[English] 日本語
Yorodumi
- PDB-4dk1: Crystal Structure of MacA-MexA chimeric protein, containing the P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dk1
TitleCrystal Structure of MacA-MexA chimeric protein, containing the Pseudomonas aeruginosa MexA alpha-hairpin domain.
ComponentsPutative MacA, Multidrug resistance protein mexA
KeywordsMEMBRANE PROTEIN / alpha-hairpin / lipoyl / beta-barrel domains / PERIPLASMIC PROTEIN
Function / homology
Function and homology information


macrolide transmembrane transporter complex / xenobiotic detoxification by transmembrane export across the plasma membrane / extrinsic component of membrane / efflux transmembrane transporter activity / transmembrane transporter activity / protein homooligomerization / transmembrane transport / response to antibiotic / identical protein binding / plasma membrane
Similarity search - Function
N-terminal domain of TfIIb - #140 / Macrolide export protein MacA / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / N-terminal domain of TfIIb ...N-terminal domain of TfIIb - #140 / Macrolide export protein MacA / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / N-terminal domain of TfIIb / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Other non-globular / Elongation Factor Tu (Ef-tu); domain 3 / Special / Prokaryotic membrane lipoprotein lipid attachment site profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Multidrug resistance protein MexA / Putative MacA
Similarity search - Component
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.499 Å
AuthorsXu, Y. / Ha, N.C.
CitationJournal: J Biol Chem / Year: 2012
Title: Assembly and channel opening of outer membrane protein in tripartite drug efflux pumps of Gram-negative bacteria.
Authors: Yongbin Xu / Arne Moeller / So-Young Jun / Minho Le / Bo-Young Yoon / Jin-Sik Kim / Kangseok Lee / Nam-Chul Ha /
Abstract: Gram-negative bacteria are capable of expelling diverse xenobiotic substances from within the cell by use of three-component efflux pumps in which the energy-activated inner membrane transporter is ...Gram-negative bacteria are capable of expelling diverse xenobiotic substances from within the cell by use of three-component efflux pumps in which the energy-activated inner membrane transporter is connected to the outer membrane channel protein via the membrane fusion protein. In this work, we describe the crystal structure of the membrane fusion protein MexA from the Pseudomonas aeruginosa MexAB-OprM pump in the hexameric ring arrangement. Electron microscopy study on the chimeric complex of MexA and the outer membrane protein OprM reveals that MexA makes a tip-to-tip interaction with OprM, which suggests a docking model for MexA and OprM. This docking model agrees well with genetic results and depicts detailed interactions. Opening of the OprM channel is accompanied by the simultaneous exposure of a protein structure resembling a six-bladed cogwheel, which intermeshes with the complementary cogwheel structure in the MexA hexamer. Taken together, we suggest an assembly and channel opening model for the MexAB-OprM pump. This study provides a better understanding of multidrug resistance in Gram-negative bacteria.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative MacA, Multidrug resistance protein mexA
B: Putative MacA, Multidrug resistance protein mexA
C: Putative MacA, Multidrug resistance protein mexA
D: Putative MacA, Multidrug resistance protein mexA


Theoretical massNumber of molelcules
Total (without water)147,3734
Polymers147,3734
Non-polymers00
Water0
1
A: Putative MacA, Multidrug resistance protein mexA
B: Putative MacA, Multidrug resistance protein mexA

A: Putative MacA, Multidrug resistance protein mexA
B: Putative MacA, Multidrug resistance protein mexA

A: Putative MacA, Multidrug resistance protein mexA
B: Putative MacA, Multidrug resistance protein mexA


Theoretical massNumber of molelcules
Total (without water)221,0606
Polymers221,0606
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area20570 Å2
ΔGint-81 kcal/mol
Surface area88850 Å2
MethodPISA
2
C: Putative MacA, Multidrug resistance protein mexA
D: Putative MacA, Multidrug resistance protein mexA

C: Putative MacA, Multidrug resistance protein mexA
D: Putative MacA, Multidrug resistance protein mexA

