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- PDB-5zfp: Structure of the ExbB/ExbD hexameric complex -

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Basic information

Entry
Database: PDB / ID: 5zfp
TitleStructure of the ExbB/ExbD hexameric complex
ComponentsBiopolymer transport protein ExbB
KeywordsTRANSPORT PROTEIN / TON SYSTEM / ION CHANNEL / ENERGIZER / TRANSPORTER / PROTON MOTIVE FORCE
Function / homology
Function and homology information


energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / protein import / plasma membrane protein complex / transmembrane transporter complex / transmembrane transporter activity / cell outer membrane / intracellular iron ion homeostasis ...energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / protein import / plasma membrane protein complex / transmembrane transporter complex / transmembrane transporter activity / cell outer membrane / intracellular iron ion homeostasis / protein stabilization / membrane / identical protein binding / plasma membrane
Similarity search - Function
TonB-system energizer ExbB type-1 / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Biopolymer transport protein ExbB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsMaki-Yonekura, S. / Matsuoka, R. / Yonekura, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
the Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research Grant15K06986 Japan
the Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research Grant16H04757 Japan
CitationJournal: Elife / Year: 2018
Title: Hexameric and pentameric complexes of the ExbBD energizer in the Ton system.
Authors: Saori Maki-Yonekura / Rei Matsuoka / Yoshiki Yamashita / Hirofumi Shimizu / Maiko Tanaka / Fumie Iwabuki / Koji Yonekura /
Abstract: Gram-negative bacteria import essential nutrients such as iron and vitamin B through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three ...Gram-negative bacteria import essential nutrients such as iron and vitamin B through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three inner membrane proteins, ExbB, ExbD and TonB. ExbB and ExbD form the proton channel that energizes uptake through TonB. Recently, crystal structures suggest that the ExbB pentamer is the scaffold. Here, we present structures of hexameric complexes of ExbB and ExbD revealed by X-ray crystallography and single particle cryo-EM. Image analysis shows that hexameric and pentameric complexes coexist, with the proportion of hexamer increasing with pH. Channel current measurement and 2D crystallography support the existence and transition of the two oligomeric states in membranes. The hexameric complex consists of six ExbB subunits and three ExbD transmembrane helices enclosed within the central channel. We propose models for activation/inactivation associated with hexamer and pentamer formation and utilization of proton motive force.
History
DepositionMar 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biopolymer transport protein ExbB
B: Biopolymer transport protein ExbB
C: Biopolymer transport protein ExbB
D: Biopolymer transport protein ExbB
E: Biopolymer transport protein ExbB
F: Biopolymer transport protein ExbB
G: Biopolymer transport protein ExbB
H: Biopolymer transport protein ExbB
I: Biopolymer transport protein ExbB
J: Biopolymer transport protein ExbB
K: Biopolymer transport protein ExbB
L: Biopolymer transport protein ExbB


Theoretical massNumber of molelcules
Total (without water)315,74812
Polymers315,74812
Non-polymers00
Water13,854769
1
A: Biopolymer transport protein ExbB
B: Biopolymer transport protein ExbB
C: Biopolymer transport protein ExbB
D: Biopolymer transport protein ExbB
E: Biopolymer transport protein ExbB
F: Biopolymer transport protein ExbB


Theoretical massNumber of molelcules
Total (without water)157,8746
Polymers157,8746
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17910 Å2
ΔGint-154 kcal/mol
Surface area60450 Å2
MethodPISA
2
G: Biopolymer transport protein ExbB
H: Biopolymer transport protein ExbB
I: Biopolymer transport protein ExbB
J: Biopolymer transport protein ExbB
K: Biopolymer transport protein ExbB
L: Biopolymer transport protein ExbB


Theoretical massNumber of molelcules
Total (without water)157,8746
Polymers157,8746
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18240 Å2
ΔGint-153 kcal/mol
Surface area60530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.470, 106.340, 163.360
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Biopolymer transport protein ExbB


Mass: 26312.322 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: exbB, b3006, JW2974 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABU7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M glycine, pH 9.0, 0.15 M CaCl2, 40 % PEG 350 MME, 0.05-0.2 M L-arginine

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→50.18 Å / Num. obs: 90711 / % possible obs: 99.3 % / Redundancy: 5 % / Biso Wilson estimate: 53.73 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.155 / Net I/σ(I): 6.67
Reflection shellResolution: 2.84→2.94 Å / Rmerge(I) obs: 0.5 / CC1/2: 0.751 / Rrim(I) all: 0.706

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SV0

5sv0


Resolution: 2.84→50.18 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.814 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.049 / SU Rfree Blow DPI: 0.382 / SU Rfree Cruickshank DPI: 0.391
RfactorNum. reflection% reflectionSelection details
Rfree0.288 4546 5.01 %RANDOM
Rwork0.245 ---
obs0.247 90711 99.3 %-
Displacement parametersBiso mean: 43.59 Å2
Baniso -1Baniso -2Baniso -3
1-12.1241 Å20 Å2-1.6974 Å2
2---7.9771 Å20 Å2
3----4.147 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: 1 / Resolution: 2.84→50.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19884 0 0 769 20653
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0120164HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1127284HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7051SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes498HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2984HARMONIC5
X-RAY DIFFRACTIONt_it20164HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion21.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2699SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23647SEMIHARMONIC4
LS refinement shellResolution: 2.84→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 341 5.08 %
Rwork0.242 6372 -
all0.244 6713 -
obs--99.39 %

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