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- PDB-8kb7: Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglu... -

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Basic information

Entry
Database: PDB / ID: 8kb7
TitleCrystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)
ComponentsProtein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
KeywordsTRANSFERASE / glycosyltransferase
Function / homology
Function and homology information


protein O-mannose beta-1,4-N-acetylglucosaminyltransferase / O-linked glycosylation / 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
alpha-D-mannopyranose / URIDINE-5'-DIPHOSPHATE / Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSatoh, T. / Umezawa, F. / Yagi, H. / Kato, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)23gm6410010h0004 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H03361 Japan
CitationJournal: To Be Published
Title: Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)
Authors: Satoh, T. / Umezawa, F. / Yagi, H. / Kato, K.
History
DepositionAug 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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


Theoretical massNumber of molelcules
Total (without water)260,82622
Polymers257,0204
Non-polymers3,80618
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.019, 150.002, 191.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA52 - 57930 - 557
21ASNASNBB52 - 57930 - 557
12THRTHRAA52 - 58030 - 558
22THRTHRCC52 - 58030 - 558
13THRTHRAA52 - 58030 - 558
23THRTHRDD52 - 58030 - 558
14ASNASNBB52 - 57930 - 557
24ASNASNCC52 - 57930 - 557
15ASNASNBB52 - 57930 - 557
25ASNASNDD52 - 57930 - 557
16THRTHRCC52 - 58030 - 558
26THRTHRDD52 - 58030 - 558

NCS ensembles :
ID
1
2
3
4
5
6

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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: 64254.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 / Plasmid: p3XFLAG-CMV-9 / Cell (production host): Expi293 / Production host: Homo sapiens (human)
References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
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
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY
Has protein modificationY

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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: 4.05 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 12% PEG4000, 0.1 M sodium citrate tribasic (pH 6.0), and 0.1 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2020
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 97911 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.5
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 31767 / CC1/2: 0.569 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→47.92 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.953 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22823 5042 4.9 %RANDOM
Rwork0.19124 ---
obs0.19304 97911 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.647 Å2
Baniso -1Baniso -2Baniso -3
1--4.61 Å20 Å20 Å2
2--6.09 Å20 Å2
3----1.47 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16633 0 236 0 16869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01317347
X-RAY DIFFRACTIONr_bond_other_d0.0010.01516374
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.66723631
X-RAY DIFFRACTIONr_angle_other_deg1.2261.58337569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.00752025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41121.284950
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.316152834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.24815131
X-RAY DIFFRACTIONr_chiral_restr0.0710.22211
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024248
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.0468.8768148
X-RAY DIFFRACTIONr_mcbond_other8.0458.8768147
X-RAY DIFFRACTIONr_mcangle_it11.1313.32810157
X-RAY DIFFRACTIONr_mcangle_other11.1313.32910158
X-RAY DIFFRACTIONr_scbond_it9.2219.799199
X-RAY DIFFRACTIONr_scbond_other9.229.7919199
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.48414.3813475
X-RAY DIFFRACTIONr_long_range_B_refined15.80618030
X-RAY DIFFRACTIONr_long_range_B_other15.80618030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A166460.04
12B166460.04
21A167040.05
22C167040.05
31A168270.04
32D168270.04
41B165450.05
42C165450.05
51B165590.05
52D165590.05
61C166620.05
62D166620.05
LS refinement shellResolution: 2.8→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 345 -
Rwork0.375 7074 -
obs--98.7 %

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