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- PDB-6idx: Crystal Structure of BAI1/ELMO2 complex -

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Basic information

Entry
Database: PDB / ID: 6idx
TitleCrystal Structure of BAI1/ELMO2 complex
Components
  • Adhesion G protein-coupled receptor B1
  • Engulfment and cell motility protein 2
KeywordsCELL ADHESION / Adhesion GPCRs
Function / homology
Function and homology information


postsynaptic actin cytoskeleton organization / engulfment of apoptotic cell / phagocytosis, recognition / positive regulation of synapse assembly / negative regulation of endothelial cell migration / muscle organ development / positive regulation of reactive oxygen species biosynthetic process / phagocytosis, engulfment / positive regulation of myoblast fusion / phosphatidylserine binding ...postsynaptic actin cytoskeleton organization / engulfment of apoptotic cell / phagocytosis, recognition / positive regulation of synapse assembly / negative regulation of endothelial cell migration / muscle organ development / positive regulation of reactive oxygen species biosynthetic process / phagocytosis, engulfment / positive regulation of myoblast fusion / phosphatidylserine binding / phagocytic cup / RHOG GTPase cycle / phagocytosis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of protein ubiquitination / negative regulation of angiogenesis / cell chemotaxis / PDZ domain binding / G protein-coupled receptor activity / cell motility / lipopolysaccharide binding / actin filament organization / FCGR3A-mediated phagocytosis / regulation of synaptic plasticity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of protein catabolic process / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / cell-cell adhesion / SH3 domain binding / transmembrane signaling receptor activity / nervous system development / postsynaptic membrane / defense response to Gram-negative bacterium / dendritic spine / postsynaptic density / cell surface receptor signaling pathway / innate immune response / focal adhesion / glutamatergic synapse / apoptotic process / dendrite / perinuclear region of cytoplasm / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
Engulfment and cell motility protein 2 / Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / GPCR, family 2, brain-specific angiogenesis inhibitor / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / GAIN domain, N-terminal ...Engulfment and cell motility protein 2 / Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / GPCR, family 2, brain-specific angiogenesis inhibitor / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / Pleckstrin homology domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Pleckstrin homology domain / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Adhesion G protein-coupled receptor B1 / Engulfment and cell motility protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsWeng, Z.F. / Lin, L. / Zhu, J.W. / Zhang, R.G.
CitationJournal: Nat Commun / Year: 2019
Title: Structure of BAI1/ELMO2 complex reveals an action mechanism of adhesion GPCRs via ELMO family scaffolds
Authors: Weng, Z. / Situ, C. / Lin, L. / Wu, Z. / Zhu, J. / Zhang, R.
History
DepositionSep 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engulfment and cell motility protein 2
C: Adhesion G protein-coupled receptor B1


Theoretical massNumber of molelcules
Total (without water)63,0642
Polymers63,0642
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-9 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.869, 92.869, 130.762
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-699-

HOH

21A-729-

HOH

31A-905-

HOH

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Components

#1: Protein Engulfment and cell motility protein 2


Mass: 59803.590 Da / Num. of mol.: 1 / Fragment: UNP residues 5-515
Source method: isolated from a genetically manipulated source
Details: there are ten residues missing due to poor electronl density
Source: (gene. exp.) Homo sapiens (human) / Gene: ELMO2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96JJ3
#2: Protein/peptide Adhesion G protein-coupled receptor B1 / Brain-specific angiogenesis inhibitor 1


Mass: 3260.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q3UHD1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.3M Ammonium Fluoride, 18% PEG3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.699→46.435 Å / Num. obs: 72368 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 23.03 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 28.4
Reflection shellResolution: 1.699→1.73 Å / Redundancy: 10 % / Rmerge(I) obs: 0.64 / Num. unique obs: 3592 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IE1

6ie1


Resolution: 1.699→46.435 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.2064 3640 5.03 %
Rwork0.1792 --
obs0.1806 72313 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.21 Å2 / Biso mean: 27.63 Å2 / Biso min: 12.4 Å2
Refinement stepCycle: final / Resolution: 1.699→46.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 0 378 4561
Biso mean---35.03 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094250
X-RAY DIFFRACTIONf_angle_d1.1575749
X-RAY DIFFRACTIONf_chiral_restr0.049662
X-RAY DIFFRACTIONf_plane_restr0.005740
X-RAY DIFFRACTIONf_dihedral_angle_d13.0111592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6991-1.72150.25951430.24422587273099
1.7215-1.74510.24951270.238826502777100
1.7451-1.770.27071320.222325762708100
1.77-1.79640.22091280.220826272755100
1.7964-1.82450.25551500.205326122762100
1.8245-1.85440.22791250.193626142739100
1.8544-1.88640.22611360.199826152751100
1.8864-1.92070.22141330.190326412774100
1.9207-1.95760.2381750.198125662741100
1.9576-1.99760.22111700.190525842754100
1.9976-2.0410.22081310.183226242755100
2.041-2.08850.21371480.191326252773100
2.0885-2.14070.19571370.184226342771100
2.1407-2.19860.23571280.178626222750100
2.1986-2.26330.19571390.183526602799100
2.2633-2.33640.19921310.175626112742100
2.3364-2.41990.22361290.178326412770100
2.4199-2.51670.20371510.187526552806100
2.5167-2.63130.22851540.181326252779100
2.6313-2.770.21811400.190426452785100
2.77-2.94350.21521540.191126232777100
2.9435-3.17070.20371260.190426782804100
3.1707-3.48970.19641470.182126852832100
3.4897-3.99440.17671310.1627052836100
3.9944-5.03160.18191290.15127342863100
5.0316-46.45180.19571460.164728342980100
Refinement TLS params.Method: refined / Origin x: -53.5964 Å / Origin y: 16.1176 Å / Origin z: 3.3737 Å
111213212223313233
T0.15 Å20.0167 Å2-0.0201 Å2-0.1747 Å2-0.0134 Å2--0.147 Å2
L0.4653 °20.436 °2-0.5342 °2-0.9312 °2-0.8486 °2--0.9712 °2
S-0.0498 Å °0.0626 Å °0.0057 Å °-0.0976 Å °0.0356 Å °0.0137 Å °0.1014 Å °-0.0805 Å °0.0217 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 515
2X-RAY DIFFRACTION1allC1471 - 1495
3X-RAY DIFFRACTION1allS1 - 479

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