[English] 日本語
Yorodumi
- PDB-9f5h: Crystal structure of MGAT5 bump-and-hole mutant in complex with U... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f5h
TitleCrystal structure of MGAT5 bump-and-hole mutant in complex with UDP and M592
ComponentsSecreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
KeywordsTRANSFERASE / Bump and hole / bioorthogonal tag
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 / viral protein processing ...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 / MGT5A-like, N-terminal
Similarity search - Domain/homology
alpha-D-mannopyranose / URIDINE-5'-DIPHOSPHATE / Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLiu, Y. / Bineva-Todd, G. / Meek, R. / Mazo, L. / Piniello, B. / Moroz, O.V. / Begum, N. / Roustan, C. / Tomita, S. / Kjaer, S. ...Liu, Y. / Bineva-Todd, G. / Meek, R. / Mazo, L. / Piniello, B. / Moroz, O.V. / Begum, N. / Roustan, C. / Tomita, S. / Kjaer, S. / Rovira, C. / Davies, G.J. / Schumann, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: A Bioorthogonal Precision Tool for Human N -Acetylglucosaminyltransferase V.
Authors: Liu, Y. / Bineva-Todd, G. / Meek, R.W. / Mazo, L. / Piniello, B. / Moroz, O. / Burnap, S.A. / Begum, N. / Ohara, A. / Roustan, C. / Tomita, S. / Kjaer, S. / Polizzi, K. / Struwe, W.B. / ...Authors: Liu, Y. / Bineva-Todd, G. / Meek, R.W. / Mazo, L. / Piniello, B. / Moroz, O. / Burnap, S.A. / Begum, N. / Ohara, A. / Roustan, C. / Tomita, S. / Kjaer, S. / Polizzi, K. / Struwe, W.B. / Rovira, C. / Davies, G.J. / Schumann, B.
History
DepositionApr 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,4219
Polymers117,7142
Non-polymers1,7077
Water4,900272
1
A: Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8425
Polymers58,8571
Non-polymers9864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5784
Polymers58,8571
Non-polymers7213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.507, 69.069, 90.993
Angle α, β, γ (deg.)108.208, 92.088, 106.747
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 / 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

-
Protein , 1 types, 2 molecules AB

#1: Protein Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A / Secreted beta-1 / 6-N-acetylglucosaminyltransferase V / Secreted GNT-V


Mass: 58856.812 Da / Num. of mol.: 2 / Mutation: F445V,F504L,E297A
Source method: isolated from a genetically manipulated source
Details: MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, and F445V, F504L bump-and-hole mutations and E297A ...Details: MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, and F445V, F504L bump-and-hole mutations and E297A mutation in the active site,MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, and F445V, F504L bump-and-hole mutations and E297A mutation in the active site
Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT5, GGNT5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09328

-
Sugars , 2 types, 4 molecules

#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: obtained synthetically / 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
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 275 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15-20% PEG3350, 0.1M Tris-HCl pH 8-8.5, 0.3M Li2SO4, 0-10% ethylene glycol, Microseed matrix screening
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.72738 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72738 Å / Relative weight: 1
ReflectionResolution: 1.97→44.1 Å / Num. obs: 68392 / % possible obs: 94.4 % / Redundancy: 3.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.116 / Rrim(I) all: 0.164 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.23-44.13.60.0196900.9980.0190.027
1.97-2.013.81.55744320.271.5542.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→44.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.1 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2418 3266 4.782 %
Rwork0.1996 65034 -
all0.202 --
obs-68300 94.644 %
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: 38.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.475 Å2-0.48 Å2-1.014 Å2
2--0.507 Å20.172 Å2
3----0.494 Å2
Refinement stepCycle: LAST / Resolution: 1.97→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8018 0 106 272 8396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128329
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167727
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.82711294
X-RAY DIFFRACTIONr_angle_other_deg0.7461.75617865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35151001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.407537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72101403
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.25510378
X-RAY DIFFRACTIONr_chiral_restr0.1060.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029634
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021906
X-RAY DIFFRACTIONr_nbd_refined0.2260.21696
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.27129
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23953
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3150.2312
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.211
X-RAY DIFFRACTIONr_nbd_other0.1710.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.211
X-RAY DIFFRACTIONr_mcbond_it2.4581.9694025
X-RAY DIFFRACTIONr_mcbond_other2.4581.9694025
X-RAY DIFFRACTIONr_mcangle_it3.7963.5325019
X-RAY DIFFRACTIONr_mcangle_other3.7953.5325020
X-RAY DIFFRACTIONr_scbond_it2.7482.1814304
X-RAY DIFFRACTIONr_scbond_other2.7322.1784301
X-RAY DIFFRACTIONr_scangle_it4.2193.9126275
X-RAY DIFFRACTIONr_scangle_other4.1963.9056270
X-RAY DIFFRACTIONr_lrange_it6.43519.8619105
X-RAY DIFFRACTIONr_lrange_other6.42419.8359079
X-RAY DIFFRACTIONr_ncsr_local_group_10.1080.0515681
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.108290.05008
12AX-RAY DIFFRACTIONLocal ncs0.108290.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0210.3532180.3474871X-RAY DIFFRACTION95.0504
2.021-2.0760.3392290.334728X-RAY DIFFRACTION95.9543
2.076-2.1360.3382350.3044577X-RAY DIFFRACTION95.3249
2.136-2.2020.3022450.2844416X-RAY DIFFRACTION95.0642
2.202-2.2740.3072130.2774276X-RAY DIFFRACTION94.8046
2.274-2.3540.2652000.2494139X-RAY DIFFRACTION94.1215
2.354-2.4420.2882360.2353927X-RAY DIFFRACTION93.2154
2.442-2.5420.2881700.2243691X-RAY DIFFRACTION90.9541
2.542-2.6540.2711550.2123434X-RAY DIFFRACTION86.8797
2.654-2.7830.2821410.2152856X-RAY DIFFRACTION77.3419
2.783-2.9330.2581750.2053431X-RAY DIFFRACTION96.4945
2.933-3.110.2521630.1893325X-RAY DIFFRACTION99.1191
3.11-3.3240.2341600.1843156X-RAY DIFFRACTION99.222
3.324-3.5880.2181530.1882913X-RAY DIFFRACTION99.3519
3.588-3.9280.2131600.162638X-RAY DIFFRACTION99.3961
3.928-4.3880.1961150.1392420X-RAY DIFFRACTION99.4508
4.388-5.0580.1631180.1242158X-RAY DIFFRACTION99.6934
5.058-6.1740.219710.1641836X-RAY DIFFRACTION99.4265
6.174-8.6480.219570.1721433X-RAY DIFFRACTION99.7991
8.648-44.10.183490.176797X-RAY DIFFRACTION99.2958
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)
10.7674-0.14010.20910.72210.18822.11040.0180.04-0.0038-0.09160.015-0.0076-0.06430.0125-0.0330.0219-0.02450.01850.17890.07090.13440.54670.9121-1.0251
20.94440.2115-0.02660.970.16131.79430.0197-0.04220.07620.0746-0.00090.026-0.0408-0.0071-0.01880.01190.00170.02280.16480.07730.12663.154439.7885-35.6928
Refinement TLS groupSelection: ALL

+
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