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- PDB-5tb5: Crystal structure of full-length farnesylated and methylated KRAS... -

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Basic information

Entry
Database: PDB / ID: 5tb5
TitleCrystal structure of full-length farnesylated and methylated KRAS4b in complex with PDE-delta (crystal form I - with partially disordered hypervariable region)
Components
  • GTPase KRas
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsONCOPROTEIN / KRAS4b / PDEdelta / PDE6delta / RAS / KRAS
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / 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 / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / SHC-mediated cascade:FGFR2 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / striated muscle cell differentiation / GRB2 events in EGFR signaling / FLT3 Signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / visual perception / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 KD Mutants / cytoplasmic vesicle membrane / Signaling by SCF-KIT / cilium / G protein activity / small GTPase binding / cytoplasmic side of plasma membrane / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / 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 / GDP binding / Signaling by BRAF and RAF1 fusions / MAPK cascade / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / cytoplasmic vesicle
Similarity search - Function
GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases ...GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Distorted Sandwich / Rab subfamily of small GTPases / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FARNESYL / GUANOSINE-5'-DIPHOSPHATE / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDharmaiah, S. / Tran, T.H. / Simanshu, D.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis of recognition of farnesylated and methylated KRAS4b by PDE delta.
Authors: Dharmaiah, S. / Bindu, L. / Tran, T.H. / Gillette, W.K. / Frank, P.H. / Ghirlando, R. / Nissley, D.V. / Esposito, D. / McCormick, F. / Stephen, A.G. / Simanshu, D.K.
History
DepositionSep 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
C: GTPase KRas
D: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,41710
Polymers76,9944
Non-polymers1,4236
Water2,882160
1
A: GTPase KRas
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2095
Polymers38,4972
Non-polymers7123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GTPase KRas
D: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2095
Polymers38,4972
Non-polymers7123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.386, 70.651, 94.307
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimer confirmed by Analytical Ultracentrifugation

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21056.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: unidentified baculovirus / References: UniProt: P01116
#2: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GMP-PDE delta / Protein p17


Mass: 17440.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli (E. coli) / References: UniProt: O43924

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Non-polymers , 4 types, 166 molecules

#3: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citrate pH 5.0 and 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 52173 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 36.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.51
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.99-2.055.70.7982.620.776198.3
2.05-2.10.623.650.892199.3
2.1-2.160.4994.510.928199.5
2.16-2.230.3426.220.969199.5
2.23-2.30.2947.30.971199.5
2.3-2.380.2249.010.985199.7
2.38-2.470.18110.830.99199.8
2.47-2.570.14213.360.994199.8
2.57-2.690.11116.420.995199.8
2.69-2.820.08819.350.9971100
2.82-2.970.06325.520.998199.9
2.97-3.150.04931.460.9981100
3.15-3.370.04136.990.9991100
3.37-3.640.03543.060.9991100
3.64-3.990.03247.250.999199.9
3.99-4.460.02950.750.999199.8
4.46-5.150.02753.020.999199.5
5.15-6.310.02652.650.999199.6
6.31-8.920.02453.030.999197.3
8.92-500.02349.920.999172.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XSCALEdata scaling
XDSdata reduction
Cootmodel building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OBE, 3T5G

4obe

3t5g


Resolution: 2→48.695 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 5200 10.09 %Random
Rwork0.2007 ---
obs0.2054 51556 99.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5117 0 94 160 5371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085362
X-RAY DIFFRACTIONf_angle_d1.0127222
X-RAY DIFFRACTIONf_dihedral_angle_d18.2853242
X-RAY DIFFRACTIONf_chiral_restr0.053792
X-RAY DIFFRACTIONf_plane_restr0.005920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.35611860.27131530X-RAY DIFFRACTION99
2.0227-2.04650.32581590.27461526X-RAY DIFFRACTION99
2.0465-2.07150.31981720.25911556X-RAY DIFFRACTION99
2.0715-2.09770.33841560.25451566X-RAY DIFFRACTION99
2.0977-2.12530.28621760.24471516X-RAY DIFFRACTION99
2.1253-2.15440.30061640.24331527X-RAY DIFFRACTION99
2.1544-2.18520.27151590.23331571X-RAY DIFFRACTION99
2.1852-2.21780.30621770.22491526X-RAY DIFFRACTION99
2.2178-2.25250.27631630.22631547X-RAY DIFFRACTION99
2.2525-2.28940.28811910.23851528X-RAY DIFFRACTION100
2.2894-2.32890.26971890.21491504X-RAY DIFFRACTION99
2.3289-2.37120.26771470.22551566X-RAY DIFFRACTION99
2.3712-2.41690.25811900.22241562X-RAY DIFFRACTION100
2.4169-2.46620.28171680.23281538X-RAY DIFFRACTION100
2.4662-2.51980.23311630.22371551X-RAY DIFFRACTION100
2.5198-2.57840.28361740.21261532X-RAY DIFFRACTION100
2.5784-2.64290.26811880.21061544X-RAY DIFFRACTION100
2.6429-2.71430.25391890.22981541X-RAY DIFFRACTION100
2.7143-2.79420.24931570.21641577X-RAY DIFFRACTION100
2.7942-2.88440.27741880.2161542X-RAY DIFFRACTION100
2.8844-2.98750.25831630.21671537X-RAY DIFFRACTION100
2.9875-3.10710.28271880.21391577X-RAY DIFFRACTION100
3.1071-3.24840.28811800.20791572X-RAY DIFFRACTION100
3.2484-3.41970.22891640.20051556X-RAY DIFFRACTION100
3.4197-3.63390.24321710.19231568X-RAY DIFFRACTION100
3.6339-3.91430.22741570.1831584X-RAY DIFFRACTION100
3.9143-4.3080.23051720.16621556X-RAY DIFFRACTION100
4.308-4.93090.20451750.15681572X-RAY DIFFRACTION99
4.9309-6.21040.18671830.1781565X-RAY DIFFRACTION100
6.2104-48.70970.24141910.20061419X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: 26.6928 Å / Origin y: -5.1397 Å / Origin z: 70.1343 Å
111213212223313233
T0.2434 Å20.0006 Å2-0.026 Å2-0.4473 Å2-0.0323 Å2--0.3551 Å2
L0.1693 °2-0.053 °20.0827 °2-0.3374 °20.0219 °2--0.198 °2
S0.0063 Å °-0.2484 Å °-0.0325 Å °0.0552 Å °-0.042 Å °0.0459 Å °-0.0434 Å °-0.1098 Å °0.0343 Å °
Refinement TLS groupSelection details: all

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