible all: 90.8

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5GGG

5ggg

Resolution: 1.424→19.175 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.28 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS

	R_factor	Num. reflection	% reflection
R_free	0.2086	3819	3.21 %
R_work	0.1867	-	-
obs	0.1874	62371	99.22 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.424→19.175 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2327	0	42	412	2781

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2428
X-RAY DIFFRACTION	f_angle_d	1.013	3296
X-RAY DIFFRACTION	f_dihedral_angle_d	22.008	884
X-RAY DIFFRACTION	f_chiral_restr	0.094	378
X-RAY DIFFRACTION	f_plane_restr	0.006	417

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 (%)
1.4237-1.4417	0.4092	116	0.3726	3467	X-RAY DIFFRACTION	81
1.4417-1.4607	0.3509	144	0.3305	4296	X-RAY DIFFRACTION	100
1.4607-1.4807	0.3109	142	0.3042	4313	X-RAY DIFFRACTION	100
1.4807-1.5018	0.2731	140	0.2924	4309	X-RAY DIFFRACTION	100
1.5018-1.5243	0.276	145	0.2762	4301	X-RAY DIFFRACTION	100
1.5243-1.5481	0.3261	140	0.27	4281	X-RAY DIFFRACTION	100
1.5481-1.5734	0.2503	142	0.2411	4330	X-RAY DIFFRACTION	100
1.5734-1.6006	0.2307	143	0.2307	4248	X-RAY DIFFRACTION	100
1.6006-1.6296	0.2255	144	0.225	4289	X-RAY DIFFRACTION	100
1.6296-1.661	0.2415	139	0.2118	4311	X-RAY DIFFRACTION	100
1.661-1.6949	0.2417	146	0.2123	4300	X-RAY DIFFRACTION	100
1.6949-1.7317	0.2399	140	0.203	4324	X-RAY DIFFRACTION	100
1.7317-1.7719	0.2237	143	0.2095	4261	X-RAY DIFFRACTION	100
1.7719-1.8162	0.2648	144	0.207	4309	X-RAY DIFFRACTION	100
1.8162-1.8653	0.2591	142	0.2041	4251	X-RAY DIFFRACTION	100
1.8653-1.9201	0.2421	144	0.1935	4363	X-RAY DIFFRACTION	100
1.9201-1.982	0.2114	144	0.1783	4301	X-RAY DIFFRACTION	100
1.982-2.0528	0.1795	136	0.1782	4254	X-RAY DIFFRACTION	100
2.0528-2.1349	0.2244	144	0.1766	4303	X-RAY DIFFRACTION	100
2.1349-2.2319	0.1902	144	0.177	4305	X-RAY DIFFRACTION	100
2.2319-2.3494	0.22	134	0.1737	4280	X-RAY DIFFRACTION	100
2.3494-2.4963	0.2394	141	0.1753	4295	X-RAY DIFFRACTION	100
2.4963-2.6886	0.2002	147	0.1757	4295	X-RAY DIFFRACTION	100
2.6886-2.9582	0.1889	146	0.174	4288	X-RAY DIFFRACTION	100
2.9582-3.3843	0.1826	143	0.1689	4289	X-RAY DIFFRACTION	100
3.3843-4.2561	0.1796	136	0.1615	4278	X-RAY DIFFRACTION	100
4.2561-19.1771	0.1692	150	0.1664	4282	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	1.2089	-0.6107	-0.3557	3.6273	1.0757	1.8864	0.047	0.0328	-0.0108	-0.2334	-0.2069	0.5403	-0.2831	-0.3492	0.1046	0.1953	0.0681	-0.0326	0.2526	-0.0167	0.1414	8.6579	10.1307	7.9963
2	0.2053	-0.0956	0.1924	0.7419	-0.753	0.7844	0.4414	0.3593	-0.1856	-1.1928	-0.5549	0.4024	-0.0355	-0.2233	0.1113	0.3383	0.1055	-0.0576	0.2419	-0.0399	0.1861	14.356	5.2172	-0.7544
3	0.8027	-0.4044	-0.0113	2.7506	0.1774	0.3517	0.0127	-0.0292	0.0496	-0.0513	-0.0108	-0.1461	-0.0365	-0.0057	0.0009	0.1233	0.0222	-0.0026	0.161	-0.0174	0.1039	22.3558	5.1567	11.6977
4	1.5046	-0.4671	0.2475	1.5238	0.1906	2.0507	0.0985	-0.1679	-0.0246	0.2822	-0.0309	0.0686	0.0253	-0.0362	-0.013	0.1593	0.0028	0.0056	0.2001	-0.0103	0.1431	17.8842	-3.5723	18.4166
5	1.3539	-0.8871	-0.4475	2.3609	0.1789	1.9174	-0.0515	-0.0614	-0.223	0.0668	-0.0581	0.4447	0.0144	-0.2402	0.0056	0.1165	0.0286	-0.0012	0.2074	0.0043	0.1906	10.5112	0.0152	14.8221
6	2.401	1.427	0.973	7.6906	4.3423	3.5516	0.0724	-0.1582	0.2044	-0.1256	-0.2602	0.3321	-0.3806	-0.3212	0.1503	0.2129	0.0708	0.0135	0.2476	0.0001	0.1412	8.8073	15.4642	17.5128
7	4.9869	0.6207	0.9159	2.6846	0.2215	1.4505	0.1206	0.6052	-0.2122	-0.2206	-0.0175	-0.4305	0.2296	0.5271	-0.1354	0.18	0.0848	0.0281	0.2514	-0.0221	0.1922	14.3664	13.9986	33.0945
8	0.0586	-0.2119	-0.2158	2.7085	0.9943	0.8736	0.1991	0.9039	-1.1488	-0.3203	-0.2762	0.0282	0.2859	0.0636	-0.0138	0.3176	0.0598	-0.024	0.3208	-0.0754	0.3529	4.304	6.4215	33.4036
9	2.4909	0.0782	0.8349	2.8898	0.1024	1.1322	0.1098	-0.4343	-0.3767	0.4248	0.0736	-0.3459	0.3487	0.1131	-0.0645	0.223	0.074	-0.0444	0.2149	-0.0005	0.1771	11.283	13.088	44.8101
10	5.318	0.0326	2.9523	1.3245	0.4636	2.0806	-0.0492	-0.3754	-0.389	0.2156	0.0679	0.1521	0.0942	-0.2897	0.0049	0.175	0.0156	0.0231	0.1798	0.0118	0.1559	-2.9509	17.3611	46.4242
11	1.8062	0.2815	0.3409	1.1649	0.4216	0.5638	-0.0005	0.0043	0.0708	-0.0044	-0.056	0.0285	-0.0267	0.0589	0.043	0.1448	0.0182	0.0075	0.1503	0.0041	0.1095	4.3667	23.5993	39.4823
12	3.8905	0.2702	1.0573	2.2636	0.2674	1.433	0.1151	0.2516	0.3417	-0.2489	-0.0935	-0.0283	-0.1539	0.0861	-0.0118	0.2402	0.0593	0.0477	0.214	-0.0246	0.1323	8.5631	21.004	30.6608

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 97 through 116 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 117 through 129 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 130 through 186 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 187 through 208 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 209 through 237 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 238 through 249 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 97 through 116 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 117 through 129 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 130 through 149 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 150 through 166 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 167 through 226 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 227 through 248 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi