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- PDB-1x86: Crystal Structure of the DH/PH domains of Leukemia-associated Rho... -

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Basic information

Entry
Database: PDB / ID: 1x86
TitleCrystal Structure of the DH/PH domains of Leukemia-associated RhoGEF in complex with RhoA
Components
  • Rho guanine nucleotide exchange factor 12
  • Transforming protein RhoA
Keywordssignaling protein/membrane protein / helical bundle (DH) / beta sandwich (PH) / alpha/beta (RhoA) / signaling protein-membrane protein COMPLEX
Function / homology
Function and homology information


aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity ...aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / negative regulation of cell size / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / regulation of small GTPase mediated signal transduction / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / motor neuron apoptotic process / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / regulation of neuron projection development / regulation of focal adhesion assembly / negative chemotaxis / RHOB GTPase cycle / myosin binding / EPHA-mediated growth cone collapse / NRAGE signals death through JNK / stress fiber assembly / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cerebral cortex cell migration / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / skeletal muscle tissue development / RHO GTPases activate PKNs / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / GTPase activator activity / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / G protein activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / G protein-coupled receptor binding / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / neuron migration / positive regulation of protein serine/threonine kinase activity
Similarity search - Function
ARHGEF12, PH domain / LARG, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. ...ARHGEF12, PH domain / LARG, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / RGS, subdomain 2 / RGS domain superfamily / Small GTPase Rho / small GTPase Rho family profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rab subfamily of small GTPases / PDZ superfamily / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Transforming protein RhoA / Rho guanine nucleotide exchange factor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsKristelly, R. / Gao, G. / Tesmer, J.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural determinants of RhoA binding and nucleotide exchange in leukemia-associated Rho guanine-nucleotide exchange factor.
Authors: Kristelly, R. / Gao, G. / Tesmer, J.J.
History
DepositionAug 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE IN THE GB (ACCESSION CODE BAA20836), IT CLEARLY SHOWS THAT 973 IS A PHE, NOT TYR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 12
B: Transforming protein RhoA
C: Rho guanine nucleotide exchange factor 12
D: Transforming protein RhoA
E: Rho guanine nucleotide exchange factor 12
F: Transforming protein RhoA
G: Rho guanine nucleotide exchange factor 12
H: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,68712
Polymers267,3078
Non-polymers3804
Water00
1
A: Rho guanine nucleotide exchange factor 12
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9223
Polymers66,8272
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-12 kcal/mol
Surface area26430 Å2
MethodPISA
2
C: Rho guanine nucleotide exchange factor 12
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9223
Polymers66,8272
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-16 kcal/mol
Surface area27100 Å2
MethodPISA
3
E: Rho guanine nucleotide exchange factor 12
F: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9223
Polymers66,8272
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-13 kcal/mol
Surface area26080 Å2
MethodPISA
4
G: Rho guanine nucleotide exchange factor 12
H: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9223
Polymers66,8272
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-20 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)296.418, 95.239, 157.338
Angle α, β, γ (deg.)90.00, 94.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Rho guanine nucleotide exchange factor 12 / Leukemia-associated RhoGEF


Mass: 44694.293 Da / Num. of mol.: 4 / Fragment: DH/PH domains / Mutation: Tyr973Phe
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF12, LARG, KIAA0382 / Plasmid: pMALc2x / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) PLYSS / References: UniProt: Q9NZN5
#2: Protein
Transforming protein RhoA / H12


Mass: 22132.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARHA, ARH12, RHO12 / Plasmid: pMALc2x / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: P61586
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4

