[English] 日本語
Yorodumi
- PDB-8pi0: NMR2 Structure of KRAS G12V (GMPPNP bound) in complex with 5-(1H-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pi0
TitleNMR2 Structure of KRAS G12V (GMPPNP bound) in complex with 5-(1H-indol-2-l)piperazin-2-one
ComponentsV-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b
KeywordsONCOPROTEIN / Complex / Fragment
Function / homology
Function and homology information


endocrine signaling / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of glial cell proliferation ...endocrine signaling / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of glial cell proliferation / glial cell proliferation / protein-membrane adaptor activity / striated muscle cell differentiation / homeostasis of number of cells within a tissue / regulation of long-term neuronal synaptic plasticity / visual learning / actin cytoskeleton organization / neuron apoptotic process / negative regulation of neuron apoptotic process / GTPase activity / positive regulation of gene expression / GTP binding / membrane
Similarity search - Function
Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBuetikofer, M. / Orts, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss Cancer LeagueKFS-4903-08-2019 Switzerland
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: NMR2-Based Drug Discovery Pipeline Presented on the Oncogenic Protein KRAS.
Authors: Butikofer, M. / Torres, F. / Kadavath, H. / Gamperli, N. / Abi Saad, M.J. / Zindel, D. / Coudevylle, N. / Riek, R. / Orts, J.
History
DepositionJun 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3842
Polymers19,1691
Non-polymers2151
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b


Mass: 19168.592 Da / Num. of mol.: 1 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, hCG_14731 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A024RAV5
#2: Chemical ChemComp-YVW / (5~{S})-5-(1~{H}-indol-2-yl)piperazin-2-one


Mass: 215.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13N3O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
151isotropic12D 1H-13C HSQC

-
Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-13C; U-15N] KRAS, 5.0 mM 5-(1H-indol-2-yl)piperazin-2-one, 100% D2O
Label: 13C_sample, 15N_sample / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMKRAS[U-13C; U-15N]1
5.0 mM5-(1H-indol-2-yl)piperazin-2-onenatural abundance1
Sample conditionsIonic strength: 125 mM / Label: conditions_1 / pH: 7.4 pD / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
HADDOCKBonvinrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4 / Conformers submitted total number: 4

+
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