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- PDB-5vcs: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransf... -

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Basic information

Entry
Database: PDB / ID: 5vcs
TitleAlpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with Bound Acceptor
ComponentsAlpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
KeywordsTRANSFERASE / glycosyltransferase / MGAT2 / Complex N-gly / Branched acceptor
Function / homology
Function and homology information


alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / Defective MGAT2 causes CDG-2a / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / : / protein N-linked glycosylation / Golgi stack / manganese ion binding / Maturation of spike protein ...alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / Defective MGAT2 causes CDG-2a / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / : / protein N-linked glycosylation / Golgi stack / manganese ion binding / Maturation of spike protein / viral protein processing / Golgi membrane / Golgi apparatus / protein homodimerization activity / membrane
Similarity search - Function
N-acetylglucosaminyltransferase II / N-acetylglucosaminyltransferase II (MGAT2) / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å
AuthorsSanders, J.H. / Kadirvelraj, R. / Wood, Z.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P01GM107012-02 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite.
Authors: Kadirvelraj, R. / Yang, J.Y. / Sanders, J.H. / Liu, L. / Ramiah, A. / Prabhakar, P.K. / Boons, G.J. / Wood, Z.A. / Moremen, K.W.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
B: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,30110
Polymers96,6962
Non-polymers2,6058
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint57 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.280, 129.160, 175.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 86 through 110 or resid 112...
21(chain B and (resid 86 through 179 or resid 181...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNALAALA(chain A and (resid 86 through 110 or resid 112...AA86 - 11058 - 82
12THRTHRPHEPHE(chain A and (resid 86 through 110 or resid 112...AA112 - 17984 - 151
13ILEILETHRTHR(chain A and (resid 86 through 110 or resid 112...AA181 - 293153 - 265
14GLYGLYTYRTYR(chain A and (resid 86 through 110 or resid 112...AA302 - 352274 - 324
15THRTHRSERSER(chain A and (resid 86 through 110 or resid 112...AA354 - 356326 - 328
16LEULEUALAALA(chain A and (resid 86 through 110 or resid 112...AA358 - 375330 - 347
17METMETARGARG(chain A and (resid 86 through 110 or resid 112...AA406 - 445378 - 417
21ASNASNPHEPHE(chain B and (resid 86 through 179 or resid 181...BB86 - 17958 - 151
22ILEILETYRTYR(chain B and (resid 86 through 179 or resid 181...BB181 - 352153 - 324
23THRTHRSERSER(chain B and (resid 86 through 179 or resid 181...BB354 - 356326 - 328
24LEULEUGLUGLU(chain B and (resid 86 through 179 or resid 181...BB358 - 415330 - 387
25VALVALARGARG(chain B and (resid 86 through 179 or resid 181...BB419 - 445391 - 417

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / Beta-1 / 2-N-acetylglucosaminyltransferase II / GlcNAc-T II / GNT-II / Mannoside ...Beta-1 / 2-N-acetylglucosaminyltransferase II / GlcNAc-T II / GNT-II / Mannoside acetylglucosaminyltransferase 2 / N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase II


Mass: 48348.117 Da / Num. of mol.: 2 / Fragment: UNP residues 29-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT2 / Production host: Homo sapiens (human)
References: UniProt: Q10469, alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(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
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam 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]/1-2-3-1-3/a4-b1_b3-c1_b6-e1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(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: 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

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Non-polymers , 3 types, 116 molecules

#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M ammonium sulfate, 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 12, 2016
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→72.668 Å / Num. obs: 25515 / % possible obs: 94.6 % / Redundancy: 4.16 % / Biso Wilson estimate: 38.48 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.166 / Χ2: 0.994 / Net I/σ(I): 8.27 / Num. measured all: 106149 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.873.9280.5941.987266196118500.7810.67494.3
2.87-2.953.9280.5492.287039188617920.8370.62295
2.95-3.043.9550.4672.626965185217610.8550.53195.1
3.04-3.133.9710.4043.136799181517120.9080.45994.3
3.13-3.233.9840.333.956478173216260.9150.37493.9
3.23-3.353.9780.2544.96412170816120.9560.28894.4
3.35-3.473.9170.2295.65931162515140.9640.2693.2
3.47-3.614.0070.1617.215986159814940.9830.18293.5
3.61-3.773.930.157.975549151414120.9830.17193.3
3.77-3.963.9440.1368.885309145713460.9860.15592.4
3.96-4.174.0030.11110.585196140412980.9890.12692.5
4.17-4.433.9410.08912.294741130112030.9930.192.5
4.43-4.734.0230.08213.074638125911530.9960.09391.6
4.73-5.114.3120.08213.494760117611040.9950.09293.9
5.11-5.65.1560.11212.565491106510650.9930.124100
5.6-6.265.1140.10212.7850539899880.9930.11399.9
6.26-7.235.060.09514.3444538818800.9920.10699.9
7.23-8.854.9640.06219.5737387537530.9970.069100
8.85-12.524.7430.04326.5728936156100.9980.04899.2
12.52-72.6684.2460.04624.914523783420.9970.05390.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VCR

5vcr


Resolution: 2.799→72.668 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.275 1284 5.04 %
Rwork0.2472 24173 -
obs0.2486 25457 94.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.15 Å2 / Biso mean: 51.7756 Å2 / Biso min: 8.2 Å2
Refinement stepCycle: final / Resolution: 2.799→72.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5638 0 171 112 5921
Biso mean--50.38 30.22 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026011
X-RAY DIFFRACTIONf_angle_d0.4458188
X-RAY DIFFRACTIONf_chiral_restr0.038900
X-RAY DIFFRACTIONf_plane_restr0.0031012
X-RAY DIFFRACTIONf_dihedral_angle_d8.6373552
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3068X-RAY DIFFRACTION6.814TORSIONAL
12B3068X-RAY DIFFRACTION6.814TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.799-2.91110.3891380.33012628276695
2.9111-3.04350.34711430.31312646278995
3.0435-3.2040.31741370.30072614275194
3.204-3.40470.30011390.26382631277094
3.4047-3.66760.28131370.23972629276693
3.6676-4.03670.27711390.22562611275092
4.0367-4.62070.24151420.20282646278892
4.6207-5.82120.2181480.21792769291796
5.8212-72.69270.25111610.24772999316099
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)
11.3713-0.2728-0.07670.3769-0.02471.2515-0.02010.1198-0.03110.0013-0.0131-0.01620.09020.066-0.00010.0839-0.05430.04350.6249-0.00070.156-18.7245-37.22728.5899
20.88330.2839-0.76790.38430.11951.6179-0.0548-0.29480.12950.04970.0577-0.00940.05950.24740.01030.2301-0.06660.05590.9558-0.03190.1583-36.8033-26.339767.452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 79 through 445 )A79 - 445
2X-RAY DIFFRACTION2chain 'B' and (resid 86 through 447 )B86 - 447

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