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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: 4.3 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG8K, sodium phosphate, sodium chloride, EDTA, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.069 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2003 / Details: mirror
RadiationMonochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.069 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 64268 / Num. obs: 60392 / Observed criterion σ(I): -1
Reflection shellResolution: 3.2→3.3 Å / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.22→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 56.153 / SU ML: 0.402 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27943 3210 5 %RANDOM
Rwork0.22697 ---
obs0.22958 60391 90.39 %-
all-64268 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.885 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å20 Å22.55 Å2
2--4.3 Å20 Å2
3----11.8 Å2
Refinement stepCycle: LAST / Resolution: 3.22→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16961 0 20 0 16981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02217258
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216070
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.97523293
X-RAY DIFFRACTIONr_angle_other_deg0.871337495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64452074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54624.495832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.615153320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91815140
X-RAY DIFFRACTIONr_chiral_restr0.0810.22645
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218713
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023295
X-RAY DIFFRACTIONr_nbd_refined0.2450.24749
X-RAY DIFFRACTIONr_nbd_other0.190.218458
X-RAY DIFFRACTIONr_nbtor_refined0.1920.28363
X-RAY DIFFRACTIONr_nbtor_other0.0890.211147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2531
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0420.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.17213502
X-RAY DIFFRACTIONr_mcbond_other0.12224177
X-RAY DIFFRACTIONr_mcangle_it1.634417015
X-RAY DIFFRACTIONr_scbond_it1.79747740
X-RAY DIFFRACTIONr_scangle_it2.72366278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.221→3.301 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 191 -
Rwork0.405 3247 -
obs--69.12 %
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)
11.0788-0.18590.19722.8729-0.26812.9006-0.0007-0.0718-0.10090.30820.12160.13120.1169-0.0417-0.12090.11130.0319-0.1150.1876-0.02840.771366.563-2.78780.514
22.8282-0.639-0.13063.38890.69544.6953-0.0837-0.02250.00690.290.11890.2784-0.00750.4181-0.03520.2793-0.0473-0.06520.89650.05920.793888.546-4.05310.184
31.99980.28050.3923.7265-1.056410.0032-0.00140.368-0.3079-0.32160.32040.44272.1481-2.1035-0.3190.3267-0.3044-0.23661.10440.09361.003742.9353.85833.063
43.5390.8055-0.46143.0933-0.0810.0859-0.5669-0.6167-0.4931-0.33160.1786-0.3181.78462.30210.38840.48420.541-0.10171.79890.0181.1168110.014-14.06255.942
57.3874-2.51122.73058.5193-1.03758.4431-0.5302-1.0180.09031.3830.8388-0.48720.022-0.2066-0.30861.05850.3133-0.13810.6294-0.07830.721465.3516.347112.696
65.78111.78662.80765.35080.119312.080.3990.2097-0.136-0.9068-0.0479-0.4218-0.25661.3951-0.35110.71890.0192-0.00011.57020.1871.091799.039.481-22.626
710.9733-2.40550.845710.9417-1.95419.00470.68590.1230.38250.7927-0.9831.51340.0446-1.02590.29710.40830.65630.18612.26320.16151.895116.32129.68632.849
820.5563-1.59162.8088.9496.331430.58090.0525-0.3905-0.64420.1807-0.2692-1.49490.85350.5970.21660.36010.25290.03251.62870.1661.7948143.673-10.20456.924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA766 - 9863 - 223
2X-RAY DIFFRACTION1BB2 - 1815 - 184
3X-RAY DIFFRACTION1BI401
4X-RAY DIFFRACTION2CC766 - 9863 - 223
5X-RAY DIFFRACTION2DD2 - 1815 - 184
6X-RAY DIFFRACTION2DJ402
7X-RAY DIFFRACTION3EE766 - 9863 - 223
8X-RAY DIFFRACTION3FF3 - 1816 - 184
9X-RAY DIFFRACTION3FK403
10X-RAY DIFFRACTION4GG766 - 9863 - 223
11X-RAY DIFFRACTION4HH3 - 1816 - 184
12X-RAY DIFFRACTION4HL404
13X-RAY DIFFRACTION5AA987 - 1063224 - 300
14X-RAY DIFFRACTION5AA1075 - 1138312 - 375
15X-RAY DIFFRACTION6CC987 - 1063224 - 300
16X-RAY DIFFRACTION6CC1075 - 1138312 - 375
17X-RAY DIFFRACTION7EE987 - 996224 - 233
18X-RAY DIFFRACTION7EE1007 - 1058244 - 295
19X-RAY DIFFRACTION7EE1077 - 1090314 - 327
20X-RAY DIFFRACTION7EE1094 - 1101331 - 338
21X-RAY DIFFRACTION7EE1108 - 1138345 - 375
22X-RAY DIFFRACTION8GG987 - 994224 - 231
23X-RAY DIFFRACTION8GG1015 - 1028252 - 265
24X-RAY DIFFRACTION8GG1037 - 1058274 - 295
25X-RAY DIFFRACTION8GG1079 - 1101316 - 338
26X-RAY DIFFRACTION8GG1108 - 1133345 - 370

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