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- PDB-5ggi: Crystal structure of human protein O-mannose beta-1,2-N-acetylglu... -

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Basic information

Entry
Database: PDB / ID: 5ggi
TitleCrystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Mn, UDP and Mannosyl-peptide
Components
  • Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
  • mannosyl-peptide
KeywordsTRANSFERASE / SUGAR BINDING PROTEIN/SUBSTRATE / glycosyltransferease / O-mannosylation / alpha-dystroglycan / SUGAR BINDING PROTEIN-SUBSTRATE complex
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 / reactive gliosis / protein O-linked mannosylation / O-glycan processing / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development ...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 / reactive gliosis / protein O-linked mannosylation / O-glycan processing / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / myelination / sensory perception of sound / gene expression / manganese ion binding / carbohydrate binding / Golgi membrane / membrane
Similarity search - Function
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain / GG-type lectin domain profile. / Glycosyl transferase, family 13 / ILEI/PANDER domain / GNT-I family / Interleukin-like EMT inducer / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
alpha-D-mannopyranose / : / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE / Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKuwabara, N. / Senda, T. / Kato, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS26840029 Japan
JSPS16K07284 Japan
CitationJournal: 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
DepositionJun 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: 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
Revision 1.5Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
F: mannosyl-peptide
G: mannosyl-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,11211
Polymers132,7394
Non-polymers1,3737
Water1,820101
1
A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1064
Polymers65,5511
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
F: mannosyl-peptide
G: mannosyl-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0077
Polymers67,1873
Non-polymers8194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.162, 126.539, 172.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABFG

#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: 65551.453 Da / Num. of mol.: 2 / Fragment: UNP residues 92-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475 / Cell line (production host): HEK-293T / Production host: Homo sapiens (human)
References: UniProt: Q8WZA1, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein/peptide mannosyl-peptide


Mass: 817.951 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 106 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: NaKPO4 / PH range: 6.6-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→46.37 Å / Num. obs: 46907 / % possible obs: 100 % / Redundancy: 26.2 % / Rmerge(I) obs: 0.338 / Net I/σ(I): 20.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.085 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGG

5ggg


Resolution: 2.6→46.372 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 2341 5 %
Rwork0.1989 --
obs0.2009 46828 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→46.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7720 0 79 101 7900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058085
X-RAY DIFFRACTIONf_angle_d0.78411024
X-RAY DIFFRACTIONf_dihedral_angle_d16.1224867
X-RAY DIFFRACTIONf_chiral_restr0.0481181
X-RAY DIFFRACTIONf_plane_restr0.0061416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.65310.42421280.36542583X-RAY DIFFRACTION100
2.6531-2.71080.3881410.31192603X-RAY DIFFRACTION100
2.7108-2.77390.3441230.2742558X-RAY DIFFRACTION100
2.7739-2.84320.32161530.24542559X-RAY DIFFRACTION100
2.8432-2.92010.27361360.22122581X-RAY DIFFRACTION100
2.9201-3.0060.27931280.22242595X-RAY DIFFRACTION100
3.006-3.1030.25721250.21962613X-RAY DIFFRACTION100
3.103-3.21390.27621380.21752574X-RAY DIFFRACTION100
3.2139-3.34250.27051310.22222609X-RAY DIFFRACTION100
3.3425-3.49460.26791400.20712589X-RAY DIFFRACTION100
3.4946-3.67880.24931480.18912589X-RAY DIFFRACTION100
3.6788-3.90910.23061480.17772595X-RAY DIFFRACTION100
3.9091-4.21080.21021410.17212644X-RAY DIFFRACTION100
4.2108-4.63420.19631350.15912627X-RAY DIFFRACTION100
4.6342-5.30390.18811250.16622678X-RAY DIFFRACTION100
5.3039-6.67920.1841310.18722699X-RAY DIFFRACTION100
6.6792-46.3790.23031700.20562791X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°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)
13.5646-0.1023-0.37876.87510.3695.00430.0633-0.1286-0.7112-0.0403-0.5941-0.69290.65651.57870.61280.59460.2520.10381.16990.28340.771739.0011145.64494.4231
21.60420.442-0.65542.1547-0.7322.5762-0.0016-0.1466-0.14980.055-0.1046-0.0909-0.02840.16920.09690.23510.0043-0.05480.28710.04120.289513.3332152.325817.5874
34.88131.0847-1.59644.2220.0455.77760.1234-0.3740.14860.4382-0.1797-0.0478-0.1020.2020.04910.2970.01330.02820.33820.07220.28233.724146.830242.9715
44.5781-1.71132.04233.8526-0.86224.15340.20290.3561-0.2772-0.279-0.04810.35560.40030.2584-0.10130.33420.010.0080.3721-0.02840.352945.8597126.935927.4621
50.8988-0.23630.04333.15541.23862.09660.01450.01390.03-0.0895-0.12250.2613-0.129-0.01390.09230.3030.0432-0.01680.36050.02490.310148.1773140.038864.1744
66.93563.28972.56088.0356-0.40462.0033-0.3148-1.1066-1.0720.9447-0.7104-1.3108-0.07410.6930.93620.8521-0.01030.09871.00590.17160.80830.7611145.61131.5116
74.19225.4941-5.41697.195-7.08716.9917-0.1048-0.29730.0045-0.3469-0.2781-0.8056-0.00451.15150.34230.7223-0.0985-0.21211.36570.39081.828330.9825139.533161.0359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 254 through 293 )
2X-RAY DIFFRACTION2chain 'A' and (resid 294 through 551 )
3X-RAY DIFFRACTION3chain 'A' and (resid 552 through 647 )
4X-RAY DIFFRACTION4chain 'B' and (resid 97 through 259 )
5X-RAY DIFFRACTION5chain 'B' and (resid 260 through 647 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 9 )
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 5 )

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