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- PDB-2vsz: Crystal Structure of the ELMO1 PH domain -

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Basic information

Entry
Database: PDB / ID: 2vsz
TitleCrystal Structure of the ELMO1 PH domain
ComponentsENGULFMENT AND CELL MOTILITY PROTEIN 1
KeywordsAPOPTOSIS / RAC SIGNALLING / SH3-BINDING / PHAGOCYTOSIS / ELMO / DOCK180 / PHOSPHOINOSITIDE BINDING / GUANINE NUCLEOTIDE EXCHANGE FACTOR
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #810 / 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 (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #810 / 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 (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Pleckstrin homology domain / Helix non-globular / Special / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Engulfment and cell motility protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKomander, D. / Patel, M. / Barford, D. / Cote, J.-F.
CitationJournal: Molecular Biology of the Cell / Year: 2008
Title: An Alpha-Helical Extension of the Elmo1 Pleckstrin Homology Domain Mediates Direct Interaction to Dock180 and is Critical in Rac Signaling.
Authors: Komander, D. / Patel, M. / Laurin, M. / Fradet, N. / Pelletier, A. / Barford, D. / Cote, J.-F.
History
DepositionMay 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENGULFMENT AND CELL MOTILITY PROTEIN 1
B: ENGULFMENT AND CELL MOTILITY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)34,2062
Polymers34,2062
Non-polymers00
Water2,864159
1
A: ENGULFMENT AND CELL MOTILITY PROTEIN 1
B: ENGULFMENT AND CELL MOTILITY PROTEIN 1

A: ENGULFMENT AND CELL MOTILITY PROTEIN 1
B: ENGULFMENT AND CELL MOTILITY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)68,4114
Polymers68,4114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area8260 Å2
ΔGint-62.7 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.016, 166.016, 81.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ENGULFMENT AND CELL MOTILITY PROTEIN 1 / CED-12 HOMOLOG / ELMO1


Mass: 17102.750 Da / Num. of mol.: 2 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 532-675
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92556
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 4.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 6.75 / Details: 2.1 M SODIUM MALONATE [PH 6.75]

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 29960 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 8.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
SHELXCDEphasing
SHARPphasing
REFMAC5.4.0066refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→144.34 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.478 / SU ML: 0.11 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES LACKING SIDE CHAIN DENSITY HAVE BEEN REFINED AS ALA OR WITH OCCU 0.01
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1505 5 %RANDOM
Rwork0.208 ---
obs0.209 28425 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.45 Å2-0 Å2
2--0.91 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→144.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 0 159 2443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222424
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9833294
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37924.643112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30415450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1821515
X-RAY DIFFRACTIONr_chiral_restr0.1240.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211839
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1381.51488
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06922405
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0643936
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8764.5881
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 91
Rwork0.23 2077
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8873-1.5509-1.24751.13230.47280.7135-0.2359-0.1013-0.21940.15580.13450.13430.19220.02080.1014-0.15170.1112-0.0017-0.02830.00190.00224.16472.8234.539
21.5901-1.9315-0.35772.5160.03891.0022-0.09260.1579-0.34890.0443-0.12730.29240.3262-0.19550.2198-0.07420.0920.0481-0.1073-0.0470.080457.6947.757-13.581
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A527 - 673
2X-RAY DIFFRACTION2B529 - 675

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