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- PDB-3kuc: Complex of Rap1A(E30D/K31E)GDP with RafRBD(A85K/N71R) -

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Basic information

Entry
Database: PDB / ID: 3kuc
TitleComplex of Rap1A(E30D/K31E)GDP with RafRBD(A85K/N71R)
Components
  • RAF proto-oncogene serine/threonine-protein kinase
  • Ras-related protein Rap-1A
KeywordsGTP binding protein/Transferase / Ras-effector complex / GTP-binding / Nucleotide-binding / Proto-oncogene / Transferase / GTP binding protein-Transferase complex
Function / homology
Function and homology information


Rap protein signal transduction / death-inducing signaling complex assembly / regulation of cell junction assembly / nerve growth factor signaling pathway / intermediate filament cytoskeleton organization / positive regulation of vasculogenesis / guanyl-nucleotide exchange factor complex / negative regulation of synaptic vesicle exocytosis / type B pancreatic cell proliferation / regulation of Rho protein signal transduction ...Rap protein signal transduction / death-inducing signaling complex assembly / regulation of cell junction assembly / nerve growth factor signaling pathway / intermediate filament cytoskeleton organization / positive regulation of vasculogenesis / guanyl-nucleotide exchange factor complex / negative regulation of synaptic vesicle exocytosis / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / anchoring junction / establishment of endothelial barrier / insulin secretion involved in cellular response to glucose stimulus / MET activates RAP1 and RAC1 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Negative feedback regulation of MAPK pathway / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / Frs2-mediated activation / p130Cas linkage to MAPK signaling for integrins / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / face development / synaptic vesicle exocytosis / pseudopodium / somatic stem cell population maintenance / neurotrophin TRK receptor signaling pathway / thyroid gland development / GRB2:SOS provides linkage to MAPK signaling for Integrins / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / positive regulation of protein kinase activity / negative regulation of protein-containing complex assembly / specific granule membrane / Schwann cell development / type II interferon-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cAMP / sperm midpiece / response to muscle stretch / activation of adenylate cyclase activity / myelination / CD209 (DC-SIGN) signaling / Integrin signaling / guanyl-nucleotide exchange factor activity / cellular response to nerve growth factor stimulus / small monomeric GTPase / G protein activity / insulin-like growth factor receptor signaling pathway / thymus development / protein localization to plasma membrane / RAF activation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron projection development / Stimuli-sensing channels / small GTPase binding / positive regulation of GTPase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Negative regulation of MAPK pathway / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Signaling by BRAF and RAF1 fusions / late endosome / presynapse / insulin receptor signaling pathway / cell junction / positive regulation of peptidyl-serine phosphorylation / nervous system development / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome membrane / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / GTPase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / Neutrophil degranulation / protein-containing complex binding / GTP binding / negative regulation of apoptotic process
Similarity search - Function
Ras-related protein Rap1 / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Ras-related protein Rap1 / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / RAF proto-oncogene serine/threonine-protein kinase / Ras-related protein Rap-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsFilchtinski, D. / Sharabi, O. / Rueppel, A. / Vetter, I.R. / Herrmann, C. / Shifman, J.M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: What makes Ras an efficient molecular switch: a computational, biophysical, and structural study of Ras-GDP interactions with mutants of Raf.
Authors: Filchtinski, D. / Sharabi, O. / Ruppel, A. / Vetter, I.R. / Herrmann, C. / Shifman, J.M.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 13, 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rap-1A
B: RAF proto-oncogene serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8545
Polymers28,3472
Non-polymers5083
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.120, 68.540, 101.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ras-related protein Rap-1A / GTP-binding protein smg-p21A / Ras-related protein Krev-1 / C21KG / G-22K


Mass: 19041.549 Da / Num. of mol.: 1 / Fragment: UNP residues 1-167 / Mutation: E30D, K31E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1A, KREV1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62834
#2: Protein RAF proto-oncogene serine/threonine-protein kinase / C-RAF / cRaf / Raf-1


Mass: 9304.958 Da / Num. of mol.: 1 / Fragment: UNP residues 51-131 / Mutation: A85K, N71R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Production host: Escherichia coli (E. coli)
References: UniProt: P04049, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 184 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-25% PEG 8000, 100 mM Tris or HEPES pH 7.2-7.6, 10-200 mM Ca Acetate or 100 mM Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00472 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 1, 2008
RadiationMonochromator: FOCUSED SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00472 Å / Relative weight: 1
ReflectionResolution: 1.92→40.84 Å / Num. all: 23787 / Num. obs: 23432 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.71 % / Rmerge(I) obs: 0.046 / Rsym value: 0.074 / Net I/σ(I): 27.27
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 7.66 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 7.52 / Rsym value: 0.384 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1gua

1gua


Resolution: 1.92→36.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.148 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20893 1184 5 %RANDOM
Rwork0.17385 ---
obs0.17559 22491 100 %-
all-22528 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.733 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--1.2 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.92→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 30 181 2157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222051
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9832779
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6645257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88224.762105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9515391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5651517
X-RAY DIFFRACTIONr_chiral_restr0.1720.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021541
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_it1.4071.51228
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34521990
X-RAY DIFFRACTIONr_scbond_it3.6723823
X-RAY DIFFRACTIONr_scangle_it5.5854.5781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 87 -
Rwork0.185 1654 -
obs--100 %
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)
10.92250.19710.33142.17072.79315.6321-0.0684-0.04080.04380.3817-0.3020.25120.4332-0.40070.37030.0864-0.04180.04530.068-0.05240.0813-8.8037-14.735726.0052
21.94880.3503-1.47992.0047-0.55343.29620.0080.0833-0.0423-0.0656-0.0623-0.03270.11410.0080.05430.01030.01710.00630.06360.01310.06923.7496-22.52693.3028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 167
2X-RAY DIFFRACTION2B56 - 131

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