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- PDB-7y4a: Crystal structure of human ELMO1 RBD-RhoG complex -

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Basic information

Entry
Database: PDB / ID: 7y4a
TitleCrystal structure of human ELMO1 RBD-RhoG complex
Components
  • Engulfment and cell motility protein 1ELMO1
  • Rho-related GTP-binding protein RhoG
KeywordsSIGNALING PROTEIN / Ras binding domain / GTPase / effector
Function / homology
Function and homology information


: / regulation of ruffle assembly / neutrophil degranulation / regulation of neutrophil migration / engulfment of apoptotic cell / guanyl-nucleotide exchange factor complex / cortical cytoskeleton organization / cell projection assembly / Nef and signal transduction / activation of GTPase activity ...: / regulation of ruffle assembly / neutrophil degranulation / regulation of neutrophil migration / engulfment of apoptotic cell / guanyl-nucleotide exchange factor complex / cortical cytoskeleton organization / cell projection assembly / Nef and signal transduction / activation of GTPase activity / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of small GTPase mediated signal transduction / establishment or maintenance of cell polarity / phagocytosis, engulfment / Rac protein signal transduction / Rho protein signal transduction / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / GPVI-mediated activation cascade / cell chemotaxis / secretory granule membrane / cell projection / actin filament organization / cell motility / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / VEGFA-VEGFR2 Pathway / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / cell cortex / regulation of cell shape / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / actin cytoskeleton organization / vesicle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / GTP binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho-related GTP-binding protein RhoG / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / Pleckstrin homology domain / Small GTPase Rho / small GTPase Rho family profile. / Pleckstrin homology domain ...Rho-related GTP-binding protein RhoG / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / Pleckstrin homology domain / Small GTPase Rho / small GTPase Rho family profile. / Pleckstrin homology domain / Small GTPase / Ras family / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Rho-related GTP-binding protein RhoG / Engulfment and cell motility protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTsuda, K. / Kukimoto-Niino, M. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
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
DepositionJun 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho-related GTP-binding protein RhoG
B: Engulfment and cell motility protein 1
C: Rho-related GTP-binding protein RhoG
D: Engulfment and cell motility protein 1
E: Rho-related GTP-binding protein RhoG
F: Engulfment and cell motility protein 1
G: Rho-related GTP-binding protein RhoG
H: Engulfment and cell motility protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,28520
Polymers122,0358
Non-polymers2,25012
Water24,2481346
1
A: Rho-related GTP-binding protein RhoG
B: Engulfment and cell motility protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0715
Polymers30,5092
Non-polymers5623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-38 kcal/mol
Surface area13840 Å2
MethodPISA
2
C: Rho-related GTP-binding protein RhoG
D: Engulfment and cell motility protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0715
Polymers30,5092
Non-polymers5623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-39 kcal/mol
Surface area13780 Å2
MethodPISA
3
E: Rho-related GTP-binding protein RhoG
F: Engulfment and cell motility protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0715
Polymers30,5092
Non-polymers5623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-38 kcal/mol
Surface area13710 Å2
MethodPISA
4
G: Rho-related GTP-binding protein RhoG
H: Engulfment and cell motility protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0715
Polymers30,5092
Non-polymers5623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-39 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.720, 63.750, 115.330
Angle α, β, γ (deg.)90.000, 100.500, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Rho-related GTP-binding protein RhoG


Mass: 21214.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOG, ARHG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P84095
#2: Protein
Engulfment and cell motility protein 1 / ELMO1 / Protein ced-12 homolog


Mass: 9294.622 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELMO1 / Cell (production host): CELL-FREE PROTEIN SYNTHESIS / Production host: Escherichia coli (E. coli) / References: UniProt: Q92556

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Non-polymers , 4 types, 1358 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1346 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.91 M potassium phosphate dibasic and 0.49 M sodium phosphate monobasic monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→42.37 Å / Num. obs: 139984 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.048 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.69 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 22384 / CC1/2: 0.788 / Rrim(I) all: 0.541

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JPP, 4G0N

6jpp

4g0n


Resolution: 1.6→42.37 Å / SU ML: 0.2111 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 25.4268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 3914 1.43 %
Rwork0.1975 269206 -
obs0.198 139937 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8264 0 136 1346 9746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00688600
X-RAY DIFFRACTIONf_angle_d0.971111748
X-RAY DIFFRACTIONf_chiral_restr0.05741316
X-RAY DIFFRACTIONf_plane_restr0.00621504
X-RAY DIFFRACTIONf_dihedral_angle_d23.60443192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.34541320.28489059X-RAY DIFFRACTION92.67
1.62-1.640.30811420.27869678X-RAY DIFFRACTION98.17
1.64-1.660.26421400.27559679X-RAY DIFFRACTION99.3
1.66-1.680.32981380.28029640X-RAY DIFFRACTION98.34
1.68-1.70.30361430.28099704X-RAY DIFFRACTION99.41
1.7-1.730.38281410.26749681X-RAY DIFFRACTION98.71
1.73-1.760.29681460.25649799X-RAY DIFFRACTION99.48
1.76-1.790.27181410.24949749X-RAY DIFFRACTION98.99
1.79-1.820.29331400.23869723X-RAY DIFFRACTION99.39
1.82-1.850.26711400.23779689X-RAY DIFFRACTION99.37
1.85-1.880.2471400.23939707X-RAY DIFFRACTION99.08
1.88-1.920.46021360.33299412X-RAY DIFFRACTION95.86
1.92-1.970.27981380.26289431X-RAY DIFFRACTION96.62
1.97-2.010.23321390.2269732X-RAY DIFFRACTION99.03
2.01-2.060.26681440.20669741X-RAY DIFFRACTION99.14
2.06-2.120.23661410.20719671X-RAY DIFFRACTION99.29
2.12-2.180.26091440.21339710X-RAY DIFFRACTION99.08
2.18-2.250.29781330.25829300X-RAY DIFFRACTION95.5
2.25-2.330.29091400.23459379X-RAY DIFFRACTION95.24
2.33-2.420.21161390.20199668X-RAY DIFFRACTION99.02
2.42-2.530.20091410.19489702X-RAY DIFFRACTION99.06
2.53-2.670.22991420.18789752X-RAY DIFFRACTION98.98
2.67-2.830.24331420.19419643X-RAY DIFFRACTION99
2.83-3.050.231390.18949738X-RAY DIFFRACTION98.96
3.05-3.360.22431390.17019685X-RAY DIFFRACTION98.8
3.36-3.850.17091390.15869536X-RAY DIFFRACTION97.81
3.85-4.840.18711410.14319693X-RAY DIFFRACTION98.75
4.84-42.370.20881340.1719305X-RAY DIFFRACTION94.89

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