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- PDB-2c5l: Structure of PLC epsilon Ras association domain with hRas -

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Basic information

Entry
Database: PDB / ID: 2c5l
TitleStructure of PLC epsilon Ras association domain with hRas
Components
  • GTPASE HRASHRAS
  • PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C PLC-EPSILON
KeywordsSIGNALING PROTEIN / SIGNALING PROTEIN-COMPLEX / RAS / UBIQUITIN SUPERFOLD / ONCOGENE / GTP-BINDING / NUCLEOTIDE- BINDING / DISEASE MUTATION / LIPOPROTEIN / PALMITATE / PRENYLATION / PROTO-ONCOGENE
Function / homology
Function and homology information


: / small GTPase binding => GO:0031267 / : / regulation of Ras protein signal transduction / inositol phosphate metabolic process / phosphoinositide phospholipase C / diacylglycerol biosynthetic process / regulation of smooth muscle contraction / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity ...: / small GTPase binding => GO:0031267 / : / regulation of Ras protein signal transduction / inositol phosphate metabolic process / phosphoinositide phospholipase C / diacylglycerol biosynthetic process / regulation of smooth muscle contraction / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity / regulation of G protein-coupled receptor signaling pathway / phospholipase C activity / glomerulus development / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of protein kinase activity / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / Synthesis of IP3 and IP4 in the cytosol / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / phosphatidylinositol-mediated signaling / 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 / Signalling to RAS / positive regulation of protein targeting to membrane / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of lamellipodium assembly / : / Schwann cell development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / lipid catabolic process / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / release of sequestered calcium ion into cytosol / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / cytoskeleton organization / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Signaling by FGFR1 in disease / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / calcium-mediated signaling / regulation of cell growth / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / RAF activation / positive regulation of MAP kinase activity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII
Similarity search - Function
: / : / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y ...: / : / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Ras association (RalGDS/AF-6) domain / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Phosphatidylinositol-specific phospholipase X-box domain profile. / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Small GTPase, Ras-type / small GTPase Ras family profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / 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) / EF-hand domain pair / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTPase HRas / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRoe, S.M. / Bunney, T.D. / Katan, M. / Pearl, L.H.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural and Mechanistic Insights Into Ras Association Domains of Phospholipase C Epsilon
Authors: Bunney, T.D. / Harris, R. / Gandarillas, N.L. / Josephs, M.B. / Roe, S.M. / Sorli, S.C. / Paterson, H.F. / Rodrigues-Lima, F. / Esposito, D. / Ponting, C.P. / Gieschik, P. / Pearl, L.H. / ...Authors: Bunney, T.D. / Harris, R. / Gandarillas, N.L. / Josephs, M.B. / Roe, S.M. / Sorli, S.C. / Paterson, H.F. / Rodrigues-Lima, F. / Esposito, D. / Ponting, C.P. / Gieschik, P. / Pearl, L.H. / Driscoll, P.C. / Katan, M.
History
DepositionOct 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPASE HRAS
B: GTPASE HRAS
C: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C PLC-EPSILON
D: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C PLC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,53212
Polymers65,0694
Non-polymers1,4638
Water8,575476
1
A: GTPASE HRAS
C: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C PLC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3587
Polymers32,5352
Non-polymers8245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GTPASE HRAS
D: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C PLC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1745
Polymers32,5352
Non-polymers6403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.416, 93.618, 111.494
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, 4 molecules ABCD

#1: Protein GTPASE HRAS / HRAS / TRANSFORMING PROTEIN P21 / H-RAS-1 / C-H-RAS


Mass: 19376.686 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P01112, small monomeric GTPase
#2: Protein PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C PLC-EPSILON


Mass: 13157.861 Da / Num. of mol.: 2 / Fragment: RA2 DOMAIN, RESIDUES 2131-2246 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: Q9HBX6, UniProt: Q9P212*PLUS, phosphoinositide phospholipase C

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Non-polymers , 4 types, 484 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsRAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE ACTIVITY ENGINEERED RESIDUE IN CHAIN A, GLY ...RAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE ACTIVITY ENGINEERED RESIDUE IN CHAIN A, GLY 12 TO VAL ENGINEERED RESIDUE IN CHAIN B, GLY 12 TO VAL ENGINEERED RESIDUE IN CHAIN C, TYR 2176 TO LEU ENGINEERED RESIDUE IN CHAIN D, TYR 2176 TO LEU
Sequence details7 N-TERMINAL RESIDUES FROM TAG. N-TERMINAL G PART OF TAG.

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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: 3 Å3/Da / Density % sol: 59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9151
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9151 Å / Relative weight: 1
ReflectionResolution: 2.8→39.87 Å / Num. obs: 18504 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.28 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.46
Reflection shellResolution: 2.8→2.82 Å / Redundancy: 4.32 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.09 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→111.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.562 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3050 5 %RANDOM
Rwork0.185 ---
obs0.187 57370 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2--0.92 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.9→111.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 90 476 4615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224285
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9865823
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0685531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70924.831207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37415766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7611529
X-RAY DIFFRACTIONr_chiral_restr0.1060.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023193
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21860
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22832
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2407
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.040.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0081.52711
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60824216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.55431832
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0324.51595
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 243 -
Rwork0.261 4179 -
obs--99.98 %

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