[English] 日本語
Yorodumi
- PDB-7e9k: Crystal Structure of POMGNT2 in complex with UDP and mono-mannosy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e9k
TitleCrystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man long peptide)
Components
  • Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
  • mono-mannosyl peptide (379Man long peptide)
KeywordsTRANSFERASE / Glycosyltransferase / O-mannose type glycosylation
Function / homology
Function and homology information


O-linked glycosylation / protein O-mannose beta-1,4-N-acetylglucosaminyltransferase / protein O-linked mannosylation / protein O-acetylglucosaminyltransferase activity / acetylglucosaminyltransferase activity / protein O-linked glycosylation / neuron migration / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Glycosyltransferase 61 / : / Glycosyltransferase 61 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-D-mannopyranose / URIDINE-5'-DIPHOSPHATE / Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKuwabara, N.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16K07284 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101083 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05648 Japan
Japan Society for the Promotion of Science (JSPS)JP17H03987 Japan
CitationJournal: Genes Cells / Year: 2021
Title: The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on alpha-dystroglycan.
Authors: Imae, R. / Kuwabara, N. / Manya, H. / Tanaka, T. / Tsuyuguchi, M. / Mizuno, M. / Endo, T. / Kato, R.
History
DepositionMar 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
B: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
D: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
E: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
C: mono-mannosyl peptide (379Man long peptide)
F: mono-mannosyl peptide (379Man long peptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,19127
Polymers250,8916
Non-polymers5,30021
Water16,358908
1
A: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
B: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
C: mono-mannosyl peptide (379Man long peptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,10514
Polymers125,4463
Non-polymers2,65911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-18 kcal/mol
Surface area44960 Å2
MethodPISA
2
D: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
E: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
F: mono-mannosyl peptide (379Man long peptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,08713
Polymers125,4463
Non-polymers2,64110
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-22 kcal/mol
Surface area45170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.150, 104.401, 148.639
Angle α, β, γ (deg.)90.000, 90.104, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules ABDECF

#1: Protein
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 / POMGnT2 / Extracellular O-linked N-acetylglucosamine transferase-like / Glycosyltransferase-like ...POMGnT2 / Extracellular O-linked N-acetylglucosamine transferase-like / Glycosyltransferase-like domain-containing protein 2


Mass: 61563.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: POMGNT2, AGO61, GTDC2 / Production host: Homo sapiens (human)
References: UniProt: Q5NDF2, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase
#2: Protein/peptide mono-mannosyl peptide (379Man long peptide)


Mass: 2317.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Sugars , 3 types, 15 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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.: 12 / 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
#7: 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 / Feature type: SUBJECT OF INVESTIGATION
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, 914 molecules

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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-HCl (pH 8.0 or 8.5), 12-16% PEG 8000, 1% tacsimate (pH 7.0)
PH range: 8.0-8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→49.57 Å / Num. obs: 163077 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Net I/σ(I): 10.8
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7958 / CC1/2: 0.761 / Rpim(I) all: 0.6 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1300018733

Resolution: 2.05→49.55 Å / SU ML: 0.2494 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2407 7922 4.87 %
Rwork0.2022 154844 -
obs0.204 162766 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.9 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17108 0 334 908 18350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002518069
X-RAY DIFFRACTIONf_angle_d0.543124650
X-RAY DIFFRACTIONf_chiral_restr0.04722795
X-RAY DIFFRACTIONf_plane_restr0.00353114
X-RAY DIFFRACTIONf_dihedral_angle_d18.72852470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.34172620.31125046X-RAY DIFFRACTION98.75
2.07-2.10.32792430.29645193X-RAY DIFFRACTION98.87
2.1-2.120.31372600.28165111X-RAY DIFFRACTION98.71
2.12-2.150.28372900.27465148X-RAY DIFFRACTION98.53
2.15-2.180.32192830.27285105X-RAY DIFFRACTION98.81
2.18-2.210.32662800.26015146X-RAY DIFFRACTION98.51
2.21-2.240.33692540.25435063X-RAY DIFFRACTION98.44
2.24-2.270.30542580.25845184X-RAY DIFFRACTION98.57
2.27-2.310.2953180.25425046X-RAY DIFFRACTION98.55
2.31-2.350.31042340.24815186X-RAY DIFFRACTION99.12
2.35-2.390.30162450.2335194X-RAY DIFFRACTION98.98
2.39-2.430.30462380.23315184X-RAY DIFFRACTION99.05
2.43-2.480.26222890.22685182X-RAY DIFFRACTION99.15
2.48-2.530.27842950.22335143X-RAY DIFFRACTION99.05
2.53-2.580.29262600.22455108X-RAY DIFFRACTION99.02
2.58-2.640.28882480.22325193X-RAY DIFFRACTION98.89
2.64-2.710.25392200.22015226X-RAY DIFFRACTION98.87
2.71-2.780.25072890.22255111X-RAY DIFFRACTION98.81
2.78-2.860.25032490.21895205X-RAY DIFFRACTION99.02
2.86-2.960.27522950.22815150X-RAY DIFFRACTION98.96
2.96-3.060.26872530.2255141X-RAY DIFFRACTION98.77
3.06-3.180.28532930.2125176X-RAY DIFFRACTION98.99
3.18-3.330.25372260.20735201X-RAY DIFFRACTION98.87
3.33-3.510.23412450.25152X-RAY DIFFRACTION98.34
3.51-3.720.22162740.18795163X-RAY DIFFRACTION97.95
3.72-4.010.22332690.17025171X-RAY DIFFRACTION99.05
4.01-4.420.18142730.15095180X-RAY DIFFRACTION98.91
4.42-5.050.17272310.14425272X-RAY DIFFRACTION99.15
5.05-6.370.18552570.1755236X-RAY DIFFRACTION99.01
6.37-49.550.17422910.17665228X-RAY DIFFRACTION97.27

+
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