[English] 日本語
Yorodumi
- PDB-9hci: structure of the double Cys-substituted cross-linked AcrB variant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hci
Titlestructure of the double Cys-substituted cross-linked AcrB variant S562C_T837C
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / RND multidrug efflux pump / antimicrobial resistance / intermediate conformational state / crosslinked structure
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / Antimicrobial resistance ...alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / Antimicrobial resistance / bile acid and bile salt transport / Secretion of toxins / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / xenobiotic transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / membrane / identical protein binding / plasma membrane
Similarity search - Function
Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
TETRADECANE / DECANE / DODECANE / nonane / HEXANE / N-OCTANE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBrandstaetter, L. / Mueller, R.T. / Pos, K.M.
Funding support Switzerland, Germany, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
University of Zurich Switzerland
German Research Foundation (DFG)SFB 807 Germany
CitationJournal: NPJ Antimicrob Resist / Year: 2026
Title: Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps.
Authors: Bornsen, C. / Muller, R.T. / Vieira Da Cruz, A. / Jimenez-Castellanos, J.C. / Meurillon, V. / Brandstatter, L. / Lodinsky, E.V. / Athar, M. / Vargiu, A.V. / Hartkoorn, R.C. / Flipo, M. / ...Authors: Bornsen, C. / Muller, R.T. / Vieira Da Cruz, A. / Jimenez-Castellanos, J.C. / Meurillon, V. / Brandstatter, L. / Lodinsky, E.V. / Athar, M. / Vargiu, A.V. / Hartkoorn, R.C. / Flipo, M. / Frangakis, A.S. / Pos, K.M.
History
DepositionNov 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.1May 20, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _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: Multidrug efflux pump subunit AcrB
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB
D: DARPIN
E: DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,32850
Polymers380,8985
Non-polymers8,43045
Water21,8881215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42140 Å2
ΔGint-21 kcal/mol
Surface area120790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.710, 165.300, 244.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 5 molecules ABCDE

#1: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 114754.398 Da / Num. of mol.: 3 / Mutation: S562C, T837C
Source method: isolated from a genetically manipulated source
Details: disulfide bond between S562C and T837C / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MG1655 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24a / Details (production host): pET24a_acrB_S562C_T837C / Production host: Escherichia coli B (bacteria) / Strain (production host): C43(DE3)DELTAacrB / References: UniProt: P31224
#2: Protein DARPIN


Mass: 18317.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Details (production host): pQE30_110819 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): XL1-Blue

-
Sugars , 1 types, 8 molecules

#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 9 types, 1252 molecules

#4: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#7: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#9: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#10: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#11: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1215 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.23 % / Description: Rod-shaped crystals
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ADA, pH 6.5, 0.2M ammonium sulfate, 8% PEG4000, 5.1% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99997 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 19, 2007
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.6→47.69 Å / Num. obs: 181397 / % possible obs: 99.94 % / Redundancy: 8.4 % / CC1/2: 0.982 / Net I/σ(I): 7.09
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 17959 / CC1/2: 0.683 / % possible all: 99.99

-
Processing

Software
NameVersionClassification
PDB-REDO8.11refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.69 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / SU B: 18.063 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 9291 5.1 %RANDOM
Rwork0.18974 ---
obs0.19177 172106 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.783 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0 Å2-0 Å2
2--0.05 Å2-0 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25975 0 576 1215 27766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01727022
X-RAY DIFFRACTIONr_bond_other_d0.0010.01626696
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.8236576
X-RAY DIFFRACTIONr_angle_other_deg0.4611.57761412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275.173535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.029104447
X-RAY DIFFRACTIONr_chiral_restr0.0610.24320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0230828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025896
X-RAY DIFFRACTIONr_mcbond_it4.4231.45613672
X-RAY DIFFRACTIONr_mcbond_other4.4211.45613672
X-RAY DIFFRACTIONr_mcangle_it6.2932.61117083
X-RAY DIFFRACTIONr_mcangle_other6.2932.61217084
X-RAY DIFFRACTIONr_scbond_it7.6212.13513350
X-RAY DIFFRACTIONr_scbond_other7.6262.13613351
X-RAY DIFFRACTIONr_scangle_other9.9673.61519494
X-RAY DIFFRACTIONr_long_range_B_refined11.44115.0730335
X-RAY DIFFRACTIONr_long_range_B_other11.45514.8830033
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 652 -
Rwork0.338 12595 -
obs--99.98 %
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)
10.6676-0.0388-0.10850.3611-0.23980.85340.1340.00060.31860.0813-0.0375-0.015-0.39540.0251-0.09650.1961-0.02560.08450.39740.00170.154829.387-15.288-16.494
20.3101-0.10070.05880.5521-0.39050.44640.08240.2758-0.006-0.2953-0.02710.13660.1796-0.0727-0.05530.19120.0363-0.08690.53640.00060.048429.191-41.57-52.379
30.57850.0241-0.07270.1513-0.0940.61080.06320.18110.1085-0.0653-0.072-0.0386-0.05190.13650.00890.05190.01880.03120.46090.06780.033167.671-26.444-34.003
42.36180.22151.30511.33660.14994.11240.0042-0.0306-0.1021-0.0123-0.06290.2638-0.0315-0.40910.05870.1154-0.1128-0.0480.3139-0.09990.18191.075-75.406-24.619
54.2351-1.6556-0.85464.24980.8592.6583-0.075-0.77330.62050.48560.1171-0.4929-0.35360.1738-0.04210.187-0.1444-0.07210.73-0.08880.115946.585-39.41927.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1044
2X-RAY DIFFRACTION2B1 - 1033
3X-RAY DIFFRACTION3C1 - 1033
4X-RAY DIFFRACTION4D12 - 166
5X-RAY DIFFRACTION5E14 - 166

+
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