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- PDB-5jyv: NMR structure of foldswitch-stablized KaiB in complex with pseudo... -

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Basic information

Entry
Database: PDB / ID: 5jyv
TitleNMR structure of foldswitch-stablized KaiB in complex with pseudo receiver domain of CikA from Thermosynechococcus elongatus
Components
  • Circadian clock protein KaiB
  • Two-component sensor histidine kinase
KeywordsSigaling protein / Circadian Clock / Signaling protein complex
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / circadian rhythm / rhythmic process / cell division / ATP binding
Similarity search - Function
Circadian clock protein KaiB / : / Circadian clock protein KaiB-like / KaiB domain / KaiB domain / KaiB / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...Circadian clock protein KaiB / : / Circadian clock protein KaiB-like / KaiB domain / KaiB domain / KaiB / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / CheY-like superfamily / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Circadian clock oscillator protein KaiB / Circadian input-output histidine kinase CikA
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTseng, R.D. / LiWang, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107521 United States
CitationJournal: Science / Year: 2017
Title: Structural basis of the day-night transition in a bacterial circadian clock.
Authors: Tseng, R. / Goularte, N.F. / Chavan, A. / Luu, J. / Cohen, S.E. / Chang, Y.G. / Heisler, J. / Li, S. / Michael, A.K. / Tripathi, S. / Golden, S.S. / LiWang, A. / Partch, C.L.
History
DepositionMay 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Two-component sensor histidine kinase
B: Circadian clock protein KaiB


Theoretical massNumber of molelcules
Total (without water)24,6802
Polymers24,6802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2250 Å2
ΔGint-10 kcal/mol
Surface area12320 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Two-component sensor histidine kinase


Mass: 12899.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: tll0899
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8DKG0
#2: Protein Circadian clock protein KaiB


Mass: 11779.870 Da / Num. of mol.: 1
Mutation: Y8A, Y94A, N29A, G89A, D91R, FLAG tag C-terminus insertion, C-terminal truncation after Residue D99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: kaiB, tlr0482
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q79V61

