[English] 日本語
Yorodumi
- PDB-8v9v: Yeh-like adhesin YhlD receptor binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v9v
TitleYeh-like adhesin YhlD receptor binding domain
ComponentsPilus assembly protein
KeywordsCELL ADHESION / Receptor / Adhesin / Intestine / EHEC / UPEC
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLopatto, E.D.B. / Tamadonfar, K.O. / Klein, R.D. / Hultgren, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2026
Title: The Yeh pilus adhesin is equipped with an alpha-helical flap motif, which contributes to pectin adherence.
Authors: Tamadonfar, K.O. / Klein, R.D. / Lopatto, E.D.B. / Zimmerman, M.I. / Azimzadeh, P.N. / Sanick, D.A. / Porter, J.R. / Villicana, J.B. / Pinkner, J.S. / Chiang, B.H. / Gualberto, N.C. / ...Authors: Tamadonfar, K.O. / Klein, R.D. / Lopatto, E.D.B. / Zimmerman, M.I. / Azimzadeh, P.N. / Sanick, D.A. / Porter, J.R. / Villicana, J.B. / Pinkner, J.S. / Chiang, B.H. / Gualberto, N.C. / Dodson, K.W. / Patnode, M.L. / Birchenough, G.M.H. / Bowman, G.R. / Hultgren, S.J.
History
DepositionDec 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)19,2051
Polymers19,2051
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.302, 104.117, 131.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

-
Components

#1: Protein Pilus assembly protein / Type-1 fimbrial protein


Mass: 19204.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: C9E67_10040, NCTC13127_02335 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A152V3W7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 95 mM sodium citrate, pH 5.6, 5% glycerol, 19% PEG4000, 19% isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.29→40.82 Å / Num. obs: 9217 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 37.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.06604 / Rpim(I) all: 0.06604 / Rrim(I) all: 0.09339 / Net I/σ(I): 9.69
Reflection shellResolution: 2.29→2.372 Å / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 904 / CC1/2: 0.515

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→40.82 Å / SU ML: 0.3723 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2631 453 4.92 %
Rwork0.2237 8761 -
obs0.2256 9214 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.75 Å2
Refinement stepCycle: LAST / Resolution: 2.29→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 0 17 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271269
X-RAY DIFFRACTIONf_angle_d0.46771726
X-RAY DIFFRACTIONf_chiral_restr0.0444205
X-RAY DIFFRACTIONf_plane_restr0.0023215
X-RAY DIFFRACTIONf_dihedral_angle_d4.5805173
LS refinement shellResolution: 2.29→2.372 Å
RfactorNum. reflection% reflection
Rfree0.3535 146 -
Rwork0.3119 2849 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: -4.25736935215 Å / Origin y: -6.26026866914 Å / Origin z: 21.1593330418 Å
111213212223313233
T0.263638799933 Å2-0.058804338393 Å2-0.042673240348 Å2-0.281700182568 Å20.00875950434893 Å2--0.280972914246 Å2
L1.67389280641 °2-0.570355320682 °20.524370061246 °2-2.2612499176 °2-1.58136348972 °2--3.2766236548 °2
S0.125043301177 Å °0.123852080077 Å °-0.149176008998 Å °0.0653285658982 Å °0.0595448454208 Å °0.126305986038 Å °0.288317855703 Å °-0.110861846216 Å °-0.137084888039 Å °
Refinement TLS groupSelection details: all

+
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