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- PDB-7xtl: Crystal structure of the C-terminal domain of human N-acetylgluco... -

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Basic information

Entry
Database: PDB / ID: 7xtl
TitleCrystal structure of the C-terminal domain of human N-acetylglucosaminyltransferase IVa
ComponentsAlpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form
KeywordsSUGAR BINDING PROTEIN / glycosyltransferase / N-glycan / N-glycosylation / Golgi / N-acetylglucosamine / carbohydrate-binding module / lectin
Function / homology
Function and homology information


alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity / glyoxylate metabolic process / alanine-glyoxylate transaminase activity / N-Glycan antennae elongation / acetylglucosaminyltransferase activity / N-glycan processing / Golgi stack / protein N-linked glycosylation / protein glycosylation ...alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity / glyoxylate metabolic process / alanine-glyoxylate transaminase activity / N-Glycan antennae elongation / acetylglucosaminyltransferase activity / N-glycan processing / Golgi stack / protein N-linked glycosylation / protein glycosylation / endoplasmic reticulum-Golgi intermediate compartment / Post-translational protein phosphorylation / peroxisome / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Maturation of spike protein / membrane => GO:0016020 / viral protein processing / endoplasmic reticulum lumen / Golgi membrane / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / metal ion binding
Similarity search - Function
Glycosyl transferase family 54
Similarity search - Domain/homology
Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 Å
AuthorsMiyazaki, T. / Oka, N. / Mori, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: Glycobiology / Year: 2022
Title: Crystal structure and sugar-binding ability of the C-terminal domain of N-acetylglucosaminyltransferase IV establish a new carbohydrate-binding module family.
Authors: Oka, N. / Mori, S. / Ikegaya, M. / Park, E.Y. / Miyazaki, T.
History
DepositionMay 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form
B: Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form


Theoretical massNumber of molelcules
Total (without water)38,5282
Polymers38,5282
Non-polymers00
Water39622
1
A: Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form


Theoretical massNumber of molelcules
Total (without water)19,2641
Polymers19,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form


Theoretical massNumber of molelcules
Total (without water)19,2641
Polymers19,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.699, 32.490, 85.629
Angle α, β, γ (deg.)90.000, 94.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form / MGAT4A


Mass: 19263.764 Da / Num. of mol.: 2 / Fragment: CBM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: MGAT4A / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UM21, alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.82 Å3/Da / Density % sol: 32.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium nitrate, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→85.34 Å / Num. obs: 20101 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.06 / Rrim(I) all: 0.216 / Net I/σ(I): 8.4
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 13 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2924 / CC1/2: 0.951 / Rpim(I) all: 0.234 / Rrim(I) all: 0.855 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 1.972→50.579 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.785 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2663 959 4.775 %
Rwork0.2204 19123 -
all0.223 --
obs-20082 99.945 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 61.557 Å2
Baniso -1Baniso -2Baniso -3
1-2.945 Å20 Å2-0.197 Å2
2--2.991 Å20 Å2
3----5.825 Å2
Refinement stepCycle: LAST / Resolution: 1.972→50.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 0 22 2353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132397
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162256
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.6393252
X-RAY DIFFRACTIONr_angle_other_deg1.2651.5785227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1175293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93924.348115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36115410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.427156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02523
X-RAY DIFFRACTIONr_nbd_refined0.20.2358
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21917
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21082
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0920.27
X-RAY DIFFRACTIONr_nbd_other0.1890.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1020.23
X-RAY DIFFRACTIONr_mcbond_it2.9694.5241175
X-RAY DIFFRACTIONr_mcbond_other2.9614.5231174
X-RAY DIFFRACTIONr_mcangle_it4.1816.7691467
X-RAY DIFFRACTIONr_mcangle_other4.1826.771468
X-RAY DIFFRACTIONr_scbond_it3.214.8641222
X-RAY DIFFRACTIONr_scbond_other3.2094.8661223
X-RAY DIFFRACTIONr_scangle_it4.7357.1491785
X-RAY DIFFRACTIONr_scangle_other4.7337.1511786
X-RAY DIFFRACTIONr_lrange_it6.60550.4592416
X-RAY DIFFRACTIONr_lrange_other6.60150.4462415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.972-2.0230.358740.3241436X-RAY DIFFRACTION99.8677
2.023-2.0790.347630.3091345X-RAY DIFFRACTION99.929
2.079-2.1390.317660.2821318X-RAY DIFFRACTION99.9278
2.139-2.2050.377440.2531304X-RAY DIFFRACTION99.7779
2.205-2.2770.313700.2321222X-RAY DIFFRACTION99.9227
2.277-2.3570.275560.2161231X-RAY DIFFRACTION100
2.357-2.4460.351620.2231160X-RAY DIFFRACTION99.8366
2.446-2.5450.359630.2361117X-RAY DIFFRACTION100
2.545-2.6580.235660.2571076X-RAY DIFFRACTION100
2.658-2.7880.34380.221027X-RAY DIFFRACTION100
2.788-2.9390.291540.2241000X-RAY DIFFRACTION100
2.939-3.1170.202530.222914X-RAY DIFFRACTION100
3.117-3.3320.226430.203899X-RAY DIFFRACTION100
3.332-3.5980.271360.199837X-RAY DIFFRACTION100
3.598-3.9410.242360.19749X-RAY DIFFRACTION100
3.941-4.4050.254350.172681X-RAY DIFFRACTION100
4.405-5.0840.228360.195630X-RAY DIFFRACTION100
5.084-6.2210.256290.239514X-RAY DIFFRACTION100
6.221-8.7750.231200.268416X-RAY DIFFRACTION100
8.775-50.5790.244150.219247X-RAY DIFFRACTION99.6198
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)
10.57350.2897-0.97161.31190.10111.9697-0.00470.0226-0.01390.1026-0.10850.02820.0775-0.09820.11310.12840.01440.06540.01890.00050.224710.6076-0.61656.9604
20.8177-0.6931.82861.89450.0596.09130.03820.3851-0.0084-0.2602-0.06070.0439-0.15131.26370.02250.0684-0.03420.03580.39240.06490.110616.1484.1358-34.5946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA387 - 534
2X-RAY DIFFRACTION2ALLB390 - 534

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