[English] 日本語
Yorodumi
- PDB-5lev: Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lev
TitleCrystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant)
ComponentsUDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
KeywordsTRANSFERASE / Protein glycosylation / integral membrane protein / congenital myasthenic syndrome 13 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / protein N-linked glycosylation / glycosyltransferase activity / intracellular membrane-bounded organelle / endoplasmic reticulum membrane ...Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / protein N-linked glycosylation / glycosyltransferase activity / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / metal ion binding / identical protein binding / membrane
Similarity search - Function
UDP-GlcNAc-dolichyl-phosphate GlcNAc phosphotransferase / : / DPAGT1 insertion domain / Glycosyl transferase, family 4 / Glycosyl transferase family 4
Similarity search - Domain/homology
Unknown ligand / UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Chu, A. / Tessitore, A. / Goubin, S. / Dong, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Berridge, G. ...Pike, A.C.W. / Dong, Y.Y. / Chu, A. / Tessitore, A. / Goubin, S. / Dong, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Berridge, G. / Wang, D. / Kupinska, K. / Belaya, K. / Beeson, D. / Burgess-Brown, N. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: Cell / Year: 2018
Title: Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design.
Authors: Dong, Y.Y. / Wang, H. / Pike, A.C.W. / Cochrane, S.A. / Hamedzadeh, S. / Wyszynski, F.J. / Bushell, S.R. / Royer, S.F. / Widdick, D.A. / Sajid, A. / Boshoff, H.I. / Park, Y. / Lucas, R. / ...Authors: Dong, Y.Y. / Wang, H. / Pike, A.C.W. / Cochrane, S.A. / Hamedzadeh, S. / Wyszynski, F.J. / Bushell, S.R. / Royer, S.F. / Widdick, D.A. / Sajid, A. / Boshoff, H.I. / Park, Y. / Lucas, R. / Liu, W.M. / Lee, S.S. / Machida, T. / Minall, L. / Mehmood, S. / Belaya, K. / Liu, W.W. / Chu, A. / Shrestha, L. / Mukhopadhyay, S.M.M. / Strain-Damerell, C. / Chalk, R. / Burgess-Brown, N.A. / Bibb, M.J. / Barry Iii, C.E. / Robinson, C.V. / Beeson, D. / Davis, B.G. / Carpenter, E.P.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9642
Polymers46,1741
Non-polymers7901
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-4 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.250, 103.250, 239.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase / GlcNAc-1-P transferase / GPT / N-acetylglucosamine-1-phosphate transferase


Mass: 46173.719 Da / Num. of mol.: 1 / Mutation: V264G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPAGT1, DPAGT2 / Plasmid: pFB-LIC-Bse / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H3H5, UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 790.145 Da / Num. of mol.: 1
Fragment: RESIDUE UNL 501 REPRESENTS AN UNIDENTIFIED LIPID BOUND TO THE TMD AND IS PRESENT IN ALL DPAGT1 DATASETS ANALYSED
Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.18 %
Preparation: EXPERIMENTAL DATA STATISTICS REPORTED ARE THOSE PRIOR TO ANISOTROPIC DATA TRUNCATION WITH STARANISO
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M bicine pH 9.0, 0.05M sodium chloride, 38% PEG300, 5mM Na2WO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.2→59.79 Å / Num. obs: 13206 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 120.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.2
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.36 / CC1/2: 0.549 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSOct 15, 2015data reduction
Aimless0.5.26data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J72

4j72


Resolution: 3.2→26.71 Å / Cor.coef. Fo:Fc: 0.8965 / Cor.coef. Fo:Fc free: 0.9095 / SU R Cruickshank DPI: 1.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.362 / SU Rfree Blow DPI: 0.366 / SU Rfree Cruickshank DPI: 0.365
Details: Data were scaled with Aimless and then anisotropically truncated with STARANISO. Structure refined with BUSTER with a single TLS group. Electron density maps were sharpened with -100A**2 ...Details: Data were scaled with Aimless and then anisotropically truncated with STARANISO. Structure refined with BUSTER with a single TLS group. Electron density maps were sharpened with -100A**2 bfactor for rebuilding in COOT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 665 5.16 %RANDOM
Rwork0.2344 ---
obs0.2347 12893 98.24 %-
Displacement parametersBiso mean: 142.51 Å2
Baniso -1Baniso -2Baniso -3
1-3.0724 Å20 Å20 Å2
2--3.0724 Å20 Å2
3----6.1448 Å2
Refine analyzeLuzzati coordinate error obs: 0.438 Å
Refinement stepCycle: 1 / Resolution: 3.2→26.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 22 14 2882
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092935HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993999HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1295SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes433HARMONIC5
X-RAY DIFFRACTIONt_it2935HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.08
X-RAY DIFFRACTIONt_other_torsion2.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion401SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3616SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.5 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2241 151 5.35 %
Rwork0.2097 2674 -
all0.2104 2825 -
obs--92.5 %
Refinement TLS params.Method: refined / Origin x: 46.1881 Å / Origin y: 50.2503 Å / Origin z: 128.211 Å
111213212223313233
T-0.5377 Å2-0.1136 Å20.0373 Å2-0.1204 Å20.166 Å2---0.3809 Å2
L4.4657 °21.5173 °2-1.3504 °2-5.2402 °2-0.5395 °2--4.4243 °2
S-0.1307 Å °0.7644 Å °0.6582 Å °-0.3363 Å °0.3576 Å °-0.332 Å °-0.4939 Å °0.8695 Å °-0.227 Å °
Refinement TLS groupSelection details: {A|8 - 403}

+
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