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HN(COCA)CB
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HBHA(CO)NH
1161isotropic13D 15N edited 1H-15N NOESY
1152isotropic13D 13C edited 1H-13C NOESY
1142isotropic13D (H)CCH-COSY
1132isotropic13D (H)CCH-TOCSY
1127isotropic13D IPAP-HNCO(CA)
1118anisotropic13D IPAP-HNCO(CA)
1107isotropic13D IPAP-HNCO
198anisotropic13D IPAP-HNCO
189isotropic12D IPAP-1H-15N HSQC
1710anisotropic12D IPAP-1H-15N HSQC
165isotropic115N, 13C edited 4D NOESY-HSQC
14515isotropic113C-edited, 12C-filtered 3D NOESY-HSQC
1443isotropic13D HN(CA)CB
1433isotropic13D HN(COCA)CB
1423isotropic13D HNCO
1413isotropic13D HN(CA)CO
1403isotropic13D HBHA(CO)NH
1393isotropic13D 15N edited 1H-15N NOESY
1384isotropic13D 13C edited 1H-13C NOESY
1374isotropic13D (H)CCH-COSY
1364isotropic13D (H)CCH-TOCSY
1354isotropic13D HCAN
1344isotropic13D HCA(CO)N
13311isotropic13D IPAP-HNCO(CA)
13212anisotropic13D IPAP-HNCO(CA)
13111isotropic13D IPAP-HNCO
13012anisotropic13D IPAP-HNCO
12913isotropic12D IPAP-1H-15N HSQC
12814anisotropic12D IPAP-1H-15N HSQC
1276isotropic115N, 13C edited 4D NOESY-HSQC
12616isotropic113C-edited, 12C-filtered 3D NOESY-HSQC
1471isotropic12D 1H-15N HSQC
1463isotropic12D 1H-15N HSQC
1492isotropic12D 1H-13C HSQC
1484isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1800 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 880 uM unlabeled KaiB mutant-N29A, 95% H2O/5% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)cika_h2095% H2O/5% D2O
solution2800 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 880 uM unlabeled KaiB mutant-N29A, 100% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)cika_d2o100% D2O
solution3800 uM [U-99% 13C; U-99% 15N] KaiB mutant-N29A, 880 uM unlabeled pseudo receiver domain of CikA, 95% H2O/5% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)KaiB_h2o95% H2O/5% D2O
solution4800 uM [U-99% 13C; U-99% 15N] KaiB mutant-N29A, 880 uM unlabeled pseudo receiver domain of CikA, 100% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)KaiB_d2o100% D2O
solution5800 uM [U-100% 15N] pseudo receiver domain of CikA, 880 uM [U-100% 13C] KaiB mutant-N29A, 95% H2O/5% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)n15_cikA_c13_tb95% H2O/5% D2O
solution6800 uM [U-100% 15N] KaiB mutant-N29A, 880 uM [U-100% 13C] pseudo receiver domain of CikA, 95% H2O/5% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)n15_tb_c13_cika95% H2O/5% D2O
gel solution7400 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 440 uM unlabeled KaiB mutant-N29A, 90% H2O/10% D2O10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)3D_cika_RDC_isotropic90% H2O/10% D2O
gel solution8650 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 715 uM unlabeled KaiB mutant-N29A, 90% H2O/10% D2O5.5% stretched polyacrylamide gel made with 5 mm diameter 10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)3D_cika_RDC_aligned90% H2O/10% D2O
gel solution9400 uM [U-99% 15N] pseudo receiver domain of CikA, 440 uM unlabeled KaiB mutant-N29A, 90% H2O/10% D2O10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)2D_cika_RDC_isotropic90% H2O/10% D2O
gel solution10400 uM [U-99% 15N] pseudo receiver domain of CikA, 440 uM unlabeled KaiB mutant-N29A, 90% H2O/10% D2O5.5% stretched polyacrylamide gel made with 5 mm diameter 10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)2D_cika_RDC_aligned90% H2O/10% D2O
gel solution11400 uM [U-99% 13C; U-99% 15N] KaiB mutant-N29A, 440 uM unlabeled pseudo receiver domain of CikA, 90% H2O/10% D2O10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)3D_tb_RDC_isotropic90% H2O/10% D2O
gel solution12700 uM [U-99% 13C; U-99% 15N] KaiB mutant-N29A, 770 uM unlabeled pseudo receiver domain of CikA, 90% H2O/10% D2O5.5% stretched polyacrylamide gel made with 5 mm diameter 10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)3D_tb_RDC_aligned90% H2O/10% D2O
gel solution13400 uM [U-99% 15N] KaiB mutant-N29A, 440 uM unlabeled pseudo receiver domain of CikA, 90% H2O/10% D2O10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)2D_tb_RDC_isotropic90% H2O/10% D2O
gel solution14400 uM [U-99% 15N] KaiB mutant-N29A, 440 uM unlabeled pseudo receiver domain of CikA, 90% H2O/10% D2O5.5% stretched polyacrylamide gel made with 5 mm diameter 10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)2D_tb_RDC_aligned90% H2O/10% D2O
solution15800 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 880 uM unlabeled KaiB mutant-N29A, 100% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)CikA_internoe_c13-c12100% D2O
solution16800 uM [U-99% 13C; U-99% 15N] KaiB mutant-N29A, 880 uM unlabeled pseudo receiver domain of CikA, 100% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)tb_internoe_c13-c12100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
800 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]1
880 uMKaiB mutant-N29Aunlabeled1
800 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]2
880 uMKaiB mutant-N29Aunlabeled2
800 uMKaiB mutant-N29A[U-99% 13C; U-99% 15N]3
880 uMpseudo receiver domain of CikAunlabeled3
800 uMKaiB mutant-N29A[U-99% 13C; U-99% 15N]4
880 uMpseudo receiver domain of CikAunlabeled4
800 uMpseudo receiver domain of CikA[U-100% 15N]5
880 uMKaiB mutant-N29A[U-100% 13C]5
800 uMKaiB mutant-N29A[U-100% 15N]6
880 uMpseudo receiver domain of CikA[U-100% 13C]6
400 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]7
440 uMKaiB mutant-N29Aunlabeled7
650 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]8
715 uMKaiB mutant-N29Aunlabeled8
400 uMpseudo receiver domain of CikA[U-99% 15N]9
440 uMKaiB mutant-N29Aunlabeled9
400 uMpseudo receiver domain of CikA[U-99% 15N]10
440 uMKaiB mutant-N29Aunlabeled10
400 uMKaiB mutant-N29A[U-99% 13C; U-99% 15N]11
440 uMpseudo receiver domain of CikAunlabeled11
700 uMKaiB mutant-N29A[U-99% 13C; U-99% 15N]12
770 uMpseudo receiver domain of CikAunlabeled12
400 uMKaiB mutant-N29A[U-99% 15N]13
440 uMpseudo receiver domain of CikAunlabeled13
400 uMKaiB mutant-N29A[U-99% 15N]14
440 uMpseudo receiver domain of CikAunlabeled14
800 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]15
880 uMKaiB mutant-N29Aunlabeled15
800 uMKaiB mutant-N29A[U-99% 13C; U-99% 15N]16
880 uMpseudo receiver domain of CikAunlabeled16
Sample conditionsIonic strength: 0.1 mM / Label: ph7 / pH: 7 / Pressure: 1 atm / Temperature: 50 C

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
PIPPGarrettpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XippGarrett DS, Powers R, Gronenborn AM, Clore GM. J Magn Reson. 2011 Dec;213(2):357-63. doi: 10.1016/j.jmr.2011.09.007. A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams http://spin.niddk.nih.gov/dgarrett/Xipp/xipp.htmlpeak picking
MARSMars - robust automatic backbone assignment of proteins Journal of Biomolecular NMR, 2004, Volume 30, Number 1, Page 11 Young-Sang Jung, Markus Zweckstetterchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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