[English] 日本語
Yorodumi
- PDB-7jih: HRAS A59E GppNHp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jih
TitleHRAS A59E GppNHp
ComponentsGTPase HRas
KeywordsONCOPROTEIN / Mutant Cancer GTPase
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 / 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 / : / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / 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 / Ras activation upon Ca2+ influx through NMDA receptor / myelination / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / 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 epithelial cell proliferation / positive regulation of GTPase activity / VEGFR2 mediated 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 / positive regulation of MAP kinase activity / regulation of long-term neuronal synaptic plasticity / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / endocytosis / 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 / GDP binding / chemotaxis / MAPK cascade / cellular senescence / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.989 Å
AuthorsJohnson, C.W. / Haigis, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA230718 United States
American Cancer Society30428-PF-17-066-01-TBG United States
Citation
Journal: Mol.Cell / Year: 2022
Title: Regulation of GTPase function by autophosphorylation.
Authors: Johnson, C.W. / Seo, H.S. / Terrell, E.M. / Yang, M.H. / KleinJan, F. / Gebregiworgis, T. / Gasmi-Seabrook, G.M.C. / Geffken, E.A. / Lakhani, J. / Song, K. / Bashyal, P. / Popow, O. / Paulo, ...Authors: Johnson, C.W. / Seo, H.S. / Terrell, E.M. / Yang, M.H. / KleinJan, F. / Gebregiworgis, T. / Gasmi-Seabrook, G.M.C. / Geffken, E.A. / Lakhani, J. / Song, K. / Bashyal, P. / Popow, O. / Paulo, J.A. / Liu, A. / Mattos, C. / Marshall, C.B. / Ikura, M. / Morrison, D.K. / Dhe-Paganon, S. / Haigis, K.M.
#1: Journal: To Be Published
Title: Characterization of KRAS4B A59E and A59T oncogenic alleles suggest a novel small GTPase function
Authors: Johnson, C.W. / Haigis, K.M.
History
DepositionJul 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTPase HRas
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1448
Polymers37,8662
Non-polymers1,2776
Water1,838102
1
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5724
Polymers18,9331
Non-polymers6393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5724
Polymers18,9331
Non-polymers6393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.675, 49.832, 57.320
Angle α, β, γ (deg.)90.000, 117.810, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 18933.227 Da / Num. of mol.: 2 / Mutation: A59E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P01112
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Starting concentration of HRAS A59T GppNHp was 18.1mg/mL in buffer containing 20mM HEPES, 50mM NaCl, 20mM MgCl2 and 1mM DTT at pH 7.5. Used a 24-well plate sealed with Vaseline and total ...Details: Starting concentration of HRAS A59T GppNHp was 18.1mg/mL in buffer containing 20mM HEPES, 50mM NaCl, 20mM MgCl2 and 1mM DTT at pH 7.5. Used a 24-well plate sealed with Vaseline and total well volumes of 0.402mL. Hanging drops were 0.001mL mother liquor to 0.001mL protein. Mother liquor contained 2.6mM NaCl, 1mM MgCl2, 15.7mM HEPES (pH7.5), 2.5mM DTT, 9.95mM Ca(OAc)2, and 19.9% PEG 3350.

-
Data collection

DiffractionMean temperature: 173.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.989→50 Å / Num. obs: 15450 / % possible obs: 80.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.18 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.051 / Rrim(I) all: 0.098 / Χ2: 0.949 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.989-2.021.40.598630.5970.5260.8010.216.7
2.02-2.061.40.5881210.7520.4710.7590.26112.6
2.06-2.11.40.3982470.8440.3120.510.32326.1
2.1-2.141.50.4743920.680.3610.6020.42641.1
2.14-2.191.80.3795680.8560.280.4760.45958.8
2.19-2.242.10.3297260.9020.2350.4080.45876.1
2.24-2.32.50.328690.8720.2160.3890.50490.5
2.3-2.362.90.2869240.9190.1840.3430.47196.4
2.36-2.433.30.2589430.9310.1610.3060.49198.8
2.43-2.513.60.2469460.9410.1450.2870.5699.6
2.51-2.63.60.1999640.9630.1160.2320.54799.8
2.6-2.73.70.1659490.9650.0960.1920.55999.9
2.7-2.823.70.1529730.980.0880.1770.60299.9
2.82-2.973.80.1159540.9870.0670.1330.62599.6
2.97-3.163.80.0949530.9910.0550.1090.81899.2
3.16-3.43.70.089720.9920.0470.0931.04699.6
3.4-3.743.70.0669530.9950.0390.0771.1699.5
3.74-4.293.60.0569640.9950.0340.0661.43798.8
4.29-5.43.50.0589710.9930.0370.0691.96898.5
5.4-503.50.069980.9950.0390.0732.45398.4

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIX1.11.1-2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K8Y

3k8y


Resolution: 1.989→29.17 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 1575 10.21 %random selection
Rwork0.196 13845 --
obs0.202 15420 80.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.85 Å2 / Biso mean: 35.3086 Å2 / Biso min: 17.62 Å2
Refinement stepCycle: final / Resolution: 1.989→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 78 102 2605
Biso mean--33.85 34.55 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072533
X-RAY DIFFRACTIONf_angle_d13435
X-RAY DIFFRACTIONf_chiral_restr0.049394
X-RAY DIFFRACTIONf_plane_restr0.005436
X-RAY DIFFRACTIONf_dihedral_angle_d10.9791509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.989-2.05290.3854190.33441349
2.0529-2.12630.3497430.281346429
2.1263-2.21140.33411030.264991759
2.2114-2.3120.30991590.2395137488
2.312-2.43380.30421780.2283151698
2.4338-2.58620.2931730.22751569100
2.5862-2.78580.26711720.22041586100
2.7858-3.06580.28631830.21061555100
3.0658-3.50880.24581840.1845156399
3.5088-4.41830.21131720.1627158399
4.4183-29.170.22871890.1793158498

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more