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- PDB-1c1y: CRYSTAL STRUCTURE OF RAP.GMPPNP IN COMPLEX WITH THE RAS-BINDING-D... -

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Basic information

Entry
Database: PDB / ID: 1c1y
TitleCRYSTAL STRUCTURE OF RAP.GMPPNP IN COMPLEX WITH THE RAS-BINDING-DOMAIN OF C-RAF1 KINASE (RAFRBD).
Components
  • PROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE RAF-1
  • RAS-RELATED PROTEIN RAP-1A
KeywordsSIGNALING PROTEIN / GTP-BINDING PROTEINS / PROTEIN-PROTEIN COMPLEX / EFFECTORS
Function / homology
Function and homology information


positive regulation of Fc receptor mediated stimulatory signaling pathway / Rap protein signal transduction / response to antineoplastic agent / regulation of cell junction assembly / nerve growth factor signaling pathway / negative regulation of collagen biosynthetic process / positive regulation of vasculogenesis / guanyl-nucleotide exchange factor complex / negative regulation of synaptic vesicle exocytosis / response to carbohydrate ...positive regulation of Fc receptor mediated stimulatory signaling pathway / Rap protein signal transduction / response to antineoplastic agent / regulation of cell junction assembly / nerve growth factor signaling pathway / negative regulation of collagen biosynthetic process / positive regulation of vasculogenesis / guanyl-nucleotide exchange factor complex / negative regulation of synaptic vesicle exocytosis / response to carbohydrate / ARMS-mediated activation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / establishment of endothelial barrier / anchoring junction / MET activates RAP1 and RAC1 / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / Frs2-mediated activation / p130Cas linkage to MAPK signaling for integrins / ERBB2-ERBB3 signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of protein kinase activity / neuromuscular junction development / regulation of cell differentiation / pseudopodium / synaptic vesicle exocytosis / positive regulation of GTPase activity / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / type II interferon-mediated signaling pathway / Schwann cell development / negative regulation of protein-containing complex assembly / specific granule membrane / myelination / Integrin signaling / phagocytic vesicle / insulin-like growth factor receptor signaling pathway / CD209 (DC-SIGN) signaling / liver regeneration / positive regulation of phagocytosis / guanyl-nucleotide exchange factor activity / cellular response to cAMP / positive regulation of D-glucose import across plasma membrane / protein localization to plasma membrane / cellular response to forskolin / adenylate cyclase activator activity / wound healing / small monomeric GTPase / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cell junction / small GTPase binding / Stimuli-sensing channels / 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 / Negative regulation of MAPK pathway / insulin receptor signaling pathway / Signaling by BRAF and RAF1 fusions / GDP binding / late endosome / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / sperm midpiece / nervous system development / presynapse / G protein activity / regulation of apoptotic process / early endosome / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / protein phosphorylation / protein kinase activity / mitochondrial outer membrane / non-specific serine/threonine protein kinase / endosome membrane / neuron projection / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / GTP binding / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / glutamatergic synapse / enzyme binding / signal transduction
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. ...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 domain 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RAF proto-oncogene serine/threonine-protein kinase / Ras-related protein Rap-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsNassar, N.
Citation
Journal: Nature / Year: 1995
Title: The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue.
Authors: Nassar, N.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Ras/Rap effector specificty determined by charge reversal.
Authors: Nassar, N.
#2: Journal: Nature / Year: 2008
Title: Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B.
Authors: Holger Rehmann / Ernesto Arias-Palomo / Michael A Hadders / Frank Schwede / Oscar Llorca / Johannes L Bos /
Abstract: Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell ...Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the structure of Epac2 in complex with a cAMP analogue (Sp-cAMPS) and RAP1B by X-ray crystallography and single particle electron microscopy. The structure represents the cAMP activated state of the Epac2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation reveals that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site towards a docking site at the Ras exchange motif domain.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAP-1A
B: PROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE RAF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4325
Polymers27,8452
Non-polymers5883
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.170, 71.880, 100.200
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


Mass: 19055.641 Da / Num. of mol.: 1 / Fragment: RAP, RESIDUES 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBKS / Production host: Escherichia coli (E. coli) / References: UniProt: P62834
#2: Protein PROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE RAF-1


Mass: 8789.290 Da / Num. of mol.: 1 / Fragment: RAFRBD, RESIDUES 51-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli)
References: UniProt: P04049, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Non-polymers , 4 types, 86 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: mmePeg5000, magnesium chloride, calcium chloride, ammonium sulphate., pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
210 %mPEG50001drop
350 mMammonium sulfate1drop
45 mM1dropCaCl2
52.5 mM1dropMgCl2
60.5 mMDTE1drop
732.2 mMTris-HCl1drop
820 %mPEG50001reservoir
90.1 Mammonium sulfate1reservoir
1010 mM1reservoirCaCl2
115 mM1reservoirMgCl2
121 mMDTE1reservoir
1364.4 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 24787 / Num. obs: 24787 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 12
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.325 / Num. unique all: 3569 / % possible all: 93.6
Reflection
*PLUS
% possible obs: 98 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 7734287.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum Likelyhood refinement using CNS_0.4.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2454 9.9 %RANDOM
Rwork0.229 ---
obs0.229 24787 97.3 %-
all-24787 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.03 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-9.12 Å20 Å20 Å2
2---2.05 Å20 Å2
3----7.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 34 83 2151
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 392 9.9 %
Rwork0.357 3569 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRPROTEIN.TOP
X-RAY DIFFRACTION2GTP.PARGTP.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.38 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.357

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