[English] 日本語
Yorodumi
- PDB-5e9u: Crystal structure of GtfA/B complex bound to UDP and GlcNAc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e9u
TitleCrystal structure of GtfA/B complex bound to UDP and GlcNAc
Components
  • Glycosyltransferase Gtf1
  • Glycosyltransferase-stabilizing protein Gtf2
KeywordsTRANSFERASE/CHAPERONE / Glycosyltransferase / Accessory protein translocation / Complex / TRANSFERASE-CHAPERONE complex
Function / homology
Function and homology information


protein O-linked glycosylation via serine / protein N-acetylglucosaminyltransferase complex / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / regulation of protein stability / nucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
Glycosyltransferase-stabilising protein GtfB / Glycosyltransferase GtfA / : / GtfA extended beta-sheet domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase stabilizing protein GtfB / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GtfA subunit
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å
AuthorsChen, Y. / Rapoport, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM052586 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mechanism of a cytosolic O-glycosyltransferase essential for the synthesis of a bacterial adhesion protein.
Authors: Chen, Y. / Seepersaud, R. / Bensing, B.A. / Sullam, P.M. / Rapoport, T.A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyltransferase Gtf1
B: Glycosyltransferase-stabilizing protein Gtf2
C: Glycosyltransferase Gtf1
D: Glycosyltransferase-stabilizing protein Gtf2
E: Glycosyltransferase Gtf1
F: Glycosyltransferase-stabilizing protein Gtf2
G: Glycosyltransferase Gtf1
H: Glycosyltransferase-stabilizing protein Gtf2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,26016
Polymers439,9128
Non-polymers1,3488
Water00
1
A: Glycosyltransferase Gtf1
B: Glycosyltransferase-stabilizing protein Gtf2
C: Glycosyltransferase Gtf1
D: Glycosyltransferase-stabilizing protein Gtf2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,6308
Polymers219,9564
Non-polymers6744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-56 kcal/mol
Surface area85300 Å2
MethodPISA
2
E: Glycosyltransferase Gtf1
F: Glycosyltransferase-stabilizing protein Gtf2
G: Glycosyltransferase Gtf1
H: Glycosyltransferase-stabilizing protein Gtf2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,6308
Polymers219,9564
Non-polymers6744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-50 kcal/mol
Surface area85330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.975, 196.005, 215.673
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Glycosyltransferase Gtf1 / Glycosyltransferase GtfA


Mass: 58399.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: M99 / Gene: gtf1, gtfA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9AET5, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein
Glycosyltransferase-stabilizing protein Gtf2 / Glycosyltransferase chaperone GtfB / orf4


Mass: 51578.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: M99 / Gene: gtf2, gtfB / Production host: Escherichia coli (E. coli) / References: UniProt: Q79T00
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#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.: 2
Source method: isolated from a genetically manipulated source
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
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, magnesium chloride, Tris, glycyl-glycyl-glycine
PH range: 7.5 - 8.0

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.84→148.98 Å / Num. obs: 60983 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 111.56 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.385 / Rpim(I) all: 0.166 / Net I/σ(I): 5.28 / Num. measured all: 448209
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) all% possible allRmerge(I) obsMean I/σ(I) obs
3.84-4.057.56627987910.5810.87699.9
12.14-148.986.41352921080.9960.03299.50.07523.4

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E9T
Resolution: 3.84→94.481 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3368 3821 3.3 %Random selection
Rwork0.2689 112079 --
obs0.2711 60748 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 309.3 Å2 / Biso mean: 115.4901 Å2 / Biso min: 31.83 Å2
Refinement stepCycle: final / Resolution: 3.84→94.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30864 0 84 0 30948
Biso mean--125.23 --
Num. residues----3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531634
X-RAY DIFFRACTIONf_angle_d0.90142899
X-RAY DIFFRACTIONf_chiral_restr0.0544662
X-RAY DIFFRACTIONf_plane_restr0.0055609
X-RAY DIFFRACTIONf_dihedral_angle_d13.918841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.84-3.88860.40491380.36244088422699
3.8886-3.93980.38451410.36464131427299
3.9398-3.99380.33511450.35594167431299
3.9938-4.05080.40491410.35374112425399
4.0508-4.11130.37641410.331141444285100
4.1113-4.17550.44471410.341241964337100
4.1755-4.2440.42271420.342641754317100
4.244-4.31720.37881380.319341354273100
4.3172-4.39570.3871460.304641744320100
4.3957-4.48020.3431410.286741774318100
4.4802-4.57170.31841430.278741124255100
4.5717-4.67110.33431420.276942124354100
4.6711-4.77970.31151430.261841304273100
4.7797-4.89920.36381430.271941204263100
4.8992-5.03170.27541430.270842204363100
5.0317-5.17980.3091420.28341404282100
5.1798-5.34690.37651360.288241564292100
5.3469-5.5380.35871430.284641444287100
5.538-5.75970.38271390.287941694308100
5.7597-6.02180.38111440.28141674311100
6.0218-6.33920.32941410.276741654306100
6.3392-6.73630.35491440.270541724316100
6.7363-7.25620.3291390.264641674306100
7.2562-7.98610.29961390.23941624301100
7.9861-9.14090.33051460.214641564302100
9.1409-11.51340.23651450.17634123426899
11.5134-94.50980.30281350.20314065420097

+
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