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

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Basic information

Entry
Database: PDB / ID: 5vcm
TitleAlpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound UDP and Manganese
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 via asparagine / Golgi stack / protein N-linked glycosylation / 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 via asparagine / Golgi stack / protein N-linked glycosylation / 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
: / URIDINE-5'-DIPHOSPHATE / Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)98,11915
Polymers96,6962
Non-polymers1,42213
Water9,800544
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A: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1047
Polymers48,3481
Non-polymers7566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0158
Polymers48,3481
Non-polymers6677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.130, 139.330, 63.210
Angle α, β, γ (deg.)90.000, 111.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 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
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 5 types, 556 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 1.96 Å3/Da / Density % sol: 37.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.7 M ammonium sulfate, 100 mM HEPES, pH 7.5, 5 mM UDP, 5 mM manganese chloride

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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: Oct 25, 2015
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: 1.6→43.044 Å / Num. obs: 97795 / % possible obs: 99.7 % / Redundancy: 7.628 % / Biso Wilson estimate: 19.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.114 / Χ2: 1.017 / Net I/σ(I): 10.97 / Num. measured all: 745960 / Scaling rejects: 18
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
1.6-1.647.3471.4081.4152119721470940.4991.51498.3
1.64-1.697.5491.1471.7953283706470580.651.23199.9
1.69-1.737.5820.9082.351709682568200.7530.97599.9
1.73-1.797.5960.7132.9150855670766950.8450.76599.8
1.79-1.857.6240.5463.8449366648464750.90.58699.9
1.85-1.917.6260.4134.9847504623562290.9390.44399.9
1.91-1.987.6330.3216.3946217605860550.9620.345100
1.98-2.067.6520.248.3443951574857440.9770.25899.9
2.06-2.167.660.1910.1542643557055670.9850.20399.9
2.16-2.267.6590.15612.1640892535253390.9880.16799.8
2.26-2.387.6980.12914.3638853505150470.9910.13899.9
2.38-2.537.6960.11615.7736933480747990.9930.12499.8
2.53-2.77.7060.09917.7534478447944740.9940.10799.9
2.7-2.927.7170.08520.5832425421142020.9950.09299.8
2.92-3.27.7320.07422.9629845386938600.9970.07999.8
3.2-3.587.730.06426.2727110351535070.9970.06899.8
3.58-4.137.7360.05928.4223766307830720.9970.06499.8
4.13-5.067.730.05629.6920161261526080.9970.0699.7
5.06-7.157.6920.05928.815577203320250.9970.06499.6
7.15-43.0447.3540.05729.088273113911250.9970.06198.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→43.044 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 4881 4.99 %
Rwork0.1857 92865 -
obs0.1874 97746 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.56 Å2 / Biso mean: 28.0761 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 1.599→43.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 77 544 6509
Biso mean--35.39 35.58 -
Num. residues----709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076252
X-RAY DIFFRACTIONf_angle_d0.8878510
X-RAY DIFFRACTIONf_chiral_restr0.053897
X-RAY DIFFRACTIONf_plane_restr0.0061073
X-RAY DIFFRACTIONf_dihedral_angle_d11.1913709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5991-1.61730.3291630.31712972313596
1.6173-1.63630.36331540.309831003254100
1.6363-1.65630.29121630.276730933256100
1.6563-1.67720.27921670.265830733240100
1.6772-1.69930.30851600.255531083268100
1.6993-1.72260.27311670.243431063273100
1.7226-1.74720.25191600.226330703230100
1.7472-1.77330.24351610.220731213282100
1.7733-1.8010.25711550.21530743229100
1.801-1.83050.26741660.20930963262100
1.8305-1.86210.24651670.203931223289100
1.8621-1.89590.24251640.202330423206100
1.8959-1.93240.25011620.200831393301100
1.9324-1.97180.23251630.187730743237100
