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- PDB-1k8r: Crystal structure of Ras-Bry2RBD complex -

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Basic information

Entry
Database: PDB / ID: 1k8r
TitleCrystal structure of Ras-Bry2RBD complex
Components
  • Protein kinase byr2
  • Transforming protein P21/H-RAS-1
KeywordsSIGNALING PROTEIN / signal transduction / cancer / GTPase / ubiquitin fold
Function / homology
Function and homology information


Oxidative Stress Induced Senescence / induction of conjugation with cellular fusion / pheromone response MAPK cascade / division septum / cell tip / mitogen-activated protein kinase kinase kinase / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity ...Oxidative Stress Induced Senescence / induction of conjugation with cellular fusion / pheromone response MAPK cascade / division septum / cell tip / mitogen-activated protein kinase kinase kinase / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / MAP kinase kinase kinase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / cell division site / defense response to protozoan / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / EGFR Transactivation by Gastrin / SHC1 events in EGFR signaling / positive regulation of protein targeting to membrane / Signalling to RAS / GRB2 events in ERBB2 signaling / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC1 events in ERBB2 signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / positive regulation of epithelial cell proliferation / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / myelination / Signaling by FGFR1 in disease / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / Signaling by ERBB2 TMD/JMD mutants / small monomeric GTPase / positive regulation of MAP kinase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Signaling by SCF-KIT / cellular senescence / cellular response to gamma radiation / positive regulation of fibroblast proliferation / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / endocytosis / positive regulation of type II interferon production / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants
Similarity search - Function
Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / : / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / small GTPase Ras family profile. / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / : / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / small GTPase Ras family profile. / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / 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. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Roll / 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 / GTPase HRas / Protein kinase byr2
Similarity search - Component
Biological speciesHomo sapiens (human)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsScheffzek, K. / Gruenewald, P. / Wohlgemuth, S. / Kabsch, W. / Tu, H. / Wigler, M. / Wittinghofer, A. / Herrmann, C.
CitationJournal: Structure / Year: 2001
Title: The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast.
Authors: Scheffzek, K. / Grunewald, P. / Wohlgemuth, S. / Kabsch, W. / Tu, H. / Wigler, M. / Wittinghofer, A. / Herrmann, C.
History
DepositionOct 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _software.name / _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.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_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: Transforming protein P21/H-RAS-1
B: Protein kinase byr2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8484
Polymers31,3012
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.030, 139.030, 112.800
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Transforming protein P21/H-RAS-1


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: GTP-binding/catalytic domain, residues 1-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Hras or Hras1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P01112
#2: Protein Protein kinase byr2


Mass: 12426.270 Da / Num. of mol.: 1 / Fragment: Ras binding domain (RBD), residues 71-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: BYR2 or STE8 or SPBC1D7.05 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P28829, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-25 mg/mlprotein1drop
220-25 %PEG33501reservoir
3100 mMTris-HCl1reservoirpH8.
40.2-0.4 M1reservoirLiSO4

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.54 Å
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Aug 6, 1996 / Details: mirrors
RadiationMonochromator: Ni Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 8592 / Num. obs: 8526 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 18.6
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / Num. unique all: 788 / Rsym value: 0.3 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / Num. measured all: 109981
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 100 % / Num. unique obs: 788 / Num. measured obs: 2634 / Rmerge(I) obs: 0.305

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
X-GENdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5p21

5p21


Resolution: 3→25 Å / Rfactor Rfree error details: 0.01 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: residues 127-139 and 166-180 of Byr2 are ill defined in electron density and are not included in the model
RfactorNum. reflection% reflectionSelection details
Rfree0.305 860 10 %random
Rwork0.235 ---
all0.24 8592 --
obs0.24 8526 99.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.4 Å
Luzzati d res low-25 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 33 0 2012
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 144 10.3 %
Rwork0.297 1253 -
obs-1253 99.9 %
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.236 / Rfactor Rfree: 0.312
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.375
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
LS refinement shell
*PLUS
Highest resolution: 3 Å / Rfactor Rfree: 0.35 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.297

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