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- PDB-6ie1: Crystal Structure of ELMO2(Engulfment and cell motility protein 2) -

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Basic information

Entry
Database: PDB / ID: 6ie1
TitleCrystal Structure of ELMO2(Engulfment and cell motility protein 2)
ComponentsEngulfment and cell motility protein 2ELMO2
KeywordsCELL ADHESION / Adhesion GPCR / BAI1-ELMO2 Complex / scaffold protein
Function / homology
Function and homology information


RHOG GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytosis / cell chemotaxis / cell motility / actin filament organization / FCGR3A-mediated phagocytosis / cell-cell adhesion / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding ...RHOG GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytosis / cell chemotaxis / cell motility / actin filament organization / FCGR3A-mediated phagocytosis / cell-cell adhesion / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / VEGFA-VEGFR2 Pathway / receptor tyrosine kinase binding / apoptotic process / membrane / cytosol
Similarity search - Function
Engulfment and cell motility protein 2 / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.48 Å
AuthorsWeng, Z.F. / Lin, L. / Zhang, R.G. / Zhu, J.W.
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 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9883
Polymers59,8041
Non-polymers1842
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.182, 119.134, 169.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Engulfment and cell motility protein 2 / ELMO2


Mass: 59803.590 Da / Num. of mol.: 1 / Fragment: UNP residues 6-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELMO2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96JJ3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium malonate pH 4.0, 12%PEG3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 27341 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 55.96 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Χ2: 0.469 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.48-2.5212.40.9213660.8980.2690.960.43799.8
2.52-2.5712.90.72113230.9390.2070.7510.429100
2.57-2.6212.70.68513720.9360.1970.7130.427100
2.62-2.6712.70.5613190.9640.1620.5840.43899.9
2.67-2.7312.70.50313590.970.1450.5240.43599.9
2.73-2.7912.80.39913390.9760.1150.4160.44799.9
2.79-2.8612.60.34313660.9850.10.3580.43999.9
2.86-2.9412.70.30613620.9840.0890.3190.4599.9
2.94-3.0312.70.23513400.9920.0680.2450.45100
3.03-3.1212.40.17613460.9940.0520.1840.465100
3.12-3.2412.10.14813600.9960.0440.1540.485100
3.24-3.3711.20.11413670.9980.0360.120.498100
3.37-3.5212.30.0913680.9980.0270.0940.51999.6
3.52-3.711.80.0713600.9980.0210.0730.529100
3.7-3.9413.40.0613600.9990.0170.0620.54599.9
3.94-4.2413.40.0513770.9990.0140.0520.55100
4.24-4.6713.60.04413740.9990.0120.0450.543100
4.67-5.3413.10.0413890.9990.0110.0420.475100
5.34-6.7312.10.04114080.9990.0120.0430.416100
6.73-5012.90.0314860.9990.0090.0320.39299.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.48→42.331 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.55
RfactorNum. reflection% reflection
Rfree0.2397 1372 5.03 %
Rwork0.2057 --
obs0.2074 27297 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.37 Å2 / Biso mean: 71.12 Å2 / Biso min: 40.83 Å2
Refinement stepCycle: final / Resolution: 2.48→42.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 0 12 26 3996
Biso mean--94.52 59.14 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044040
X-RAY DIFFRACTIONf_angle_d0.7335477
X-RAY DIFFRACTIONf_chiral_restr0.028638
X-RAY DIFFRACTIONf_plane_restr0.003704
X-RAY DIFFRACTIONf_dihedral_angle_d12.3111494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4796-2.56820.30471380.28972497263597
2.5682-2.6710.30031290.281825592688100
2.671-2.79250.33281340.293725792713100
2.7925-2.93970.3741270.282125922719100
2.9397-3.12380.32321480.275925522700100
3.1238-3.36490.29911280.264725942722100
3.3649-3.70340.25361360.230125952731100
3.7034-4.23890.22541590.188325842743100
4.2389-5.33880.18661500.164326132763100
5.3388-42.33760.18451230.152527602883100
Refinement TLS params.Method: refined / Origin x: 55.9743 Å / Origin y: 56.6634 Å / Origin z: 72.9737 Å
111213212223313233
T0.3896 Å2-0.0247 Å2-0.0422 Å2-0.5725 Å2-0.0633 Å2--0.4466 Å2
L0.8853 °20.7685 °2-0.8905 °2-0.9448 °2-0.6009 °2--0.8236 °2
S0.0137 Å °0.0566 Å °0.0594 Å °0.01 Å °0.0545 Å °0.0761 Å °-0.101 Å °0.0131 Å °-0.0499 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 513
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allS1 - 33

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