[English] 日本語
Yorodumi
- PDB-1k8r: Crystal structure of Ras-Bry2RBD complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k8r
TitleCrystal structure of Ras-Bry2RBD complex
Components
  • Protein kinase byr2
  • Transforming protein P21/H-RAS-1
KeywordsSIGNALING PROTEIN / signal transduction / cancer / GTPase / ubiquitin fold
Function / homology
Function and homology information


induction of conjugation with cellular fusion / Oxidative Stress Induced Senescence / pheromone response MAPK cascade / division septum / mitogen-activated protein kinase kinase kinase / cell tip / phospholipase C activator activity / GTPase complex / positive regulation of ruffle assembly / oncogene-induced cell senescence ...induction of conjugation with cellular fusion / Oxidative Stress Induced Senescence / pheromone response MAPK cascade / division septum / mitogen-activated protein kinase kinase kinase / cell tip / phospholipase C activator activity / GTPase complex / positive regulation of ruffle assembly / oncogene-induced cell senescence / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / cell division site / defense response to protozoan / p38MAPK cascade / 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 / positive regulation of protein targeting to membrane / Activated NTRK2 signals through RAS / MAP kinase kinase kinase activity / SHC1 events in ERBB4 signaling / Signalling to RAS / adipose tissue development / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / 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 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / JNK cascade / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / EGFR Transactivation by Gastrin / positive regulation of GTPase activity / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / positive regulation of MAP kinase activity / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / animal organ morphogenesis / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / cellular response to gamma radiation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / endocytosis / Regulation of RAS by GAPs / RAS processing / chemotaxis / Signaling by RAF1 mutants / Negative regulation of MAPK pathway
Similarity search - Function
Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / SAM domain profile. / small GTPase Ras family profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / SAM domain profile. / small GTPase Ras family profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / Protein kinase byr2
Similarity search - Component
Biological speciesHomo sapiens (human)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsScheffzek, K. / Gruenewald, P. / Wohlgemuth, S. / Kabsch, W. / Tu, H. / Wigler, M. / Wittinghofer, A. / Herrmann, C.
CitationJournal: Structure / Year: 2001
Title: The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast.
Authors: Scheffzek, K. / Grunewald, P. / Wohlgemuth, S. / Kabsch, W. / Tu, H. / Wigler, M. / Wittinghofer, A. / Herrmann, C.
History
DepositionOct 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _software.name / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transforming protein P21/H-RAS-1
B: Protein kinase byr2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8484
Polymers31,3012
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.030, 139.030, 112.800
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Transforming protein P21/H-RAS-1


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: GTP-binding/catalytic domain, residues 1-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Hras or Hras1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P01112
#2: Protein Protein kinase byr2


Mass: 12426.270 Da / Num. of mol.: 1 / Fragment: Ras binding domain (RBD), residues 71-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: BYR2 or STE8 or SPBC1D7.05 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P28829, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-25 mg/mlprotein1drop
220-25 %PEG33501reservoir
3100 mMTris-HCl1reservoirpH8.
40.2-0.4 M1reservoirLiSO4

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.54 Å
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Aug 6, 1996 / Details: mirrors
RadiationMonochromator: Ni Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 8592 / Num. obs: 8526 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 18.6
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / Num. unique all: 788 / Rsym value: 0.3 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / Num. measured all: 109981
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 100 % / Num. unique obs: 788 / Num. measured obs: 2634 / Rmerge(I) obs: 0.305

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
X-GENdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5p21

5p21


Resolution: 3→25 Å / Rfactor Rfree error details: 0.01 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: residues 127-139 and 166-180 of Byr2 are ill defined in electron density and are not included in the model
RfactorNum. reflection% reflectionSelection details
Rfree0.305 860 10 %random
Rwork0.235 ---
all0.24 8592 --
obs0.24 8526 99.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.4 Å
Luzzati d res low-25 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 33 0 2012
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 144 10.3 %
Rwork0.297 1253 -
obs-1253 99.9 %
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.236 / Rfactor Rfree: 0.312
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.375
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
LS refinement shell
*PLUS
Highest resolution: 3 Å / Rfactor Rfree: 0.35 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.297

+
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://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