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- PDB-4c48: Crystal structure of AcrB-AcrZ complex -

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Basic information

Entry
Database: PDB / ID: 4c48
TitleCrystal structure of AcrB-AcrZ complex
Components
  • ACRIFLAVINE RESISTANCE PROTEIN B
  • DARPIN
  • UNCHARACTERIZED MEMBRANE PROTEIN YBHT
KeywordsTRANSPORT PROTEIN / DRUG EFFLUX / TRANSMEMBRANE PROTEIN
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 / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid transmembrane transporter activity / xenobiotic transport ...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 / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / cell outer membrane / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2480 / : / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2480 / : / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / Ankyrin repeat-containing domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
SYNTHETIC CONSTRUCT (others)
Escherichia coli str. K-12 substr. W3110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDu, D. / James, N. / Klimont, E. / Luisi, B.F.
CitationJournal: Nature / Year: 2014
Title: Structure of the AcrAB-TolC multidrug efflux pump.
Authors: Dijun Du / Zhao Wang / Nathan R James / Jarrod E Voss / Ewa Klimont / Thelma Ohene-Agyei / Henrietta Venter / Wah Chiu / Ben F Luisi /
Abstract: The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of ...The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of these transporters form multicomponent 'pumps' that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component. A model system for such a pump is the acridine resistance complex of Escherichia coli. This pump assembly comprises the outer-membrane channel TolC, the secondary transporter AcrB located in the inner membrane, and the periplasmic AcrA, which bridges these two integral membrane proteins. The AcrAB-TolC efflux pump is able to transport vectorially a diverse array of compounds with little chemical similarity, thus conferring resistance to a broad spectrum of antibiotics. Homologous complexes are found in many Gram-negative species, including in animal and plant pathogens. Crystal structures are available for the individual components of the pump and have provided insights into substrate recognition, energy coupling and the transduction of conformational changes associated with the transport process. However, how the subunits are organized in the pump, their stoichiometry and the details of their interactions are not known. Here we present the pseudo-atomic structure of a complete multidrug efflux pump in complex with a modulatory protein partner from E. coli. The model defines the quaternary organization of the pump, identifies key domain interactions, and suggests a cooperative process for channel assembly and opening. These findings illuminate the basis for drug resistance in numerous pathogenic bacterial species.
History
DepositionSep 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Nov 21, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACRIFLAVINE RESISTANCE PROTEIN B
B: DARPIN
C: UNCHARACTERIZED MEMBRANE PROTEIN YBHT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,66513
Polymers137,0113
Non-polymers4,65410
Water63135
1
A: ACRIFLAVINE RESISTANCE PROTEIN B
B: DARPIN
C: UNCHARACTERIZED MEMBRANE PROTEIN YBHT
hetero molecules

A: ACRIFLAVINE RESISTANCE PROTEIN B
B: DARPIN
C: UNCHARACTERIZED MEMBRANE PROTEIN YBHT
hetero molecules

A: ACRIFLAVINE RESISTANCE PROTEIN B
B: DARPIN
C: UNCHARACTERIZED MEMBRANE PROTEIN YBHT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)424,99539
Polymers411,0339
Non-polymers13,96330
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
Buried area44080 Å2
ΔGint-263.6 kcal/mol
Surface area170090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.010, 145.010, 538.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ACRIFLAVINE RESISTANCE PROTEIN B / ACRB


Mass: 113388.898 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-1047
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Description: NOVAGEN / Variant: NOVABLUE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P31224
#2: Protein DARPIN


Mass: 18317.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: NOVAGEN / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43

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Protein/peptide / Sugars , 2 types, 10 molecules C

#3: Protein/peptide UNCHARACTERIZED MEMBRANE PROTEIN YBHT / ACRZ


Mass: 5304.423 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. W3110
Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): XL1-BLUE / References: UniProt: P0AAW9
#4: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 2 types, 36 molecules

#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.6 % / Description: CHAIN A
Crystal growpH: 7.5
Details: CRYSTALLISATION SOLUTION 100 MM HEPES, PH 7.5, 10 MM MGCL2 AND 12% (W/V) PEG 3350. SAMPLE BUFFER 10 MM HEPES PH: 7.5, 50 MM SODIUM CHLORIDE, 0.03% DDM N-DODECYL BETA-D-MALTOPYRANOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 33271 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11
Reflection shellResolution: 3.3→3.46 Å / Redundancy: 5 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DX5

4dx5


Resolution: 3.3→29.67 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.832 / SU B: 31.407 / SU ML: 0.518 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. PORTIONS OF ACRB AND DARPIN WERE DISORDERED AND WERE MODELLED STEREOCHEMICALLY. THE N AND C TERMINI OF ACRZ ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. PORTIONS OF ACRB AND DARPIN WERE DISORDERED AND WERE MODELLED STEREOCHEMICALLY. THE N AND C TERMINI OF ACRZ ARE NOT AS WELL ORGANISED AS THE CENTRAL REGION AND HAVE HIGHER B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.322 1656 5 %RANDOM
Rwork0.28142 ---
obs0.28343 31614 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.041 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å21.22 Å20 Å2
2--1.22 Å20 Å2
3----3.97 Å2
Refinement stepCycle: LAST / Resolution: 3.3→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9259 0 96 35 9390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199518
X-RAY DIFFRACTIONr_bond_other_d0.0020.029397
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.97512903
X-RAY DIFFRACTIONr_angle_other_deg0.786321557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81251226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56924.823367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.149151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3781538
X-RAY DIFFRACTIONr_chiral_restr0.0720.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022062
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 123 -
Rwork0.34 2254 -
obs--99.96 %

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