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- PDB-6amb: Crystal Structure of the Afadin RA1 domain in complex with HRAS -

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Basic information

Entry
Database: PDB / ID: 6amb
TitleCrystal Structure of the Afadin RA1 domain in complex with HRAS
Components
  • Afadin
  • GTPase HRas
KeywordsSIGNALING PROTEIN / GTPase / adhesion / RA domain / RBD domain
Function / homology
Function and homology information


regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / protein localization to cell junction / Adherens junctions interactions / pore complex assembly / neuroepithelial cell differentiation / telencephalon development / cell-cell adhesion mediated by cadherin ...regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / protein localization to cell junction / Adherens junctions interactions / pore complex assembly / neuroepithelial cell differentiation / telencephalon development / cell-cell adhesion mediated by cadherin / phospholipase C activator activity / GTPase complex / brain morphogenesis / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / apical junction complex / positive regulation of wound healing / defense response to protozoan / pore complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / regulation of postsynapse assembly / homeostasis of number of cells / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / adipose tissue development / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / cell adhesion molecule binding / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / protein-membrane adaptor activity / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / presynaptic active zone membrane / Signaling by FGFR2 in disease / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / myelination / Signaling by FLT3 fusion proteins / FLT3 Signaling / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / intrinsic apoptotic signaling pathway / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / hippocampal mossy fiber to CA3 synapse / VEGFR2 mediated cell proliferation / animal organ morphogenesis / positive regulation of epithelial cell proliferation / small monomeric GTPase / adherens junction / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / RAF activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / postsynaptic density membrane / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / cerebral cortex development
Similarity search - Function
: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Small GTPase, Ras-type / Small GTPase Ras domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / Afadin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSmith, M.J. / Ishiyama, N. / Ikura, M.
CitationJournal: Nat Commun / Year: 2017
Title: Evolution of AF6-RAS association and its implications in mixed-lineage leukemia.
Authors: Smith, M.J. / Ottoni, E. / Ishiyama, N. / Goudreault, M. / Haman, A. / Meyer, C. / Tucholska, M. / Gasmi-Seabrook, G. / Menezes, S. / Laister, R.C. / Minden, M.D. / Marschalek, R. / Gingras, ...Authors: Smith, M.J. / Ottoni, E. / Ishiyama, N. / Goudreault, M. / Haman, A. / Meyer, C. / Tucholska, M. / Gasmi-Seabrook, G. / Menezes, S. / Laister, R.C. / Minden, M.D. / Marschalek, R. / Gingras, A.C. / Hoang, T. / Ikura, M.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: 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_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: Afadin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4624
Polymers30,9162
Non-polymers5472
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-14 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.239, 57.152, 73.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 19386.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01112
#2: Protein Afadin / Afadin adherens junction formation factor / Protein Af-6


Mass: 11529.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Afdn, Af6, Mllt4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9QZQ1
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.63 Å3/Da / Density % sol: 24.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 8.9 / Details: PEG3350, K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 7437 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Χ2: 0.993 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.20.5573580.8530.2410.6090.756100
2.54-2.596.90.5563660.9010.2280.6020.82999.7
2.59-2.647.10.4793480.930.1930.5170.819100
2.64-2.697.10.4423810.9170.1760.4760.889100
2.69-2.757.10.4583620.9150.1850.4950.894100
2.75-2.827.10.3553680.9270.1430.3830.9100
2.82-2.897.10.2863590.9510.1150.3081.011100
2.89-2.967.10.2523580.960.1020.2721.074100
2.96-3.0570.2083670.9860.0840.2251.035100
3.05-3.1570.1633630.9880.0660.1771.109100
3.15-3.2670.1483700.9890.060.161.057100
3.26-3.3970.1353680.9890.0550.1461.147100
3.39-3.5570.1153670.9910.0470.1241.2100
3.55-3.7370.13740.9940.0410.1081.099100
3.73-3.976.90.0833660.9950.0340.091.078100
3.97-4.276.90.0763730.9960.0310.0820.993100
4.27-4.76.80.0673850.9970.0280.0730.963100
4.7-5.386.60.0673870.9970.0280.0730.974100
5.38-6.786.40.0683900.9960.0290.0740.961100
6.78-505.90.0694270.9960.0310.0761.02798.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DDC

3ddc


Resolution: 2.5→40.301 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.51
RfactorNum. reflection% reflection
Rfree0.2655 725 10.03 %
Rwork0.2184 --
obs0.2232 7226 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.91 Å2 / Biso mean: 54.2805 Å2 / Biso min: 27.18 Å2
Refinement stepCycle: final / Resolution: 2.5→40.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 33 10 2010
Biso mean--38.51 45.2 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022037
X-RAY DIFFRACTIONf_angle_d0.5222758
X-RAY DIFFRACTIONf_chiral_restr0.041311
X-RAY DIFFRACTIONf_plane_restr0.003351
X-RAY DIFFRACTIONf_dihedral_angle_d17.4411223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4991-2.6920.33381340.23831200133493
2.692-2.96290.40711420.25741255139796
2.9629-3.39140.26971450.23231307145299
3.3914-4.27210.26061470.209513271474100
4.2721-40.30590.22471570.20714121569100

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