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- PDB-1gua: HUMAN RAP1A, RESIDUES 1-167, DOUBLE MUTANT (E30D,K31E) COMPLEXED ... -

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Entry
Database: PDB / ID: 1gua
TitleHUMAN RAP1A, RESIDUES 1-167, DOUBLE MUTANT (E30D,K31E) COMPLEXED WITH GPPNHP AND THE RAS-BINDING-DOMAIN OF HUMAN C-RAF1, RESIDUES 51-131
Components
  • C-RAF1
  • RAP1A
KeywordsCOMPLEX (GTP-BINDING/ATP-BINDING) / ONCOGENE PROTEIN/KINASE/EFFECTOR PROTEIN GTP-BINDING-PROTEIN / COMPLEX (GTP-BINDING-ATP-BINDING) / COMPLEX (GTP-BINDING-ATP-BINDING) complex
Function / homology
Function and homology information


Rap protein signal transduction / death-inducing signaling complex assembly / regulation of cell junction assembly / intermediate filament cytoskeleton organization / nerve growth factor signaling pathway / 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 / intermediate filament cytoskeleton organization / nerve growth factor signaling pathway / 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 / establishment of endothelial barrier / MET activates RAP1 and RAC1 / insulin secretion involved in cellular response to glucose stimulus / anchoring junction / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / GP1b-IX-V activation signalling / Frs2-mediated activation / p130Cas linkage to MAPK signaling for integrins / ERBB2-ERBB3 signaling pathway / face development / pseudopodium / neurotrophin TRK receptor signaling pathway / regulation of cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / synaptic vesicle exocytosis / thyroid gland development / somatic stem cell population maintenance / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / type II interferon-mediated signaling pathway / positive regulation of protein kinase activity / negative regulation of protein-containing complex assembly / Schwann cell development / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / specific granule membrane / activation of adenylate cyclase activity / positive regulation of peptidyl-serine phosphorylation / cellular response to cAMP / response to muscle stretch / sperm midpiece / myelination / Integrin signaling / positive regulation of GTPase activity / CD209 (DC-SIGN) signaling / insulin-like growth factor receptor signaling pathway / guanyl-nucleotide exchange factor activity / thymus development / small monomeric GTPase / protein localization to plasma membrane / RAF activation / wound healing / cellular response to nerve growth factor stimulus / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of neuron projection development / small GTPase binding / Stimuli-sensing channels / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Signaling by BRAF and RAF1 fusions / cell junction / MAPK cascade / late endosome / insulin receptor signaling pathway / nervous system development / presynapse / G protein activity / regulation of apoptotic process / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / early endosome / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity
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 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / RAF proto-oncogene serine/threonine-protein kinase / Ras-related protein Rap-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsNassar, N. / Wittinghofer, A.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Ras/Rap effector specificity determined by charge reversal.
Authors: Nassar, N. / Horn, G. / Herrmann, C. / Block, C. / Janknecht, R. / Wittinghofer, A.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Quantitative Structure-Activity Analysis Correlating Ras/Raf Interaction in Vitro to Raf Activation in Vivo
Authors: Block, C. / Janknecht, R. / Herrmann, C. / Nassar, N. / Wittinghofer, A.
#2: Journal: J.Biol.Chem. / Year: 1995
Title: Quantitative Analysis of the Complex between P21Ras and the Ras-Binding Domain of the Human Raf-1 Protein Kinase
Authors: Herrmann, C. / Martin, G.A. / Wittinghofer, A.
#3: 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. / Horn, G. / Herrmann, C. / Scherer, A. / Mccormick, F. / Wittinghofer, A.
History
DepositionJun 18, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_database_status.process_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_asym_id / _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_asym_id / _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_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 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAP1A
B: C-RAF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8325
Polymers28,2452
Non-polymers5873
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.500, 71.800, 100.300
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 RAP1A


Mass: 19041.549 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-167 / Mutation: E30D, K31E, DEL(168-186)
Source method: isolated from a genetically manipulated source
Details: COMPLEXED TO 5'-GUANOSYL-IMIDO-TRIPHOSPHATE / Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN C-RAF1 GENE RESIDUES 51 / Plasmid: PTAC / Gene (production host): HUMAN RAP1A GENE / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P62834
#2: Protein C-RAF1


Mass: 9203.765 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-131
Source method: isolated from a genetically manipulated source
Details: HUMAN RAP1A AND C-RAF1 / Source: (gene. exp.) Homo sapiens (human)
Description: PURIFIED AS A GST-FUSION PROTEIN WITH THROMBIN CLEAVAGE SITE
Gene: HUMAN C-RAF1 GENE RESIDUES 51 / Plasmid: PGEX-RAFRBD / Species (production host): Escherichia coli / Gene (production host): HUMAN C-RAF1 GENE, RESIDUES 51-131 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P04049, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Non-polymers , 4 types, 92 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#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.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 51 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 %PEG40001reservoir
22 mMdithiothreitol1reservoir
380 mMTris-HCl1reservoir
45 mM1reservoirMgCl2
520-50 mMcalcium acetate1reservoir
615 mg/mlRap/RafRBD1drop
711 %PEG40001drop
82 mMdithiothreitol1drop
980 mMTris-HCl1drop
105 mM1dropMgCl2
1120-50 mMcalcium acetate1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21975 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.049
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 26720 / Rmerge(I) obs: 0.041

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / σ(F): 0
Details: THE ELECTRON DENSITY FOR THE SIDE CHAINS OF RESIDUES 104 - 107 FROM RBD (CHAIN B) IS WEAK.
RfactorNum. reflection
Rwork0.22 -
obs0.22 21693
Displacement parametersBiso mean: 16.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 34 89 2063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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