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- PDB-121p: STRUKTUR UND GUANOSINTRIPHOSPHAT-HYDROLYSEMECHANISMUS DES C-TERMI... -

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Basic information

Entry
Database: PDB / ID: 121p
TitleSTRUKTUR UND GUANOSINTRIPHOSPHAT-HYDROLYSEMECHANISMUS DES C-TERMINAL VERKUERZTEN MENSCHLICHEN KREBSPROTEINS P21-H-RAS
ComponentsH-RAS P21 PROTEIN
KeywordsONCOGENE PROTEIN
Function / homologySmall GTP-binding protein domain / Signalling to RAS / SHC-related events triggered by IGF1R / DAP12 signaling / EGFR Transactivation by Gastrin / Tie2 Signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / SHC1 events in EGFR signaling / GRB2 events in EGFR signaling ...Small GTP-binding protein domain / Signalling to RAS / SHC-related events triggered by IGF1R / DAP12 signaling / EGFR Transactivation by Gastrin / Tie2 Signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / SHC1 events in EGFR signaling / GRB2 events in EGFR signaling / p38MAPK events / Signaling by SCF-KIT / NCAM signaling for neurite out-growth / SHC1 events in ERBB4 signaling / SHC1 events in ERBB2 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Activation of RAS in B cells / SOS-mediated signalling / small GTPase Ras family profile. / Ras family / P-loop containing nucleoside triphosphate hydrolase / Small GTPase superfamily, Ras-type / FCERI mediated MAPK activation / EPHB-mediated forward signaling / Signaling by RAS mutants / SHC-mediated cascade:FGFR4 / Signaling by moderate kinase activity BRAF mutants / Negative regulation of MAPK pathway / MAP2K and MAPK activation / RAF/MAP kinase cascade / RAF activation / Regulation of RAS by GAPs / Signaling by FGFR1 in disease / Signaling by FGFR4 in disease / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / Ras activation upon Ca2+ influx through NMDA receptor / FRS-mediated FGFR3 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR1 / Constitutive Signaling by EGFRvIII / CD209 (DC-SIGN) signaling / VEGFR2 mediated cell proliferation / Small GTPase / Signaling by high-kinase activity BRAF mutants / Signaling by BRAF and RAF fusions / Activated NTRK3 signals through RAS / Activated NTRK2 signals through FRS2 and FRS3 / Activated NTRK2 signals through RAS / Signaling by FGFR3 point mutants in cancer / Signaling by FGFR3 fusions in cancer / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Insulin receptor signalling cascade / Paradoxical activation of RAF signaling by kinase inactive BRAF / RAS signaling downstream of NF1 loss-of-function variants / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of ruffle assembly / positive regulation of miRNA metabolic process / positive regulation of wound healing / negative regulation of GTPase activity / T-helper 1 type immune response / response to isolation stress / positive regulation of Ras protein signal transduction / cellular senescence / defense response to protozoan / mitotic cell cycle checkpoint / positive regulation of actin cytoskeleton reorganization / intrinsic apoptotic signaling pathway / positive regulation of protein targeting to membrane / positive regulation of phospholipase C activity / positive regulation of DNA replication / animal organ morphogenesis / positive regulation of JNK cascade / regulation of long-term neuronal synaptic plasticity / positive regulation of interferon-gamma production / GDP binding / positive regulation of epithelial cell proliferation / cellular response to gamma radiation / ephrin receptor signaling pathway / protein heterooligomerization / positive regulation of GTPase activity / stimulatory C-type lectin receptor signaling pathway / cell cycle arrest / endocytosis / Ras protein signal transduction / positive regulation of MAP kinase activity / chemotaxis / T cell receptor signaling pathway / positive regulation of MAPK cascade / negative regulation of neuron apoptotic process / protein C-terminus binding / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / glutamatergic synapse / MAPK cascade / negative regulation of gene expression
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / 1.54 Å resolution
AuthorsKrengel, U. / Scheffzek, K. / Scherer, A. / Kabsch, W. / Wittinghofer, A. / Pai, E.F.
Citation
Journal: Thesis / Year: 1991
Title: Struktur Und Guanosintriphosphat-Hydrolysemechanismus Des C-Terminal Verkuerzten Menschlichen Krebsproteins P21-H-Ras
Authors: Krengel, U.
#1: Journal: Nato Asi Ser.,Ser.A / Year: 1991
Title: The Three-Dimensional Structure of P21 in the Catalytically Active Conformation and Analysis of Oncogenic Mutants
Authors: Krengel, U. / Schlichting, I. / Scheidig, A. / Frech, M. / John, J. / Lautwein, A. / Wittinghofer, F. / Kabsch, W. / Pai, E.F.
#2: Journal: Embo J. / Year: 1990
Title: Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 Angstroms Resolution: Implications for the Mechanism of GTP Hydrolysis
Authors: Pai, E.F. / Krengel, U. / Petsko, G.A. / Goody, R.S. / Kabsch, W. / Wittinghofer, A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 6, 1991 / Release: Jan 31, 1994
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 31, 1994Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-RAS P21 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4213
Polyers18,8751
Non-polymers5462
Water3,513195
1
A: H-RAS P21 PROTEIN
hetero molecules

A: H-RAS P21 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8416
Polyers37,7502
Non-polymers1,0914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
γ
α
β
Length a, b, c (Å)40.200, 40.200, 161.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP 32 2 1
Atom site foot note1: RESIDUES 61 - 64 (GLN - GLU - GLU - TYR) ADOPT SEVERAL CONFORMATIONS IN THE CRYSTAL. THE COORDINATES GIVEN APPROXIMATE ONE OF THESE. THE ELECTRON DENSITY FOR THIS PART OF THE STRUCTURE IS NOT AS WELL DEFINED AS FOR THE REST OF THE STRUCTURE.

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Components

#1: Protein/peptide H-RAS P21 PROTEIN


Mass: 18875.191 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / References: UniProt: P01112
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Formula: C11H18N5O13P3 / Comment: GMP-PCP (energy-carrying molecule analogue) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Formula: H2O / Water
Compound detailsSECONDARY STRUCTURE ELEMENTS HAVE BEEN ASSIGNED ACCORDING TO THE PROGRAM DSSP (W.KABSCH AND C. ...SECONDARY STRUCTURE ELEMENTS HAVE BEEN ASSIGNED ACCORDING TO THE PROGRAM DSSP (W.KABSCH AND C.SANDER, 1983, BIOPOLYMERS 22:2577-2637).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 / Density percent sol: 38.32 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefineDetails: RESIDUES 61 - 64 (GLN - GLU - GLU - TYR) ADOPT SEVERAL CONFORMATIONS IN THE CRYSTAL. THE COORDINATES GIVEN APPROXIMATE ONE OF THESE. THE ELECTRON DENSITY FOR THIS PART OF THE STRUCTURE IS NOT AS WELL DEFINED AS FOR THE REST OF THE STRUCTURE.
Least-squares processR factor R work: 0.195 / R factor obs: 0.195 / Highest resolution: 1.54 Å
Refine hist #LASTHighest resolution: 1.54 Å
Number of atoms included #LASTProtein: 1322 / Nucleic acid: 0 / Ligand: 33 / Solvent: 195 / Total: 1550
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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