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- PDB-6nu4: Solution structure of the Arabidopsis thaliana RALF8 peptide -

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Basic information

Entry
Database: PDB / ID: 6nu4
TitleSolution structure of the Arabidopsis thaliana RALF8 peptide
ComponentsProtein RALF-like 8
KeywordsPLANT PROTEIN / Rapid alkalinization factor-8 / cysteine-rich plant peptide / plant growth / pollen tube generation
Function / homologyRapid ALkalinization Factor / Rapid ALkalinization Factor (RALF) / regulation of root meristem growth / apoplast / calcium-mediated signaling / hormone activity / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / Protein RALF-like 8
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / molecular dynamics
AuthorsLee, W. / Markley, J.L. / Frederick, R.O. / Miyoshi, H. / Tonelli, M. / Cornilescu, G. / Cornilescu, C. / Sussman, M.R.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA073808 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 RR02301 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM66326 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RR02781 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RR08438 United States
National Science Foundation (NSF, United States)DMB-8415048 United States
National Science Foundation (NSF, United States)OIA-9977486 United States
National Science Foundation (NSF, United States)BIR-9214394 United States
CitationJournal: Protein Sci. / Year: 2019
Title: Function and solution structure of the Arabidopsis thaliana RALF8 peptide.
Authors: Frederick, R.O. / Haruta, M. / Tonelli, M. / Lee, W. / Cornilescu, G. / Cornilescu, C.C. / Sussman, M.R. / Markley, J.L.
History
DepositionJan 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / 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
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein RALF-like 8


Theoretical massNumber of molelcules
Total (without water)6,2481
Polymers6,2481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6840 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 Protein RALF-like 8


Mass: 6248.083 Da / Num. of mol.: 1 / Fragment: residues 27-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RALFL8, At1g61563, T25B24 / Plasmid: pE-SUMO(Kan) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1ECR9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D HN(CA)CB
131isotropic23D CBCA(CO)NH
141isotropic23D HN(CA)CO
151isotropic23D HNCO
1111isotropic22D 1H-13C HSQC
1101isotropic23D C(CO)NH
191isotropic23D HBHA(CO)NH
181isotropic23D (H)CCH-TOCSY
171isotropic13D 1H-15N NOESY
161isotropic23D 1H-13C NOESY aliphatic

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-13C; U-15N] Rapid ALkalinization Factor-8 (RALF8), 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: Rapid ALkalinization Factor-8 (RALF8) / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 200 mM / Label: conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Varian VNMRSVarianVNMRS8002

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SMILEJ. Ying, F. Delaglio, D.A. Torchia, and A. Baxprocessing
NMRFAM-SPARKYW. Lee, M. Tonelli, J.L. Markleypeak picking
NMRFAM-SPARKYW. Lee, M. Tonelli, J.L. Markleychemical shift assignment
I-PINEW. Lee, A. Bahrami, H. Dashti, H.R. Eghbalnia, M. Tonelli, W.M. Westler, J.L. Markleychemical shift assignment
TALOS-NY. Shen, A. Baxstructure calculation
PECANEghbalnia, Wang, Bahrami, Assadi, and Markleystructure calculation
PONDEROSA-C/SW. Lee, J.L. Stark, J.L. Markleystructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AUDANAW. Lee, C.M. Petit, G. Cornilescu, J.L. Stark, J.L. Markleystructure calculation
PONDEROSA-C/SW. Lee, J.L. Stark, J.L. Markleyrefinement
RefinementMethod: molecular dynamics / Software ordinal: 11 / Details: torsion angle dynamics, simulated annealing
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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