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- PDB-4dly: Set 1 CaCl2/DTT, ordered off -

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Basic information

Entry
Database: PDB / ID: 4dly
TitleSet 1 CaCl2/DTT, 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 / negative regulation of GTPase 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 / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase 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 / 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 / Schwann cell development / 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 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / protein-membrane adaptor activity / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / myelination / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / EPHB-mediated forward signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FLT3 fusion proteins / 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 / intrinsic apoptotic signaling pathway / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / 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 / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / positive regulation of MAP kinase activity / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / positive regulation of type II interferon production / 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 / MAPK cascade / positive regulation of fibroblast proliferation / cellular senescence / Signaling by BRAF and RAF1 fusions / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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)19,8769
Polymers18,8761
Non-polymers1,0008
Water3,243180
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)119,25454
Polymers113,2576
Non-polymers5,99748
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 area15530 Å2
ΔGint-243 kcal/mol
Surface area41030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.207, 88.207, 134.142
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-203-

MG

21A-205-

CA

31A-362-

HOH

41A-370-

HOH

51A-378-

HOH

61A-383-

HOH

71A-388-

HOH

81A-455-

HOH

91A-475-

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, 188 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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / 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.: 180 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 200 mM CaCl2, 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-BM / 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: 1.57→50 Å / Num. all: 28221 / Num. obs: 28221 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.363 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.57-1.690.29512900.859192.9
1.6-1.6310.20.26814050.9061100
1.63-1.66110.2414070.9211100
1.66-1.69110.2114120.8851100
1.69-1.7311.10.18613890.931100
1.73-1.77110.1613920.9611100
1.77-1.8111.10.13614000.9561100
1.81-1.86110.11814150.9921100
1.86-1.9211.10.10414111.111100
1.92-1.9811.10.0913991.1551100
1.98-2.0511.10.07814121.181100
2.05-2.1311.10.07314031.3011100
2.13-2.2311.10.06514111.2841100
2.23-2.3511.10.06314191.4461100
2.35-2.4911.10.05814191.4041100
2.49-2.6811.10.05914191.6821100
2.68-2.95110.06414342.171100
2.95-3.3810.90.0614352.5421100
3.38-4.2610.90.04814472.1921100
4.26-5010.40.04415022.176199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_336refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→28.226 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.9142 / SU ML: 0.16 / σ(F): 0.23 / Phase error: 15.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 1976 7.12 %
Rwork0.1584 --
all0.1599 27768 -
obs0.1599 27768 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.044 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 62.5 Å2 / Biso mean: 17.2477 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.4114 Å20 Å20 Å2
2---0.4114 Å20 Å2
3---0.8227 Å2
Refinement stepCycle: LAST / Resolution: 1.57→28.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 53 180 1546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081393
X-RAY DIFFRACTIONf_angle_d1.2721891
X-RAY DIFFRACTIONf_chiral_restr0.336213
X-RAY DIFFRACTIONf_plane_restr0.004242
X-RAY DIFFRACTIONf_dihedral_angle_d15.833525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5701-1.62620.18221920.15762438263095
1.6262-1.69130.17871910.14822513270496
1.6913-1.76830.17311930.1442515270897
1.7683-1.86150.1761950.14372559275498
1.8615-1.97810.16031990.14112551275098
1.9781-2.13080.16281960.14492583277999
2.1308-2.34510.17941990.15512607280699
2.3451-2.68420.18672010.157826332834100
2.6842-3.38090.17672010.164526582859100
3.3809-28.23060.17842090.165127352944100

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