[English] 日本語
Yorodumi
- PDB-8t5g: SOS2 co-crystal structure with fragment bound (compound 12) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t5g
TitleSOS2 co-crystal structure with fragment bound (compound 12)
ComponentsSon of sevenless homolog 2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / Interleukin-15 signaling / Activation of RAC1 / NRAGE signals death through JNK / regulation of T cell proliferation / B cell homeostasis / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / insulin receptor signaling pathway ...regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / Interleukin-15 signaling / Activation of RAC1 / NRAGE signals death through JNK / regulation of T cell proliferation / B cell homeostasis / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / insulin receptor signaling pathway / G alpha (12/13) signalling events / Ras protein signal transduction / protein heterodimerization activity / plasma membrane / cytosol
Similarity search - Function
Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain ...Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / : / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Histone-fold / PH-like domain superfamily
Similarity search - Domain/homology
TACRINE / Son of sevenless homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsGunn, R.J. / Lawson, J.D. / Ivetac, A. / Ulaganathan, T. / Coulombe, R. / Fethiere, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of Five SOS2 Fragment Hits with Binding Modes Determined by SOS2 X-Ray Cocrystallography.
Authors: Smith, C.R. / Chen, D. / Christensen, J.G. / Coulombe, R. / Fethiere, J. / Gunn, R.J. / Hollander, J. / Jones, B. / Ketcham, J.M. / Khare, S. / Kuehler, J. / Lawson, J.D. / Marx, M.A. / ...Authors: Smith, C.R. / Chen, D. / Christensen, J.G. / Coulombe, R. / Fethiere, J. / Gunn, R.J. / Hollander, J. / Jones, B. / Ketcham, J.M. / Khare, S. / Kuehler, J. / Lawson, J.D. / Marx, M.A. / Olson, P. / Pearson, K.E. / Ren, C. / Tsagris, D. / Ulaganathan, T. / Van't Veer, I. / Wang, X. / Ivetac, A.
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Son of sevenless homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0317
Polymers57,3711
Non-polymers6616
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.576, 52.339, 60.932
Angle α, β, γ (deg.)84.84, 75.48, 75.95
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Son of sevenless homolog 2 / SOS-2


Mass: 57370.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07890
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-THA / TACRINE


Mass: 198.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: 10% Peg 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.92→43.9 Å / Num. obs: 40046 / % possible obs: 97 % / Redundancy: 3.6 % / CC1/2: 0.99 / Net I/σ(I): 8.43
Reflection shellResolution: 1.92→1.97 Å / Num. unique obs: 2819 / CC1/2: 0.27

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata processing
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EIE

6eie


Resolution: 1.92→43.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.55 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24032 1919 4.8 %RANDOM
Rwork0.19835 ---
obs0.20039 38129 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.152 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0.11 Å20.12 Å2
2--0.37 Å2-1.21 Å2
3----1.17 Å2
Refinement stepCycle: 1 / Resolution: 1.92→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 39 202 4080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133984
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173755
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.6545392
X-RAY DIFFRACTIONr_angle_other_deg1.2921.5738727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13921.532235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60815733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9971535
X-RAY DIFFRACTIONr_chiral_restr0.0720.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0823.8811847
X-RAY DIFFRACTIONr_mcbond_other3.0833.8781846
X-RAY DIFFRACTIONr_mcangle_it4.3385.7972305
X-RAY DIFFRACTIONr_mcangle_other4.3375.82306
X-RAY DIFFRACTIONr_scbond_it3.8664.352137
X-RAY DIFFRACTIONr_scbond_other3.8654.3512138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8766.3413085
X-RAY DIFFRACTIONr_long_range_B_refined8.66146.1134624
X-RAY DIFFRACTIONr_long_range_B_other8.6646.1124625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å
RfactorNum. reflection% reflection
Rfree0.35 129 -
Rwork0.35 2682 -
obs--92.01 %

+
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