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- PDB-3i3s: Crystal Structure of H-Ras with Thr50 replaced by Isoleucine -

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Basic information

Entry
Database: PDB / ID: 3i3s
TitleCrystal Structure of H-Ras with Thr50 replaced by Isoleucine
ComponentsGTPase HRas
KeywordsSIGNALING PROTEIN / GTPases / H-Ras / Noonan Syndrome / Cell membrane / Disease mutation / Golgi apparatus / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Palmitate / Prenylation / Proto-oncogene / S-nitrosylation
Function / homology
Function and homology information


GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / 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 / positive regulation of protein targeting to membrane / Signalling to RAS / 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 / : / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / 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 / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / positive regulation of MAP kinase activity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / Regulation of RAS by GAPs / endocytosis / Negative regulation of MAPK pathway / RAS processing / 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 / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / insulin receptor signaling pathway / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsGremer, L. / Dvorsky, R. / Merbitz-Zahradnik, T. / Wittinghofer, A. / Ahmadian, M.R.
CitationJournal: Nat.Genet. / Year: 2010
Title: A restricted spectrum of NRAS mutations causes Noonan syndrome.
Authors: Cirstea, I.C. / Kutsche, K. / Dvorsky, R. / Gremer, L. / Carta, C. / Horn, D. / Roberts, A.E. / Lepri, F. / Merbitz-Zahradnik, T. / Konig, R. / Kratz, C.P. / Pantaleoni, F. / Dentici, M.L. / ...Authors: Cirstea, I.C. / Kutsche, K. / Dvorsky, R. / Gremer, L. / Carta, C. / Horn, D. / Roberts, A.E. / Lepri, F. / Merbitz-Zahradnik, T. / Konig, R. / Kratz, C.P. / Pantaleoni, F. / Dentici, M.L. / Joshi, V.A. / Kucherlapati, R.S. / Mazzanti, L. / Mundlos, S. / Patton, M.A. / Silengo, M.C. / Rossi, C. / Zampino, G. / Digilio, C. / Stuppia, L. / Seemanova, E. / Pennacchio, L.A. / Gelb, B.D. / Dallapiccola, B. / Wittinghofer, A. / Ahmadian, M.R. / Tartaglia, M. / Zenker, M.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5226
Polymers18,8871
Non-polymers6355
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: GTPase HRas
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)117,13536
Polymers113,3236
Non-polymers3,81130
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area12820 Å2
ΔGint-227 kcal/mol
Surface area41370 Å2
MethodPISA
3
R: GTPase HRas
hetero molecules

R: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,04512
Polymers37,7742
Non-polymers1,27010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
Buried area3180 Å2
ΔGint-68 kcal/mol
Surface area14880 Å2
MethodPISA
4
R: GTPase HRas
hetero molecules

R: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,04512
Polymers37,7742
Non-polymers1,27010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area3260 Å2
ΔGint-49 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.210, 89.210, 134.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11R-170-

MG

21R-171-

MG

31R-260-

HOH

41R-271-

HOH

51R-273-

HOH

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Components

#1: Protein GTPase HRas / Transforming protein p21 / p21ras / H-Ras-1 / c-H-ras / Ha-Ras / GTPase HRas / N-terminally processed


Mass: 18887.246 Da / Num. of mol.: 1 / Fragment: UNP residues 1-166 / Mutation: T50I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 285 K / Method: hanging drop / pH: 7.5
Details: 17% PEG 6000, 200 mM CaCl2, pH 7.5, hanging drop, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.36→99 Å / Num. all: 44436 / Num. obs: 44357 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.869 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 25.36
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.36-1.40.2954.616391365399.9
1.4-1.50.2268.861991753799.9
1.5-1.60.12914.7489205792100
1.6-1.80.07822.1686438071100
1.8-20.05131.344198517099.9
2-2.30.04835.2405644798100
2.3-2.60.05135.6236632849100
2.6-30.04240.818749222699.9
3-3.50.03745.713568156799.4
3.5-40.03961.21210388299.7
4-50.03272.81197787399.3
5-70.02571.3495960599.5
7-100.02671.9175323097
10-150.02368.45127783.7
15-250.02560.61272369.7
250.03657.215430.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5P21

5p21


Resolution: 1.36→30.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.375 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2218 5 %RANDOM
Rwork0.159 ---
obs0.16 44353 100 %-
all-44436 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 42.05 Å2 / Biso mean: 18.969 Å2 / Biso min: 7.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.36→30.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 36 102 1458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221639
X-RAY DIFFRACTIONr_bond_other_d0.0020.021105
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.982254
X-RAY DIFFRACTIONr_angle_other_deg0.93932710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9824.39691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9621515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021885
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02338
X-RAY DIFFRACTIONr_nbd_refined0.2820.2318
X-RAY DIFFRACTIONr_nbd_other0.2150.21130
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2742
X-RAY DIFFRACTIONr_nbtor_other0.0820.2838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.280
X-RAY DIFFRACTIONr_metal_ion_refined0.050.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5670.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4190.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0560.21
X-RAY DIFFRACTIONr_mcbond_it1.3111.51013
X-RAY DIFFRACTIONr_mcbond_other0.4781.5390
X-RAY DIFFRACTIONr_mcangle_it1.87421575
X-RAY DIFFRACTIONr_scbond_it2.4263737
X-RAY DIFFRACTIONr_scangle_it3.2894.5661
X-RAY DIFFRACTIONr_rigid_bond_restr1.22533028
X-RAY DIFFRACTIONr_sphericity_free6.4123106
X-RAY DIFFRACTIONr_sphericity_bonded2.49832696
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 164 -
Rwork0.161 3113 -
all-3277 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -2.7361 Å / Origin y: -21.1472 Å / Origin z: -31.657 Å
111213212223313233
T-0.0302 Å2-0.0097 Å2-0.0106 Å2--0.0109 Å2-0.0039 Å2---0.0354 Å2
L0.7606 °2-0.1971 °2-0.2665 °2-1.1527 °20.0608 °2--0.5163 °2
S0.0489 Å °-0.0531 Å °-0.0088 Å °0.0156 Å °-0.0461 Å °-0.0728 Å °0.0199 Å °-0.0065 Å °-0.0028 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1R1 - 166
2X-RAY DIFFRACTION1R1 - 168
3X-RAY DIFFRACTION1R1 - 171
4X-RAY DIFFRACTION1R1 - 273

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