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- PDB-6jpp: Solution structure of ELMO1 RBD -

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Basic information

Entry
Database: PDB / ID: 6jpp
TitleSolution structure of ELMO1 RBD
ComponentsEngulfment and cell motility protein 1
KeywordsSIGNALING PROTEIN / ELMO / RAS BINDING DOMAIN / RBD / UBIQUITIN FOLD / RHOG / PROTEIN BINDING
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / Nef and signal transduction / phagocytosis, engulfment / Rac protein signal transduction / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cell motility / actin filament organization / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway ...guanyl-nucleotide exchange factor complex / Nef and signal transduction / phagocytosis, engulfment / Rac protein signal transduction / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cell motility / actin filament organization / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / SH3 domain binding / actin cytoskeleton organization / apoptotic process / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / Pleckstrin homology domain / Pleckstrin homology domain / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Engulfment and cell motility protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTsuda, K. / Kukimoto-Niino, M. / Shirouzu, M.
CitationJournal: Commun Biol / Year: 2023
Title: Targeting Ras-binding domain of ELMO1 by computational nanobody design.
Authors: Tam, C. / Kukimoto-Niino, M. / Miyata-Yabuki, Y. / Tsuda, K. / Mishima-Tsumagari, C. / Ihara, K. / Inoue, M. / Yonemochi, M. / Hanada, K. / Matsumoto, T. / Shirouzu, M. / Zhang, K.Y.J.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engulfment and cell motility protein 1


Theoretical massNumber of molelcules
Total (without water)12,7651
Polymers12,7651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9740 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Engulfment and cell motility protein 1 / Protein ced-12 homolog


Mass: 12765.462 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELMO1, KIAA0281 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92556

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-13C NOESY
121isotropic23D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] Elmo1 RBD, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Elmo1 RBD / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7.0 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz / Details: cryoprobe

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificdata analysis
KUJIRAKobayashi, Ndata analysis
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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