C: Putative MacA, Multidrug resistance protein mexA
D: Putative MacA, Multidrug resistance protein mexA


Theoretical massNumber of molelcules
Total (without water)221,0606
Polymers221,0606
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area20440 Å2
ΔGint-77 kcal/mol
Surface area89450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.708, 151.708, 216.953
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 42:74 OR RESSEQ 76:238 OR RESSEQ 242:255 OR RESSEQ 257:282 )
211CHAIN B AND (RESSEQ 42:74 OR RESSEQ 76:238 OR RESSEQ 242:255 OR RESSEQ 257:282 )
311CHAIN C AND (RESSEQ 42:74 OR RESSEQ 76:238 OR RESSEQ 242:255 OR RESSEQ 257:282 )
411CHAIN D AND (RESSEQ 42:74 OR RESSEQ 76:238 OR RESSEQ 242:255 OR RESSEQ 257:282 )

-
Components

#1: Protein
Putative MacA, Multidrug resistance protein mexA


Mass: 36843.281 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 30-88, 95-158, 181-394
Source method: isolated from a genetically manipulated source
Details: The chimeric protein of MacA (RESIDUES 30-88), mexA (RESIDUES 95-158), and MacA (RESIDUES 181-394)
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: PAO1 / Gene: mexA, PA0425 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2EHL9, UniProt: P52477
Sequence detailsTHESE RESIDUES DERIVE FROM A VARIANT OF THE STRAIN OF THE BACTERIA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.89 Å3/Da / Density % sol: 74.85 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 7.5
Details: 0.16M CaCl2, 0.1M Hepes (pH 7.5) 23.5% PEG 400, EVAPORATION, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: Double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.499→20 Å / Num. all: 36819 / Num. obs: 33690 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.5→3.56 Å / % possible all: 95

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.499→19.951 Å / SU ML: 1.47 / σ(F): 1.68 / Phase error: 34.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.368 1709 5.08 %Random
Rwork0.3141 ---
all0.3168 33685 --
obs0.3168 33667 91.35 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0.129 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.013 Å20 Å20 Å2
2---11.013 Å2-0 Å2
3---22.026 Å2
Refinement stepCycle: LAST / Resolution: 3.499→19.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8568 0 0 0 8568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0258652
X-RAY DIFFRACTIONf_angle_d2.97311739
X-RAY DIFFRACTIONf_dihedral_angle_d26.0383219
X-RAY DIFFRACTIONf_chiral_restr0.2071442
X-RAY DIFFRACTIONf_plane_restr0.0151514
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1802X-RAY DIFFRACTIONPOSITIONAL
12B1802X-RAY DIFFRACTIONPOSITIONAL0.119
13C1802X-RAY DIFFRACTIONPOSITIONAL0.11
14D1802X-RAY DIFFRACTIONPOSITIONAL0.111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4989-3.60130.41721400.4286269394
3.6013-3.71680.43621530.4087282198
3.7168-3.84870.36711490.3552270995
3.8487-4.00170.36511330.3183236481
4.0017-4.18220.38731130.3079228379
4.1822-4.40050.38311420.2786258790
4.4005-4.67280.35551410.283247485
4.6728-5.02830.30251540.2503263891
5.0283-5.52450.35211470.2687268892
5.5245-6.30180.33771400.2819281895
6.3018-7.85810.34611600.2686285097
7.8581-19.95110.37741370.3261303398
Refinement TLS params.Method: refined / Origin x: -21.0638 Å / Origin y: 78.0611 Å / Origin z: 137.541 Å
111213212223313233
T-0.0137 Å2-0.0182 Å2-0.0663 Å2-0.0058 Å20.0701 Å2---0.044 Å2
L0.0049 °2-0.0025 °2-0.0265 °2-0.0152 °20.0089 °2--0.0229 °2
S0.0273 Å °0.2699 Å °0.0049 Å °-0.2777 Å °-0.0144 Å °0.0799 Å °0.0036 Å °-0.0131 Å °-0.003 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