[English] 日本語
Yorodumi
- PDB-5jqi: Crystal structure of FimH A62S from E. coli UTI89 bound to FimG N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jqi
TitleCrystal structure of FimH A62S from E. coli UTI89 bound to FimG N-terminal extension
Components
  • FimG N-terminal extension
  • Type 1 fimbiral adhesin FimH
KeywordsSUGAR BINDING PROTEIN / lectin / immunoglobulin fold / carbohydrate binding protein / donor strand exchange
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / metal ion binding
Similarity search - Function
Fimbrial-type adhesion domain / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like ...Fimbrial-type adhesion domain / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Type 1 fimbiral adhesin FimH / Type 1 fimbriae minor subunit FimG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli UTI89 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.962 Å
AuthorsKalas, V. / Hultgren, S.J.
CitationJournal: Sci Adv / Year: 2017
Title: Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions.
Authors: Vasilios Kalas / Jerome S Pinkner / Thomas J Hannan / Michael E Hibbing / Karen W Dodson / Alex S Holehouse / Hao Zhang / Niraj H Tolia / Michael L Gross / Rohit V Pappu / James Janetka / Scott J Hultgren /
Abstract: Positive selection in the two-domain type 1 pilus adhesin FimH enhances fitness in urinary tract infection (UTI). We report a comprehensive atomic-level view of FimH in two-state conformational ...Positive selection in the two-domain type 1 pilus adhesin FimH enhances fitness in urinary tract infection (UTI). We report a comprehensive atomic-level view of FimH in two-state conformational ensembles in solution, composed of one low-affinity tense (T) and multiple high-affinity relaxed (R) conformations. Positively selected residues allosterically modulate the equilibrium between these two conformational states, each of which engages mannose through distinct binding orientations. A FimH variant that only adopts the R state is severely attenuated early in a mouse model of uncomplicated UTI but is proficient at colonizing catheterized bladders in vivo or bladder transitional-like epithelial cells in vitro. Thus, the bladder habitat has barrier(s) to R state-mediated colonization possibly conferred by the terminally differentiated bladder epithelium and/or decoy receptors in urine. Together, our studies reveal the conformational landscape in solution, binding mechanisms, and adhesive strength of an allosteric two-domain adhesin that evolved "moderate" affinity to optimize persistence in the bladder during UTI.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 27, 2023Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: FimG N-terminal extension
H: Type 1 fimbiral adhesin FimH
A: FimG N-terminal extension
B: Type 1 fimbiral adhesin FimH
C: FimG N-terminal extension
D: Type 1 fimbiral adhesin FimH
E: FimG N-terminal extension
F: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,63712
Polymers122,2688
Non-polymers3684
Water16,033890
1
G: FimG N-terminal extension
H: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,5672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-10 kcal/mol
Surface area13130 Å2
MethodPISA
2
A: FimG N-terminal extension
B: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,5672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area13280 Å2
MethodPISA
3
C: FimG N-terminal extension
D: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,5672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-10 kcal/mol
Surface area12980 Å2
MethodPISA
4
E: FimG N-terminal extension
F: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,5672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.440, 75.560, 78.440
Angle α, β, γ (deg.)68.35, 69.00, 77.43
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide
FimG N-terminal extension


Mass: 1513.776 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli UTI89 (bacteria) / References: UniProt: Q1R2J5*PLUS
#2: Protein
Type 1 fimbiral adhesin FimH


Mass: 29053.260 Da / Num. of mol.: 4 / Fragment: UNP residues 22-300 / Mutation: A62S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain UTI89 / UPEC) (bacteria)
Strain: UTI89 / UPEC / Gene: fimH, UTI89_C5017 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2J4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium Acetate, 0.1 M HEPES 7.5, 10% PEG 8000
PH range: 5-8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.96→48.67 Å / Num. obs: 75411 / % possible obs: 94.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.5
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2 / % possible all: 90.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JWN

3jwn


Resolution: 1.962→48.666 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.08
RfactorNum. reflection% reflection
Rfree0.2394 3735 4.95 %
Rwork0.1888 --
obs0.1913 75394 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.962→48.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8491 0 24 890 9405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048724
X-RAY DIFFRACTIONf_angle_d0.7911966
X-RAY DIFFRACTIONf_dihedral_angle_d11.0072962
X-RAY DIFFRACTIONf_chiral_restr0.0311448
X-RAY DIFFRACTIONf_plane_restr0.0041548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9621-1.98690.31741360.30312389X-RAY DIFFRACTION87
1.9869-2.0130.3241380.24562618X-RAY DIFFRACTION91
2.013-2.04060.31491270.24492556X-RAY DIFFRACTION92
2.0406-2.06980.30231420.23542593X-RAY DIFFRACTION92
2.0698-2.10070.31641430.24072584X-RAY DIFFRACTION92
2.1007-2.13350.31061400.24212550X-RAY DIFFRACTION92
2.1335-2.16850.28221410.23042642X-RAY DIFFRACTION93
2.1685-2.20590.31681450.22392585X-RAY DIFFRACTION93
2.2059-2.2460.28081360.22072640X-RAY DIFFRACTION93
2.246-2.28920.31731350.22432621X-RAY DIFFRACTION93
2.2892-2.33590.2831310.22372663X-RAY DIFFRACTION93
2.3359-2.38670.2991340.21692579X-RAY DIFFRACTION94
2.3867-2.44220.28171150.21122744X-RAY DIFFRACTION94
2.4422-2.50330.24961270.20942600X-RAY DIFFRACTION94
2.5033-2.57090.25561610.20462653X-RAY DIFFRACTION95
2.5709-2.64660.26921400.20692655X-RAY DIFFRACTION94
2.6466-2.7320.2431290.19472702X-RAY DIFFRACTION95
2.732-2.82960.25791480.19842672X-RAY DIFFRACTION95
2.8296-2.94290.24541360.20132707X-RAY DIFFRACTION96
2.9429-3.07680.25241310.19542692X-RAY DIFFRACTION96
3.0768-3.2390.24251610.18982728X-RAY DIFFRACTION96
3.239-3.44190.21171460.16552692X-RAY DIFFRACTION96
3.4419-3.70760.20561430.17532731X-RAY DIFFRACTION97
3.7076-4.08050.17981430.15942753X-RAY DIFFRACTION97
4.0805-4.67060.17061250.13482776X-RAY DIFFRACTION98
4.6706-5.88280.17171320.13762761X-RAY DIFFRACTION98
5.8828-48.68140.18911500.15362773X-RAY DIFFRACTION98

+
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