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- PDB-3v4f: H-Ras PEG 400/CaCl2, ordered off -

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Basic information

Entry
Database: PDB / ID: 3v4f
TitleH-Ras PEG 400/CaCl2, ordered off
ComponentsGTPase HRasHRAS
KeywordsSIGNALING PROTEIN / GTP-BINDING / NUCLEOTIDE BINDING
Function / homology
Function and homology information


Activation of RAS in B cells / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / MET activates RAS signaling / p38MAPK events / GRB2 events in ERBB2 signaling / Tie2 Signaling / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling ...Activation of RAS in B cells / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / MET activates RAS signaling / p38MAPK events / GRB2 events in ERBB2 signaling / Tie2 Signaling / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / FLT3 Signaling / CD209 (DC-SIGN) signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / mitotic cell cycle checkpoint signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / EGFR Transactivation by Gastrin / Signaling by SCF-KIT / : / : / RAF activation / Downstream signal transduction / Regulation of RAS by GAPs / regulation of cell cycle => GO:0051726 / DAP12 signaling / VEGFR2 mediated cell proliferation / Estrogen-stimulated signaling through PRKCZ / NCAM signaling for neurite out-growth / Negative regulation of MAPK pathway / FCERI mediated MAPK activation / : / MAP2K and MAPK activation / response to isolation stress / EPHB-mediated forward signaling / positive regulation of Ras protein signal transduction / positive regulation of ruffle assembly / RAF/MAP kinase cascade / 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 / small GTPase-mediated signal transduction / positive regulation of wound healing / defense response to protozoan / positive regulation of protein targeting to membrane / positive regulation of phospholipase C activity / intrinsic apoptotic signaling pathway / small monomeric GTPase / liver development / positive regulation of DNA replication / positive regulation of epithelial cell proliferation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / cellular response to gamma radiation / positive regulation of MAP kinase activity / positive regulation of GTPase activity / endocytosis / GDP binding / cellular senescence / positive regulation of type II interferon production / T cell receptor signaling pathway / Ras protein signal transduction / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / Golgi membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / GTPase activity / glutamatergic synapse / apoptotic process / positive regulation of cell population proliferation / protein-containing complex binding / GTP binding / positive regulation of gene expression / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Small GTPase / Ras family / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.391 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
DepositionDec 14, 2011Deposition 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 8, 2017Group: Refinement description / Category: software / Item: _software.name
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)19,6817
Polymers18,8761
Non-polymers8056
Water3,117173
1
A: GTPase HRas
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)118,08842
Polymers113,2576
Non-polymers4,83136
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 area13800 Å2
ΔGint-199 kcal/mol
Surface area41260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.521, 88.521, 134.060
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-194-

MG

21A-196-

CA

31A-370-

HOH

41A-392-

HOH

51A-396-

HOH

61A-407-

HOH

71A-440-

HOH

81A-1486-

HOH

91A-1497-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GTPase HRas / HRAS / H-Ras-1 / 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.) Rattus norvegicus (Norway rat) / Gene: Hras, Hras1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20171

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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-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.: 173 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350 200 mM CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: APS / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2011
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→35 Å / Num. obs: 40675 / % possible obs: 99.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.063 / Χ2: 1.878 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.39-1.4150.79619791.3198.4
1.41-1.446.20.73419951.311199.8
1.44-1.477.70.64820241.261100
1.47-1.59.20.58320131.2181100
1.5-1.5310.10.50120341.2821100
1.53-1.5710.70.40520161.2681100
1.57-1.610.90.33820041.2451100
1.6-1.65110.27820201.3341100
1.65-1.7110.23620361.4141100
1.7-1.7511.10.19820111.5541100
1.75-1.8111.10.15720171.7031100
1.81-1.8911.10.12820551.8111100
1.89-1.97110.10220182.041100
1.97-2.08110.08420252.2211100
2.08-2.21110.07220462.4241100
2.21-2.3810.80.06420362.6741100
2.38-2.6210.80.05420672.6311100
2.62-2.9910.70.04620422.5351100
2.99-3.7710.50.0420912.631100
3.77-359.70.0421462.767199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.391→33.274 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 18.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 1999 4.92 %
Rwork0.1828 --
obs0.1836 40649 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.857 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso max: 65.09 Å2 / Biso mean: 20.8433 Å2 / Biso min: 7.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.0946 Å20 Å20 Å2
2---1.0946 Å20 Å2
3---2.1892 Å2
Refinement stepCycle: LAST / Resolution: 1.391→33.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 44 173 1526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071397
X-RAY DIFFRACTIONf_angle_d1.1691901
X-RAY DIFFRACTIONf_chiral_restr0.068214
X-RAY DIFFRACTIONf_plane_restr0.005244
X-RAY DIFFRACTIONf_dihedral_angle_d14.37530
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 (%)
1.3906-1.42540.34371370.38262634277196
1.4254-1.4640.32561420.312127262868100
1.464-1.5070.29351420.257627552897100
1.507-1.55570.21411410.208427412882100
1.5557-1.61130.1871420.186327492891100
1.6113-1.67580.18491420.179927412883100
1.6758-1.75210.20081420.173527422884100
1.7521-1.84440.18671430.164927772920100
1.8444-1.960.19221420.15927522894100
1.96-2.11130.2071430.173227742917100
2.1113-2.32370.18391440.174627692913100
2.3237-2.65980.18471440.181227812925100
2.6598-3.35060.19041450.176928072952100
3.3506-33.28390.18951500.174329023052100

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