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- PDB-8vsx: NMR Structure of GCAP5 R22A -

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Basic information

Entry
Database: PDB / ID: 8vsx
TitleNMR Structure of GCAP5 R22A
ComponentsGuanylyl cyclase-activating protein 1
KeywordsMETAL BINDING PROTEIN / EF-hand / GCAP5 / Phototransduction / Retinal guanylyl cyclase
Function / homology
Function and homology information


guanylate cyclase activator activity / calcium sensitive guanylate cyclase activator activity / response to stimulus / photoreceptor outer segment / visual perception / ferrous iron binding / calcium ion binding / identical protein binding
Similarity search - Function
Guanylyl cyclase-activating protein 1 / Recoverin family / EF-hand domain pair / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Guanylate cyclase activator 1A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsCudia, D.L. / Ames, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY012347 United States
CitationJournal: Biochemistry / Year: 2024
Title: NMR Structure of Retinal Guanylate Cyclase Activating Protein 5 (GCAP5) with R22A Mutation That Abolishes Dimerization and Enhances Cyclase Activation.
Authors: Cudia, D.L. / Ahoulou, E.O. / Bej, A. / Janssen, A.N. / Scholten, A. / Koch, K.W. / Ames, J.B.
History
DepositionJan 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanylyl cyclase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)22,4031
Polymers22,4031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area620 Å2
ΔGint2 kcal/mol
Surface area10580 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Guanylyl cyclase-activating protein 1 / Guanylate cyclase activator 1A


Mass: 22403.266 Da / Num. of mol.: 1 / Mutation: R22A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: GUCA1E, guca1e / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MAC8
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-15N HSQC
122isotropic13D HNCO
132isotropic13D HN(CA)CB
192isotropic13D HNCACBi
142isotropic13D HNCA
152isotropic13D CBCA(CO)NH
182isotropic13D HN(COCA)CB
172isotropic13D HBHA(CO)NH
162isotropic13D HBHANH
1102isotropic12D (HB)CB(CGCD)HD
1142isotropic12D (HB)CB(CGCDCE)HE
1132isotropic22D 1H-13C HSQC aliphatic
1122isotropic23D (H)CCH-TOCSY
1112isotropic13D C(CO)NH
1152isotropic23D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution30.75 mM [U-100% 15N] Guanylyl Cyclase Activating Protein-5 (GCAP5) with R22A Mutation, 5 mM [U-99% 2H] TRIS-d11, 2 mM [U-99% 2H] DTT-d10, 93% H2O/7% D2O15N_sample93% H2O/7% D2O
solution20.75 mM [U-100% 13C; U-100% 15N] Guanylyl Cyclase Activating Protein-5 (GCAP5) with R22A Mutation, 5 mM [U-99% 2H] TRIS-d11, 2 mM [U-99% 2H] DTT-d10, 93% H2O/7% D2O13C/15N_sample93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMGuanylyl Cyclase Activating Protein-5 (GCAP5) with R22A Mutation[U-100% 15N]3
5 mMTRIS-d11[U-99% 2H]3
2 mMDTT-d10[U-99% 2H]3
0.75 mMGuanylyl Cyclase Activating Protein-5 (GCAP5) with R22A Mutation[U-100% 13C; U-100% 15N]2
5 mMTRIS-d11[U-99% 2H]2
2 mMDTT-d10[U-99% 2H]2
Sample conditionsIonic strength: 5 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / Conformers submitted total number: 10

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