[English] 日本語
Yorodumi
- PDB-6yjv: Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycopro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yjv
TitleCrystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with UDP-2-deoxy-2-fluoroglucose and biantennary pentasaccharide M592
ComponentsAlpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
KeywordsTRANSFERASE / Carbohydrate / Enzyme / N-glycosylation / GlcNAc
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 / negative regulation of protein tyrosine phosphatase activity / 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 / negative regulation of protein tyrosine phosphatase activity / 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
Chem-U2F / Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWu, L. / Darby, J.F. / Gilio, A.K. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ErC-2012-AdG-322942 United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Substrate Engagement and Catalytic Mechanisms of N-Acetylglucosaminyltransferase V
Authors: Darby, J.F. / Gilio, A.K. / Piniello, B. / Roth, C. / Blagova, E. / Rovira, C. / Hubbard, R.E. / Davies, G.J. / Wu, L.
History
DepositionApr 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,92214
Polymers117,9942
Non-polymers2,92812
Water9,170509
1
AAA: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6237
Polymers58,9971
Non-polymers1,6266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2997
Polymers58,9971
Non-polymers1,3026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.520, 69.210, 90.650
Angle α, β, γ (deg.)108.420, 92.250, 106.540
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#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

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-1-2/a3-b1_a6-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 519 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H23FN2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→44.14 Å / Num. obs: 106002 / % possible obs: 94.7 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.028 / Net I/σ(I): 11.1
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 1.085 / Mean I/σ(I) obs: 1 / Num. unique obs: 7858 / CC1/2: 0.547 / Rpim(I) all: 0.705

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zic

5zic


Resolution: 1.7→44.14 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.426 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2115 3663 3.456 %
Rwork0.1754 --
all0.177 --
obs-106001 94.657 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.149 Å2
Baniso -1Baniso -2Baniso -3
1--2.177 Å20.272 Å2-0.545 Å2
2--1.371 Å21.706 Å2
3----0.719 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8127 0 184 509 8820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138547
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177858
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.66611572
X-RAY DIFFRACTIONr_angle_other_deg1.2741.59218341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0751002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92323.035425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.265151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6031538
X-RAY DIFFRACTIONr_chiral_restr0.0780.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029223
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021745
X-RAY DIFFRACTIONr_nbd_refined0.2020.21522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.27515
X-RAY DIFFRACTIONr_nbtor_refined0.1630.24046
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2394
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0720.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.224
X-RAY DIFFRACTIONr_nbd_other0.2250.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.227
X-RAY DIFFRACTIONr_mcbond_it3.4574.2794026
X-RAY DIFFRACTIONr_mcbond_other3.4564.2794025
X-RAY DIFFRACTIONr_mcangle_it4.7336.4045022
X-RAY DIFFRACTIONr_mcangle_other4.7336.4045023
X-RAY DIFFRACTIONr_scbond_it4.3124.7974521
X-RAY DIFFRACTIONr_scbond_other4.2994.7814498
X-RAY DIFFRACTIONr_scangle_it6.5696.9786550
X-RAY DIFFRACTIONr_scangle_other6.5726.9536515
X-RAY DIFFRACTIONr_lrange_it8.39249.5719285
X-RAY DIFFRACTIONr_lrange_other8.39449.4229212
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.0516485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74400.3137856X-RAY DIFFRACTION95.0399
1.744-1.79200.2917711X-RAY DIFFRACTION95.0216
1.792-1.84400.2757445X-RAY DIFFRACTION95.1316
1.844-1.9010.25930.2577167X-RAY DIFFRACTION95.4761
1.901-1.9630.263270.2376635X-RAY DIFFRACTION94.3105
1.963-2.0320.2483310.2156594X-RAY DIFFRACTION95.9407
2.032-2.1080.2423290.2016232X-RAY DIFFRACTION94.9219
2.108-2.1940.2512830.2056002X-RAY DIFFRACTION95.9103
2.194-2.2920.2452840.1965780X-RAY DIFFRACTION94.6169
2.292-2.4040.232740.1835549X-RAY DIFFRACTION95.3808
2.404-2.5340.2412400.1875206X-RAY DIFFRACTION95.0602
2.534-2.6870.2272430.194917X-RAY DIFFRACTION93.9377
2.687-2.8730.2292390.1994629X-RAY DIFFRACTION94.3777
2.873-3.1020.2232230.1894244X-RAY DIFFRACTION93.179
3.102-3.3980.2271830.1773848X-RAY DIFFRACTION91.6553
3.398-3.7980.2231620.1493536X-RAY DIFFRACTION92.7282
3.798-4.3840.1751560.1223143X-RAY DIFFRACTION94.6085
4.384-5.3660.1551440.1222662X-RAY DIFFRACTION94.1611
5.366-7.5740.1991010.1552041X-RAY DIFFRACTION93.2521
7.574-44.140.174510.1451141X-RAY DIFFRACTION93.8583

+
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