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

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Basic information

Entry
Database: PDB / ID: 7jhn
TitleStructure of human beta 1,3-N-acetylglucosaminyltransferase 2 with UDP and trisaccharide GlcNAc-beta1-3Gal-beta1-4GlcNAc
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
URIDINE-5'-DIPHOSPHATE / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 21, 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 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: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5188
Polymers43,3001
Non-polymers2,2187
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.916, 76.865, 66.786
Angle α, β, γ (deg.)90.000, 105.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.: 1
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 , 3 types, 3 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.: 1
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2-1/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 1 / 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 , 4 types, 111 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17836 / % possible obs: 86.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.25 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Χ2: 0.923 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.242.70.5065260.7490.3370.6110.86951.3
2.24-2.282.90.4345510.8290.2830.520.92454.9
2.28-2.3230.4426200.8220.2860.5290.88360.4
2.32-2.373.10.3246770.9360.2040.3830.82264.8
2.37-2.423.20.4356910.850.2720.5150.89269.9
2.42-2.483.20.3537820.9560.2180.4160.89675.3
2.48-2.543.30.2828340.9540.1730.3320.9480.6
2.54-2.613.30.2638680.9590.1610.3090.8985.9
2.61-2.693.40.2299670.9670.140.2690.94593.1
2.69-2.773.50.1759780.9840.1070.2050.94897.2
2.77-2.873.60.16910170.9860.1010.1971.00699.2
2.87-2.993.80.14110540.9890.0840.1641.039100
2.99-3.123.80.10710080.9910.0630.1241.026100
3.12-3.293.80.07910230.9930.0470.0921.013100
3.29-3.493.80.05710390.9970.0330.0660.964100
3.49-3.763.80.04410290.9980.0260.0520.915100
3.76-4.143.80.04810340.9960.0280.0561.092100
4.14-4.743.80.04310320.9960.0250.050.986100
4.74-5.973.80.03610440.9970.0210.0420.698100
5.97-503.70.0310620.9980.0190.0360.57199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7jhi


Resolution: 2.2→39.8938 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 753 5.03 %
Rwork0.1955 14227 -
obs0.1984 14980 72.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.41 Å2 / Biso mean: 38.9464 Å2 / Biso min: 4.85 Å2
Refinement stepCycle: final / Resolution: 2.2→39.8938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 143 107 2946
Biso mean--56.38 34.43 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042939
X-RAY DIFFRACTIONf_angle_d0.6874004
X-RAY DIFFRACTIONf_chiral_restr0.044452
X-RAY DIFFRACTIONf_plane_restr0.004493
X-RAY DIFFRACTIONf_dihedral_angle_d15.8121736
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.36860.3595600.228126532
2.3686-2.60690.23941020.2462209754
2.6069-2.98410.30161540.2399307378
2.9841-3.75920.29242210.2009383599
3.7592-39.89380.21412160.16753957100

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