[English] 日本語
Yorodumi
- PDB-2ks6: NMR solution structure of ALG13 --- obtained with iterative CS-Ro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ks6
TitleNMR solution structure of ALG13 --- obtained with iterative CS-Rosetta from backbone NMR data.
ComponentsUDP-N-acetylglucosamine transferase subunit ALG13
KeywordsTRANSFERASE / CS-Rosetta / Cyclic N-oxides / Endoplasmic reticulum / Glycosyltransferase
Function / homology
Function and homology information


N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase / N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity / UDP-N-acetylglucosamine transferase complex / dolichol-linked oligosaccharide biosynthetic process / cytoplasmic side of Golgi membrane / endoplasmic reticulum / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Glycosyl transferase, family 28, C-terminal / Glycosyltransferase family 28 C-terminal domain / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine transferase subunit ALG13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / iterative CS-Rosetta
AuthorsLange, O.F. / Wang, X. / Prestegard, J.H. / Baker, D.
CitationJournal: Science / Year: 2010
Title: NMR structure determination for larger proteins using backbone-only data.
Authors: Raman, S. / Lange, O.F. / Rossi, P. / Tyka, M. / Wang, X. / Aramini, J. / Liu, G. / Ramelot, T.A. / Eletsky, A. / Szyperski, T. / Kennedy, M.A. / Prestegard, J. / Montelione, G.T. / Baker, D.
History
DepositionDec 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 1, 2014Group: Refinement description
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine transferase subunit ALG13


Theoretical massNumber of molelcules
Total (without water)22,5531
Polymers22,5531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein UDP-N-acetylglucosamine transferase subunit ALG13 / Asparagine-linked glycosylation protein 13


Mass: 22552.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ALG13, YGL047W / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)
References: UniProt: P53178, N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: This structure has been determined only from backbone NMR data: chemical shifts, RDCs and HN-HN NOEs. This data is a subset of the data used for related entry 2jzc.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D HN(CA)CB
1323D HN(CO)CA
1423D HN(COCA)CB
1513D 1H-15N NOESY
1633D 1H-15N NOESY
1713D 1H-13C NOESY
1843D 1H-13C NOESY
1952D S3-TROSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.35 mM [U-15N; U-2H; 13C,1H Leu, Val, Ile.CD1 methyl] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.35 mM [U-13C; U-15N; U-2H] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.35 mM [U-15N; U-2H; 13C,1H Leu, Val, Ile.cd1 labeled; 1H Phe labeled] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
40.35 mM [U-15N; U-2H; 13C,1H Leu, Val, Ile.cd1 labeled; 1H Phe labeled] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 100% D2O100% D2O
50.35 mM [U-13C; U-15N; U-2H] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 3.5 w/v acrylamide, 3.5 w/v (3-acrylamidopropyl)-trimethylammonium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-15N; U-2H; 13C,1H Leu, Val, Ile.CD1 methyl]1
20 mMsodium phosphate1
100 mMsodium chloride1
0.02 %sodium azide1
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-13C; U-15N; U-2H]2
20 mMsodium phosphate2
100 mMsodium chloride2
0.02 %sodium azide2
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-15N; U-2H; 13C,1H Leu, Val, Ile.cd1 labeled; 1H Phe labeled]3
20 mMsodium phosphate3
100 mMsodium chloride3
0.02 %sodium azide3
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-15N; U-2H; 13C,1H Leu, Val, Ile.cd1 labeled; 1H Phe labeled]4
20 mMsodium phosphate4
100 mMsodium chloride4
0.02 %sodium azide4
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-13C; U-15N; U-2H]5
20 mMsodium phosphate5
100 mMsodium chloride5
0.02 %sodium azide5
3.5 w/vacrylamide5
3.5 w/v(3-acrylamidopropyl)-trimethylammonium chloride5
Sample conditionsIonic strength: 0.1 / pH: 6.7 / Pressure: ambient / Temperature: 297 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA9002

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.processing
NMRViewJohnson, B. et al.data analysis
CYANAGuntert, P. et al.data analysis
CS-ROSETTAShen, Y. et al.refinement
RefinementMethod: iterative CS-Rosetta / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

+
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