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- PDB-7e9j: Crystal Structure of POMGNT2 in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 7e9j
TitleCrystal Structure of POMGNT2 in complex with UDP
ComponentsProtein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
KeywordsTRANSFERASE / Glycosyltransferase / O-mannose type glycosylation
Function / homology
Function and homology information


O-linked glycosylation / protein O-mannose beta-1,4-N-acetylglucosaminyltransferase / protein O-linked mannosylation / protein O-acetylglucosaminyltransferase activity / acetylglucosaminyltransferase activity / protein O-linked glycosylation / neuron migration / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
: / Glycosyltransferase 61 / Glycosyltransferase 61 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKuwabara, N.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16K07284 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101083 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05648 Japan
Japan Society for the Promotion of Science (JSPS)JP17H03987 Japan
CitationJournal: Genes Cells / Year: 2021
Title: The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on alpha-dystroglycan.
Authors: Imae, R. / Kuwabara, N. / Manya, H. / Tanaka, T. / Tsuyuguchi, M. / Mizuno, M. / Endo, T. / Kato, R.
History
DepositionMar 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: 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

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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-1,4-N-acetylglucosaminyltransferase 2
B: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9439
Polymers123,1282
Non-polymers1,8157
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-26 kcal/mol
Surface area44280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.129, 106.233, 132.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 / POMGnT2 / Extracellular O-linked N-acetylglucosamine transferase-like / Glycosyltransferase-like ...POMGnT2 / Extracellular O-linked N-acetylglucosamine transferase-like / Glycosyltransferase-like domain-containing protein 2


Mass: 61563.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: POMGNT2, AGO61, GTDC2 / Production host: Homo sapiens (human)
References: UniProt: Q5NDF2, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.0 or 8.5), 12-16 % PEG 8000, 1 % tacsimate (pH 7.0)
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.0718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.4→49.3 Å / Num. obs: 56436 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 1.858 / Num. unique obs: 5292 / CC1/2: 0.442 / Rpim(I) all: 0.518

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.3 Å / SU ML: 0.321 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0105
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 2771 5.16 %
Rwork0.2048 50894 -
obs0.2065 53665 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8285 0 114 242 8641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348646
X-RAY DIFFRACTIONf_angle_d0.626411813
X-RAY DIFFRACTIONf_chiral_restr0.0451324
X-RAY DIFFRACTIONf_plane_restr0.00391504
X-RAY DIFFRACTIONf_dihedral_angle_d14.28521161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.36571410.33262494X-RAY DIFFRACTION100
2.44-2.490.37091270.33072530X-RAY DIFFRACTION100
2.49-2.530.37391400.31642525X-RAY DIFFRACTION100
2.53-2.590.32081370.29592485X-RAY DIFFRACTION100
2.59-2.640.3161290.28062529X-RAY DIFFRACTION99.96
2.64-2.70.30591370.26922506X-RAY DIFFRACTION100
2.7-2.770.31321380.25692513X-RAY DIFFRACTION100
2.77-2.850.27441370.23332529X-RAY DIFFRACTION99.96
2.85-2.930.26181600.23682500X-RAY DIFFRACTION100
2.93-3.020.24311420.22542526X-RAY DIFFRACTION99.96
3.02-3.130.25881570.22852505X-RAY DIFFRACTION100
3.13-3.260.29661530.22622511X-RAY DIFFRACTION100
3.26-3.410.27111500.212529X-RAY DIFFRACTION100
3.41-3.580.23261280.20622560X-RAY DIFFRACTION100
3.58-3.810.2271240.18312553X-RAY DIFFRACTION99.96
3.81-4.10.2181330.17662563X-RAY DIFFRACTION100
4.1-4.520.18211320.1512568X-RAY DIFFRACTION100
4.52-5.170.15041390.14232585X-RAY DIFFRACTION100
5.17-6.510.20031280.1792646X-RAY DIFFRACTION100
6.51-49.30.19471390.18742737X-RAY DIFFRACTION99.79
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)
11.12934318978-0.0197013664778-0.3061364131520.625099998581-0.5272918455483.60091163609-0.09503184910860.0549064023994-0.156738372924-0.05151204249180.07045367534450.03878717828760.210787424786-0.1769599831460.0409708605610.254465524656-0.0152085716788-0.008523629027490.2135450990990.02165346574030.25944595476787.1963568329106.334994033149.143425564
25.69775135227-3.05220461479-0.653746105854.931666852690.8626793981814.6546082112-0.01084965039050.06870179879950.1772855219970.2425597610130.01617658622890.147206897167-0.41483469281-0.4964708876070.01089726227620.390336109658-0.0653825197811-0.02094605452510.3610533380890.1038985599870.22333955626282.2423491699122.196640199128.662578738
33.076588197792.93075258511.134151664024.609831967431.447016961831.16070433036-0.07768844901820.2106935282740.0343404423667-0.0913837465588-0.0795135693256-0.114606173284-0.1290020981820.001561903573760.1612913115640.3122518288030.08992289667470.02154235653460.5918893314310.1106197334670.353784604717129.205992223121.995984713150.126793226
42.25727931713-0.6501270334340.6451625542031.404319736430.2642658032383.4666508874-0.313435210268-0.5814177719590.08627138997270.3320496365060.154585657283-0.287798783179-0.08646009970420.03073028765240.06884087887520.3233954291050.0620750335894-0.1026329115830.4166596953410.04020194330240.349262903099109.220999992108.964137108176.411110646
51.750572400440.04319841721390.8843540252272.266528099240.1717518388812.78343525709-0.609137693178-0.8269756272290.5693598878990.2682424881280.0639884239901-0.417750512382-0.9024774992780.1766602191920.4939504736470.9190912332250.184646913684-0.4161742632140.882513934502-0.2205439954610.781654015205110.551241659129.498633527192.740785172
63.16103170873-1.002396476091.575895580124.43169624783-2.873149062324.5619632345-0.453146939842-0.5935893789230.2992922170680.3251691125580.4397636669480.238396490247-0.54161206854-0.4424932849430.05121115487190.3289669133330.100579591608-0.03645905685340.515405532322-0.04590546263920.29288297079266.7808350021126.021794078171.090752352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 400 )
2X-RAY DIFFRACTION2chain 'A' and (resid 401 through 473 )
3X-RAY DIFFRACTION3chain 'A' and (resid 474 through 580 )
4X-RAY DIFFRACTION4chain 'B' and (resid 52 through 375 )
5X-RAY DIFFRACTION5chain 'B' and (resid 376 through 474 )
6X-RAY DIFFRACTION6chain 'B' and (resid 475 through 580 )

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