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- PDB-4jpb: The structure of a ternary complex between CheA domains P4 and P5... -

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Basic information

Entry
Database: PDB / ID: 4jpb
TitleThe structure of a ternary complex between CheA domains P4 and P5 with CheW and with an unzipped fragment of TM14, a chemoreceptor analog from Thermotoga maritima.
Components
  • Chemotaxis protein CheA
  • Chemotaxis protein CheW
  • Methyl-accepting chemotaxis protein
KeywordsIMMUNE SYSTEM / Ternary complex / Transmembrane Signaling Two component system Receptor / Histidine Kinase Adaptor protein / Membrane
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / chemotaxis / lysozyme activity / protein domain specific binding / signal transduction / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3200 / CheA-289, Domain 4 / Chemotaxis protein CheW / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / Chemotaxis protein CheA, P2 response regulator-binding / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3200 / CheA-289, Domain 4 / Chemotaxis protein CheW / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / Chemotaxis protein CheA, P2 response regulator-binding / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / SH3 Domains / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Helix non-globular / Histidine kinase/HSP90-like ATPase superfamily / Special / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chemotaxis protein CheA / Chemotaxis protein CheW / Methyl-accepting chemotaxis protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.186 Å
AuthorsLi, X. / Bayas, C. / Bilwes, A.M. / Crane, B.R.
CitationJournal: Biochemistry / Year: 2013
Title: The 3.2 angstrom resolution structure of a receptor: CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays.
Authors: Li, X. / Fleetwood, A.D. / Bayas, C. / Bilwes, A.M. / Ortega, D.R. / Falke, J.J. / Zhulin, I.B. / Crane, B.R.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein CheA
W: Chemotaxis protein CheW
B: Methyl-accepting chemotaxis protein
C: Methyl-accepting chemotaxis protein


Theoretical massNumber of molelcules
Total (without water)72,3334
Polymers72,3334
Non-polymers00
Water00
1
A: Chemotaxis protein CheA
W: Chemotaxis protein CheW

A: Chemotaxis protein CheA
W: Chemotaxis protein CheW

A: Chemotaxis protein CheA
W: Chemotaxis protein CheW


Theoretical massNumber of molelcules
Total (without water)157,1426
Polymers157,1426
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8970 Å2
ΔGint-60 kcal/mol
Surface area38420 Å2
MethodPISA
2
B: Methyl-accepting chemotaxis protein
C: Methyl-accepting chemotaxis protein

B: Methyl-accepting chemotaxis protein
C: Methyl-accepting chemotaxis protein


Theoretical massNumber of molelcules
Total (without water)39,9054
Polymers39,9054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area14860 Å2
ΔGint-151 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.588, 213.588, 208.838
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe receptor fragment is dimerized by crystal symmetry to produce a 4-helix bundle. The assembly state of the receptor kinase arrays is complex and extended, but the ring structure formed by the alternating CheA and CheW units built by the crystal symmetry of this structure are thought to be important features of the assembled system.

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Components

#1: Protein Chemotaxis protein CheA


Mass: 35403.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: cheA, TM_0702 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL-21 (RIL DE3) / References: UniProt: Q56310, histidine kinase
#2: Protein Chemotaxis protein CheW


Mass: 16976.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: cheW, TM_0701 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (RIL DE3) / References: UniProt: Q56311
#3: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis sensory transducer / Chemoreceptor Tm00014


Mass: 9976.237 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: ThemaDRAFT_1422, Tm00014, TM_0014 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (RIL DE3) / References: UniProt: Q7DFA3

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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: 6.34 Å3/Da / Density % sol: 80.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Cubic shaped crystals (50x50x50 um3) were grown from a mixture of 520 uM Tm14s, 457 uM CheA 354 and 121 uM CheW after 1 month by vapor diffusion from a 2 ul drop (1:1 mixture of protein and ...Details: Cubic shaped crystals (50x50x50 um3) were grown from a mixture of 520 uM Tm14s, 457 uM CheA 354 and 121 uM CheW after 1 month by vapor diffusion from a 2 ul drop (1:1 mixture of protein and reservoir: 500 ul reservoir of 0.2 M sodium acetate trihydrate, 0.1 M Tris (pH 8.5), 15% w/v polyethylene glycol 4,000), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2012 / Details: Rh-coated Si mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.186→46.2 Å / Num. all: 30645 / Num. obs: 30554 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 20.3
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.186→46.156 Å / SU ML: 0.38 / σ(F): 1.34 / σ(I): 0 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1998 6.55 %Random 6.5%
Rwork0.1961 ---
obs0.1977 30516 99.38 %-
all-30607 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a free: 0.58 Å
Refinement stepCycle: LAST / Resolution: 3.186→46.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 0 0 3447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113488
X-RAY DIFFRACTIONf_angle_d1.3314699
X-RAY DIFFRACTIONf_dihedral_angle_d19.0811352
X-RAY DIFFRACTIONf_chiral_restr0.086581
X-RAY DIFFRACTIONf_plane_restr0.004604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.186-3.29990.3391960.33682790X-RAY DIFFRACTION98
3.2999-3.4320.35391980.28222836X-RAY DIFFRACTION100
3.432-3.58810.28281990.26062834X-RAY DIFFRACTION100
3.5881-3.77720.26141990.22772839X-RAY DIFFRACTION100
3.7772-4.01370.2272010.20242863X-RAY DIFFRACTION100
4.0137-4.32340.23351980.16422846X-RAY DIFFRACTION100
4.3234-4.75810.16672020.14982873X-RAY DIFFRACTION100
4.7581-5.44570.17632020.15942872X-RAY DIFFRACTION100
5.4457-6.85740.22422000.19942872X-RAY DIFFRACTION100
6.8574-46.16070.19912030.19012893X-RAY DIFFRACTION97

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