[English] 日本語
Yorodumi
- PDB-6ts8: Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ts8
TitleChaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) double cysteine mutant G177C/A786C.
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsPROTEIN BINDING / Endoplasmic Reticulum / Glycoprotein Folding / ERQC / UGGT
Function / homology
Function and homology information


UDP-glucose:glycoprotein glucosyltransferase activity / protein N-linked glycosylation via asparagine / ERAD pathway / unfolded protein binding / endoplasmic reticulum lumen / nucleotide binding / metal ion binding
Similarity search - Function
UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Glucosyltransferase 24, catalytic domain ...UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Glucosyltransferase 24, catalytic domain / Glucosyltransferase 24 / UDP-glucose:Glycoprotein Glucosyltransferase / Nucleotide-diphospho-sugar transferases / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.6 Å
AuthorsRoversi, P. / Zitzmann, N. / Ibba, R. / Hensen, M. / Chandran, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust204801/Z/16/Z United Kingdom
Wellcome Trust106272/Z/14/Z United Kingdom
Wellcome Trust214090/Z/18/Z United Kingdom
CitationJournal: Structure / Year: 2021
Title: Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose: Glycoprotein glucosyltransferase.
Authors: Modenutti, C.P. / Blanco Capurro, J.I. / Ibba, R. / Alonzi, D.S. / Song, M.N. / Vasiljevic, S. / Kumar, A. / Chandran, A.V. / Tax, G. / Marti, L. / Hill, J.C. / Lia, A. / Hensen, M. / ...Authors: Modenutti, C.P. / Blanco Capurro, J.I. / Ibba, R. / Alonzi, D.S. / Song, M.N. / Vasiljevic, S. / Kumar, A. / Chandran, A.V. / Tax, G. / Marti, L. / Hill, J.C. / Lia, A. / Hensen, M. / Waksman, T. / Rushton, J. / Rubichi, S. / Santino, A. / Marti, M.A. / Zitzmann, N. / Roversi, P.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.title / _citation.year
Revision 1.3Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 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: UDP-glucose-glycoprotein glucosyltransferase-like protein
B: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)312,7102
Polymers312,7102
Non-polymers00
Water00
1
A: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)156,3551
Polymers156,3551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)156,3551
Polymers156,3551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.047, 139.047, 176.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 28 - 1409 / Label seq-ID: 1 - 1382

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein UDP-glucose-glycoprotein glucosyltransferase-like protein


Mass: 156354.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) double cysteine mutant G177C/A786C.
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Plasmid: pHLsec / Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 16.54% w/v PEG 4,000, 0.03 M citric acid pH 5.3, 0.07 M citric Acid pH 6.0, 12.75% v/v isopropanol

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 4.59→139.05 Å / Num. obs: 22051 / % possible obs: 87.8 % / Redundancy: 4.3 % / CC1/2: 0.982 / Rmerge(I) obs: 0.278 / Rpim(I) all: 0.147 / Rrim(I) all: 0.316 / Net I/σ(I): 4.6
Reflection shellResolution: 4.717→5.576 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1744 / CC1/2: 0.589 / Rpim(I) all: 0.52 / Rrim(I) all: 1.338 / % possible all: 69.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nv4

5nv4


Resolution: 4.6→139.04 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.887 / SU B: 258.499 / SU ML: 1.351 / Cross valid method: THROUGHOUT / ESU R Free: 2.993 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23403 318 5.3 %RANDOM
Rwork0.20315 ---
obs0.20472 5723 32.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 160.355 Å2
Baniso -1Baniso -2Baniso -3
1--3.16 Å20 Å2-0 Å2
2---3.16 Å20 Å2
3---6.32 Å2
Refinement stepCycle: 1 / Resolution: 4.6→139.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20112 0 0 0 20112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01320590
X-RAY DIFFRACTIONr_bond_other_d0.0020.01719148
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6427926
X-RAY DIFFRACTIONr_angle_other_deg1.3461.57544384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00752500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2722.1521134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.324153532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.09615142
X-RAY DIFFRACTIONr_chiral_restr0.0910.22612
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222960
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024434
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.22312.6910024
X-RAY DIFFRACTIONr_mcbond_other4.22312.68810023
X-RAY DIFFRACTIONr_mcangle_it7.8219.0212516
X-RAY DIFFRACTIONr_mcangle_other7.81919.02212517
X-RAY DIFFRACTIONr_scbond_it2.73812.75210566
X-RAY DIFFRACTIONr_scbond_other2.73812.75410567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4919.03115411
X-RAY DIFFRACTIONr_long_range_B_other16.3940126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 40282 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 4.6→4.707 Å
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.184 23 -
obs--1.67 %
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)
10.0637-0.06130.09480.451-0.03250.16140.04840.04160.037-0.0103-0.0446-0.05190.04190.0135-0.00380.6614-0.02010.02160.6920.00040.621711.2166-32.18210.6884
20.14580.03950.1230.0330.04680.1463-0.11450.0235-0.01050.00870.11770.00550.03220.0625-0.00320.67510.02410.04850.60850.02940.007-37.3296-80.7851-0.2497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 1409
2X-RAY DIFFRACTION2B28 - 1409

+
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