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- PDB-7jhl: Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 wit... -

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Basic information

Entry
Database: PDB / ID: 7jhl
TitleStructure of human beta 1,3-N-acetylglucosaminyltransferase 2 with UDP-N-acetylglucosamine
ComponentsN-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
KeywordsTRANSFERASE / glycosyltransferase / poly-N-acetyl-lactosamine
Function / homology
Function and homology information


N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / keratan sulfate proteoglycan biosynthetic process / poly-N-acetyllactosamine biosynthetic process / N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity / Keratan sulfate biosynthesis / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / axon guidance ...N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / keratan sulfate proteoglycan biosynthetic process / poly-N-acetyllactosamine biosynthetic process / N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity / Keratan sulfate biosynthesis / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / axon guidance / cellular response to leukemia inhibitory factor / sensory perception of smell / Golgi membrane
Similarity search - Function
Glycosyl transferase, family 31 / Galactosyltransferase
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsHao, Y. / Huang, X.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structures and mechanism of human glycosyltransferase beta 1,3-N-acetylglucosaminyltransferase 2 (B3GNT2), an important player in immune homeostasis.
Authors: Hao, Y. / Crequer-Grandhomme, A. / Javier, N. / Singh, A. / Chen, H. / Manzanillo, P. / Lo, M.C. / Huang, X.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
B: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,37314
Polymers86,6012
Non-polymers3,77312
Water4,972276
1
A: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1247
Polymers43,3001
Non-polymers1,8236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2507
Polymers43,3001
Non-polymers1,9496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.654, 76.638, 134.206
Angle α, β, γ (deg.)90.000, 105.270, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 / Beta-1 / 3-N-acetylglucosaminyltransferase 1 / Beta3Gn-T1 / 3-galactosyltransferase 7 / b3Gal-T7 / ...Beta-1 / 3-N-acetylglucosaminyltransferase 1 / Beta3Gn-T1 / 3-galactosyltransferase 7 / b3Gal-T7 / Beta-3-Gx-T7 / UDP-Gal:beta-GlcNAc beta-1 / UDP-GlcNAc:betaGal beta-1 / 3-N-acetylglucosaminyltransferase 2 / Beta3Gn-T2 / UDP-galactose:beta-N-acetylglucosamine beta-1


Mass: 43300.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B3GNT2, B3GALT7, B3GNT1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NY97, N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 2 / 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

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Non-polymers , 5 types, 284 molecules

#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 24% PEG1500, 20% glycerol

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Data collection

DiffractionMean temperature: 87 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→46.42 Å / Num. obs: 37963 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.64 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.063 / Rrim(I) all: 0.165 / Net I/σ(I): 9.4 / Num. measured all: 255698 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.26-2.3370.9782412634700.8130.3981.0572.4100
9.04-46.426.60.05441756330.9970.0230.05922.299.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JHI

7jhi


Resolution: 2.26→46.42 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 1833 4.84 %
Rwork0.1747 36071 -
obs0.1771 37904 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.44 Å2 / Biso mean: 39.0774 Å2 / Biso min: 14.05 Å2
Refinement stepCycle: final / Resolution: 2.26→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 243 276 5959
Biso mean--50.85 42.44 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045918
X-RAY DIFFRACTIONf_angle_d0.6898063
X-RAY DIFFRACTIONf_chiral_restr0.044895
X-RAY DIFFRACTIONf_plane_restr0.0041006
X-RAY DIFFRACTIONf_dihedral_angle_d13.7663508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.26-2.32110.28511490.23082741100
2.3211-2.38940.28931490.23012785100
2.3894-2.46660.34261320.22072730100
2.4666-2.55470.23631390.20822768100
2.5547-2.6570.30041490.19832765100
2.657-2.77790.22351350.18662761100
2.7779-2.92430.23851420.18772784100
2.9243-3.10750.26461460.1822743100
3.1075-3.34740.23431310.17682802100
3.3474-3.68410.2241540.16142759100
3.6841-4.21690.17821330.14082798100
4.2169-5.31160.17981290.14562824100
5.3116-46.420.19131450.1788281198

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