[English] 日本語
Yorodumi
- PDB-6nu4: Solution structure of the Arabidopsis thaliana RALF8 peptide -

+
Open data


ID or keywords:

Loading...

-
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) / apoplast / calcium-mediated signaling / hormone activity / cell-cell signaling / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein RALF-like 8


Theoretical massNumber of molelcules
Total (without water)6,2481
Polymers6,2481
Non-polymers00
Water0
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more