[English] 日本語
Yorodumi
- PDB-8ce3: Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ce3
TitleCrystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 3D fragment 2548
ComponentsAlpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
KeywordsCARBOHYDRATE / Glycosyltransferase / fragment
Function / homology
Function and homology information


alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / protein N-linked glycosylation via asparagine / : / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein ...alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / protein N-linked glycosylation via asparagine / : / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein / viral protein processing / positive regulation of cell migration / Golgi membrane / Golgi apparatus / extracellular exosome / membrane
Similarity search - Function
Glycosyltransferase family 18 / Domain of unknown function DUF4525 / : / Glycosyltransferase family 18 / Domain of unknown function (DUF4525)
Similarity search - Domain/homology
: / Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGilio, A.K. / Darby, J.F. / Wu, L. / Davies, G.J.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N008332/1 United Kingdom
Marie Sklodowska-Curie Actions, FragNET ITN675899European Union
Royal SocietyINF/R1/191028 United Kingdom
CitationJournal: To Be Published
Title: A Modular 3-D Fragment Collection: Design, Synthesis and Screening
Authors: Downes, T.D. / Jones, S.P. / Firth, J.D. / Darby, J.F. / Gilio, A.K. / Klein, H.F. / Blakemore, D.C. / de Fusco, C. / Roughley, S.D. / Vidler, L.R. / Whatton, M.A. / Woolford, A.J.A. / ...Authors: Downes, T.D. / Jones, S.P. / Firth, J.D. / Darby, J.F. / Gilio, A.K. / Klein, H.F. / Blakemore, D.C. / de Fusco, C. / Roughley, S.D. / Vidler, L.R. / Whatton, M.A. / Woolford, A.J.A. / Wrigley, G.L. / Hubbard, R.E. / Wu, L. / Davies, G.J. / O'Brien, P.
History
DepositionFeb 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
B: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,93823
Polymers117,9942
Non-polymers1,94521
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a single peak at expected retention time for a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-100 kcal/mol
Surface area41820 Å2
Unit cell
Length a, b, c (Å)46.860, 68.540, 91.310
Angle α, β, γ (deg.)107.300, 92.160, 107.050
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 214 - 728 / Label seq-ID: 1 - 515

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A / Alpha-mannoside beta-1 / 6-N-acetylglucosaminyltransferase V / GlcNAc-T V / GNT-V / Mannoside ...Alpha-mannoside beta-1 / 6-N-acetylglucosaminyltransferase V / GlcNAc-T V / GNT-V / Mannoside acetylglucosaminyltransferase 5 / N-acetylglucosaminyl-transferase V


Mass: 58996.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT5, GGNT5 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q09328, alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-UE0 / (3~{S})-1-ethanoyl-3-(4-methylphenyl)piperidine-3-carboxylic acid


Mass: 261.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 8.0, 0.3 M Li2SO4, 30 % (w/v) PEG 3350, 10 % (v/v) ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.89→60.47 Å / Num. obs: 80017 / % possible obs: 97.26 % / Redundancy: 3.5 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 13.6
Reflection shellResolution: 1.89→1.92 Å / Num. unique obs: 5618 / CC1/2: 0.6 / Rrim(I) all: 1.297

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→60.465 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.197 / SU B: 4.945 / SU ML: 0.137 / Average fsc free: 0.9498 / Average fsc work: 0.9652 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2327 3795 4.743 %
Rwork0.1897 76222 -
all0.192 --
obs-80017 97.259 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.819 Å2
Baniso -1Baniso -2Baniso -3
1--0.258 Å21.025 Å20.567 Å2
2---0.062 Å21.78 Å2
3----1.538 Å2
Refinement stepCycle: LAST / Resolution: 1.89→60.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8033 0 112 349 8494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128332
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167912
X-RAY DIFFRACTIONr_angle_refined_deg1.511.65111245
X-RAY DIFFRACTIONr_angle_other_deg0.4871.57718271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.242539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.187101482
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.50110384
X-RAY DIFFRACTIONr_chiral_restr0.0740.21203
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021911
X-RAY DIFFRACTIONr_nbd_refined0.2180.21625
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.27374
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23944
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.2355
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.215
X-RAY DIFFRACTIONr_nbd_other0.190.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.215
X-RAY DIFFRACTIONr_mcbond_it5.4565.3583959
X-RAY DIFFRACTIONr_mcbond_other5.4565.3583959
X-RAY DIFFRACTIONr_mcangle_it6.8399.6094933
X-RAY DIFFRACTIONr_mcangle_other6.8399.6094934
X-RAY DIFFRACTIONr_scbond_it6.4595.9624373
X-RAY DIFFRACTIONr_scbond_other6.4595.9634374
X-RAY DIFFRACTIONr_scangle_it9.08710.676312
X-RAY DIFFRACTIONr_scangle_other9.08710.6716313
X-RAY DIFFRACTIONr_lrange_it10.51354.6039233
X-RAY DIFFRACTIONr_lrange_other10.51254.6029233
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.0515860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.101790.05008
12AX-RAY DIFFRACTIONLocal ncs0.101790.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.89-1.9390.3422590.33356180.33360810.9020.9196.64530.33
1.939-1.9920.3042880.29454410.29559230.9340.93796.72460.288
1.992-2.050.3222730.27553410.27757990.9290.94896.80980.263
2.05-2.1130.2872670.25851340.2655860.940.95396.68810.243
2.113-2.1820.3362530.24449610.24853770.9330.96196.96860.224
2.182-2.2590.2962470.2248560.22452700.9490.96996.83110.201
2.259-2.3440.2642130.20447950.20651490.9560.97497.26160.186
2.344-2.4390.2592140.20644790.20948110.9540.97497.54730.188
2.439-2.5470.2542100.20143690.20346920.9620.97697.59160.183
2.547-2.6720.2631990.18641570.1944620.960.97997.62440.174
2.672-2.8160.262070.19139260.19442390.9580.97897.49940.181
2.816-2.9860.2722050.20737600.2140490.9530.97497.92540.201
2.986-3.1920.2541810.19534570.19837290.9620.97897.55970.195
3.192-3.4470.2141550.20633030.20635420.9670.97897.62850.21
3.447-3.7750.251340.18630240.18932300.9640.98297.77090.198
3.775-4.2180.1871330.15927390.1629430.9780.98797.58750.178
4.218-4.8670.1661450.13123710.13325720.9830.9997.82270.155
4.867-5.9510.191990.16120460.16221810.9810.98798.34940.19
5.951-8.3750.222710.18715850.18916880.9730.98398.10430.222
8.375-60.4650.225420.1828600.1849470.9660.97995.24820.25

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more