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- PDB-4dlr: H-Ras PEG 400/Ca(OAc)2, ordered off -

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Basic information

Entry
Database: PDB / ID: 4dlr
TitleH-Ras PEG 400/Ca(OAc)2, ordered off
ComponentsGTPase HRasHRAS
KeywordsSIGNALING PROTEIN / GTP-BINDING / NUCLEOTIDE BINDING
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 / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / 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 / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / 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 / positive regulation of protein targeting to membrane / 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 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / 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 / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / 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 / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / intrinsic apoptotic signaling pathway / 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 / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / animal organ morphogenesis / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / Constitutive Signaling by EGFRvIII / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / 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 / chemotaxis / positive regulation of fibroblast proliferation / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling
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
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.319 Å
AuthorsHolzapfel, G. / Mattos, C.
CitationJournal: Biochemistry / Year: 2012
Title: Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition.
Authors: Holzapfel, G. / Buhrman, G. / Mattos, C.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Structure summary
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _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: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7469
Polymers18,8761
Non-polymers8708
Water3,189177
1


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


Theoretical massNumber of molelcules
Total (without water)118,47554
Polymers113,2576
Non-polymers5,21848
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation4_464y-1,x+1,-z-11
crystal symmetry operation5_674x-y+1,-y+2,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area14600 Å2
ΔGint-239 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.415, 87.415, 133.471
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
11A-205-

CA

21A-206-

MG

31A-207-

MG

41A-361-

HOH

51A-369-

HOH

61A-380-

HOH

71A-388-

HOH

81A-409-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18876.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01112

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Non-polymers , 5 types, 185 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 200 mM Ca Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.319→35 Å / Num. all: 37269 / Num. obs: 37269 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.059 / Χ2: 2.384 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.42-1.4410.70.33518281.4991100
1.44-1.4710.90.30818521.5791100
1.47-1.510.90.27218621.671100
1.5-1.5310.90.23418491.8161100
1.53-1.5610.90.21118412.0081100
1.56-1.610.90.19218462.079199.9
1.6-1.6410.90.17318362.2071100
1.64-1.6810.90.15718552.3181100
1.68-1.7310.90.14418512.3991100
1.73-1.7910.90.12318292.5911100
1.79-1.8510.90.10718662.7341100
1.85-1.9310.90.09318612.8171100
1.93-2.0110.90.08218442.9681100
2.01-2.1210.90.07518673.1841100
2.12-2.2510.90.0718673.2941100
2.25-2.43110.06218763.0881100
2.43-2.6711.10.05318712.7151100
2.67-3.0611.10.04518942.3531100
3.06-3.8511.10.03718912.2121100
3.85-3510.50.03519832.087199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.319→32.924 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.9102 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 15.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 1999 4.32 %
Rwork0.1697 --
all0.1704 46257 -
obs0.1704 -99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.256 Å2 / ksol: 0.432 e/Å3
Displacement parametersBiso max: 58.31 Å2 / Biso mean: 15.9037 Å2 / Biso min: 6.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.0005 Å20 Å20 Å2
2---1.0005 Å2-0 Å2
3---2.001 Å2
Refinement stepCycle: LAST / Resolution: 1.319→32.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 46 177 1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071400
X-RAY DIFFRACTIONf_angle_d1.1681905
X-RAY DIFFRACTIONf_chiral_restr0.069213
X-RAY DIFFRACTIONf_plane_restr0.005246
X-RAY DIFFRACTIONf_dihedral_angle_d14.786532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3192-1.35220.30921380.28043084322299
1.3522-1.38880.24861420.239131283270100
1.3888-1.42960.23311420.19931643306100
1.4296-1.47580.20121410.184931053246100
1.4758-1.52850.19171430.15631673310100
1.5285-1.58970.15021420.152431273269100
1.5897-1.66210.17871410.149931403281100
1.6621-1.74970.16041420.157131423284100
1.7497-1.85930.18651440.154131703314100
1.8593-2.00290.16951420.156531523294100
2.0029-2.20440.16751430.166131703313100
2.2044-2.52320.18051440.16431853329100
2.5232-3.17860.17261460.170632123358100
3.1786-32.93470.19911490.171233123461100

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