[English] 日本語
Yorodumi
- PDB-4q1q: Crystal structure of TibC-catalyzed hyper-glycosylated TibA55-350... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q1q
TitleCrystal structure of TibC-catalyzed hyper-glycosylated TibA55-350 fragment
ComponentsAdhesin/invasin TibA autotransporter
KeywordsCELL ADHESION / Beta-helix / Adhesion
Function / homology
Function and homology information


: / : / periplasmic space / cell adhesion / cell surface / extracellular region
Similarity search - Function
Adhesin of bacterial autotransporter system / Adhesin of bacterial autotransporter system, probable stalk / Pertactin virulence factor family / Pertactin, central region / Pertactin / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain ...Adhesin of bacterial autotransporter system / Adhesin of bacterial autotransporter system, probable stalk / Pertactin virulence factor family / Pertactin, central region / Pertactin / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
D-glycero-alpha-D-manno-heptopyranose / Adhesin/invasin TibA autotransporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.11 Å
AuthorsYao, Q. / Lu, Q. / Shao, F.
Citation
Journal: Cell Host Microbe / Year: 2014
Title: An iron-containing dodecameric heptosyltransferase family modifies bacterial autotransporters in pathogenesis
Authors: Lu, Q. / Yao, Q. / Xu, Y. / Li, L. / Li, S. / Liu, Y. / Gao, W. / Niu, M. / Sharon, M. / Ben-Nissan, G. / Zamyatina, A. / Liu, X. / Chen, S. / Shao, F.
#1: Journal: Elife / Year: 2014
Title: A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family.
Authors: Qing Yao / Qiuhe Lu / Xiaobo Wan / Feng Song / Yue Xu / Mo Hu / Alla Zamyatina / Xiaoyun Liu / Niu Huang / Ping Zhu / Feng Shao /
Abstract: A large group of bacterial virulence autotransporters including AIDA-I from diffusely adhering E. coli (DAEC) and TibA from enterotoxigenic E. coli (ETEC) require hyperglycosylation for functioning. ...A large group of bacterial virulence autotransporters including AIDA-I from diffusely adhering E. coli (DAEC) and TibA from enterotoxigenic E. coli (ETEC) require hyperglycosylation for functioning. Here we demonstrate that TibC from ETEC harbors a heptosyltransferase activity on TibA and AIDA-I, defining a large family of bacterial autotransporter heptosyltransferases (BAHTs). The crystal structure of TibC reveals a characteristic ring-shape dodecamer. The protomer features an N-terminal β-barrel, a catalytic domain, a β-hairpin thumb, and a unique iron-finger motif. The iron-finger motif contributes to back-to-back dimerization; six dimers form the ring through β-hairpin thumb-mediated hand-in-hand contact. The structure of ADP-D-glycero-β-D-manno-heptose (ADP-D,D-heptose)-bound TibC reveals a sugar transfer mechanism and also the ligand stereoselectivity determinant. Electron-cryomicroscopy analyses uncover a TibC-TibA dodecamer/hexamer assembly with two enzyme molecules binding to one TibA substrate. The complex structure also highlights a high efficient hyperglycosylation of six autotransporter substrates simultaneously by the dodecamer enzyme complex.
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Jun 24, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations
Category: pdbx_chem_comp_identifier / struct_conn ...pdbx_chem_comp_identifier / struct_conn / struct_site / struct_site_gen
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._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 1.4Apr 3, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adhesin/invasin TibA autotransporter
B: Adhesin/invasin TibA autotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,05772
Polymers60,3442
Non-polymers14,71370
Water1,33374
1
A: Adhesin/invasin TibA autotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,52936
Polymers30,1721
Non-polymers7,35635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adhesin/invasin TibA autotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,52936
Polymers30,1721
Non-polymers7,35635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.807, 62.166, 97.288
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Adhesin/invasin TibA autotransporter / Adhesin/invasin TibA / Glycoprotein TibA / Adhesin/invasin TibA translocator


Mass: 30172.199 Da / Num. of mol.: 2 / Fragment: UNP residues 55-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ETEC H10407 / Gene: tibA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9XD84
#2: Sugar...
ChemComp-289 / D-glycero-alpha-D-manno-heptopyranose / D-glycero-alpha-D-manno-heptose / D-glycero-D-manno-heptose / D-glycero-manno-heptose


Type: D-saccharide, alpha linking / Mass: 210.182 Da / Num. of mol.: 70
Source method: isolated from a genetically manipulated source
Formula: C7H14O7
IdentifierTypeProgram
D-gro-a-D-manHeppIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
DDmanHepSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 20%(w/v) PEG 8000, 100mM magnesium acetate, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 31760 / Num. obs: 31569 / % possible obs: 99.4 % / Redundancy: 7.5 %

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementStarting model: SAD

Resolution: 2.11→19.87 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.778 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1598 5.1 %RANDOM
Rwork0.2055 29958 --
obs0.2076 31556 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.95 Å2 / Biso mean: 55.873 Å2 / Biso min: 28.72 Å2
Baniso -1Baniso -2Baniso -3
1--3.48 Å20 Å2-1.75 Å2
2--2.63 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.11→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 910 74 4712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194742
X-RAY DIFFRACTIONr_bond_other_d0.0050.024152
X-RAY DIFFRACTIONr_angle_refined_deg1.8642.1346344
X-RAY DIFFRACTIONr_angle_other_deg0.7739646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.02124.848132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24515524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9961516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024608
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02884
LS refinement shellResolution: 2.112→2.167 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 86 -
Rwork0.275 1831 -
all-1917 -
obs--80.14 %

+
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://pdbjlvh1.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