1.9718-2.01470.1951640.183430893253100
2.0147-2.06160.20521630.182230883251100
2.0616-2.11310.24461640.183731483312100
2.1131-2.17030.23891610.175830413202100
2.1703-2.23410.20811620.184530943256100
2.2341-2.30620.23591680.172231213289100
2.3062-2.38870.21691550.168430933248100
2.3887-2.48430.18791660.176130973263100
2.4843-2.59730.20521620.172731163278100
2.5973-2.73430.2221690.173731203289100
2.7343-2.90550.19831630.17430833246100
2.9055-3.12980.21271630.181631153278100
3.1298-3.44470.23091660.166530873253100
3.4447-3.94280.18321680.164331473315100
3.9428-4.96640.18071570.156531073264100
4.9664-43.05910.22341580.20923129328799
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)
11.6883-0.3168-0.42382.4336-0.99191.95390.04110.12450.129-0.15840.04550.1983-0.0258-0.1217-0.0920.13880.0255-0.01770.08370.02770.136-0.7377-12.684-33.4757
22.4424-1.3964-0.76432.24220.46830.5350.08050.1544-0.0693-0.2232-0.03030.1790.12040.0062-0.05580.23550.0344-0.01820.15150.03830.162.8556-15.3694-40.1125
36.3831-1.3689-2.61996.75920.84528.5961-0.02490.3459-0.21190.38090.01010.0343-0.0451-0.02310.02050.25740.04660.00050.1948-0.04480.156420.8417-36.941-47.764
42.3096-0.6115-0.75791.8636-0.05591.71340.0137-0.09340.05220.02050.0476-0.0004-0.11690.026-0.020.11080.0131-0.01490.05750.02650.08476.7697-18.1183-28.2404
52.6387-0.3315-0.97351.2378-0.68841.5098-0.0544-0.645-0.31940.34160.23030.0977-0.2167-0.2048-0.08870.20090.05780.0330.27110.08370.195-1.4123-24.9007-10.7459
62.4053-0.0867-0.38890.976-0.86831.7941-0.2072-0.0805-0.4687-0.1090.15970.15910.3527-0.11660.01810.20330.03250.04690.2060.0470.23914.6701-30.1177-16.7742
72.3744-0.3451-0.43611.046-0.63161.0096-0.0803-0.2011-0.1505-0.0110.11930.10250.11460.04650.07830.14740.01040.00550.10930.03670.165710.4926-28.8134-23.0861
82.92571.20322.03242.84711.69975.4628-0.1067-0.503-0.4424-0.03690.23490.2253-0.1314-0.3388-0.0490.15670.06890.0520.26020.09510.2733-15.4-27.1713-18.018
93.342-2.1514-2.48531.7310.65494.1017-0.7876-1.0715-0.55140.4330.54980.16341.10820.87790.38340.33820.07770.07990.44410.12460.402910.324-37.6242-13.6197
103.8665-0.55460.26067.5087-0.93944.47290.00270.05230.40690.0991-0.0998-0.206-0.27380.0930.07330.17880.01740.03290.11910.01190.161620.6153-23.5116-36.6256
112.07470.80360.00991.42990.11280.9082-0.02650.076-0.1907-0.0686-0.00380.08450.1784-0.0045-0.00940.14870.0021-0.00080.1041-0.0320.1955-17.5583-68.2263-18.5014
122.5845-1.9849-1.84482.11331.7551.7603-0.0813-0.0893-0.04590.1984-0.01940.09540.0408-0.15250.07140.1470.00610.00160.193-0.02820.1538-25.0956-52.51230.3016
133.10890.51710.00461.33470.25653.047-0.01790.07960.34980.04010.107-0.1639-0.44040.5329-0.07780.215-0.01620.00660.2623-0.03680.23060.8278-54.2557-16.8983
141.53860.2908-0.33731.0656-0.08643.4077-0.07710.15380.1497-0.17420.1351-0.0299-0.09880.2362-0.0410.1796-0.0445-0.00660.1601-0.01740.2103-5.6637-49.542-13.6948
156.21150.2271-0.08961.79250.27311.20150.0032-0.18170.0038-0.1491-0.0537-0.29010.10530.20280.09110.16530.02950.02730.2123-0.02530.1209-11.6962-49.63241.2455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 86 through 157 )A86 - 157
2X-RAY DIFFRACTION2chain 'A' and (resid 158 through 191 )A158 - 191
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 224 )A192 - 224
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 267 )A225 - 267
5X-RAY DIFFRACTION5chain 'A' and (resid 268 through 305 )A268 - 305
6X-RAY DIFFRACTION6chain 'A' and (resid 306 through 324 )A306 - 324
7X-RAY DIFFRACTION7chain 'A' and (resid 325 through 387 )A325 - 387
8X-RAY DIFFRACTION8chain 'A' and (resid 388 through 411 )A388 - 411
9X-RAY DIFFRACTION9chain 'A' and (resid 412 through 427 )A412 - 427
10X-RAY DIFFRACTION10chain 'A' and (resid 428 through 447 )A428 - 447
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 176 )B78 - 176
12X-RAY DIFFRACTION12chain 'B' and (resid 177 through 243 )B177 - 243
13X-RAY DIFFRACTION13chain 'B' and (resid 244 through 324 )B244 - 324
14X-RAY DIFFRACTION14chain 'B' and (resid 325 through 414 )B325 - 414
15X-RAY DIFFRACTION15chain 'B' and (resid 417 through 445 )B417 - 445

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