[English] 日本語
Yorodumi
- PDB-9btn: Structure of human SHOC2 in complex with a cyclic peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9btn
TitleStructure of human SHOC2 in complex with a cyclic peptide
Components
  • Leucine-rich repeat protein SHOC-2
  • cyclic peptide
KeywordsSTRUCTURAL PROTEIN / SHOC2 / RAS / PP1C / MAPK / Inhibitor / Complex
Function / homology
Function and homology information


cellular response to growth hormone stimulus / negative regulation of neural precursor cell proliferation / protein phosphatase type 1 complex / volume-sensitive anion channel activity / nerve growth factor signaling pathway / cyclic-GMP-AMP transmembrane import across plasma membrane / protein phosphatase 1 binding / protein phosphatase regulator activity / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling ...cellular response to growth hormone stimulus / negative regulation of neural precursor cell proliferation / protein phosphatase type 1 complex / volume-sensitive anion channel activity / nerve growth factor signaling pathway / cyclic-GMP-AMP transmembrane import across plasma membrane / protein phosphatase 1 binding / protein phosphatase regulator activity / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of Ras protein signal transduction / regulation of MAPK cascade / negative regulation of neuron differentiation / fibroblast growth factor receptor signaling pathway / positive regulation of neuron differentiation / RAF activation / positive regulation of neuron projection development / protein phosphatase binding / intracellular signal transduction / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich repeat protein SHOC-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsHauseman, Z.J. / Dhembi, A. / King, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Nature / Year: 2025
Title: Targeting the SHOC2-RAS interaction in RAS-mutant cancers.
Authors: Hauseman, Z.J. / Stauffer, F. / Beyer, K.S. / Molle, S. / Cavicchioli, E. / Marchand, J.R. / Fodor, M. / Viscomi, J. / Dhembi, A. / Katz, S. / Faggion, B. / Lanter, M. / Kerr, G. / ...Authors: Hauseman, Z.J. / Stauffer, F. / Beyer, K.S. / Molle, S. / Cavicchioli, E. / Marchand, J.R. / Fodor, M. / Viscomi, J. / Dhembi, A. / Katz, S. / Faggion, B. / Lanter, M. / Kerr, G. / Schildknecht, D. / Handl, C. / Maddalo, D. / Pissot Soldermann, C. / Brady, J. / Shrestha, O. / Nguyen, Z. / Leder, L. / Cremosnik, G. / Lopez Romero, S. / Hassiepen, U. / Stams, T. / Linder, M. / Galli, G.G. / Guthy, D.A. / King, D.A. / Maira, S.M. / Thoma, C.R. / Ehmke, V. / Tordella, L.
History
DepositionMay 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine-rich repeat protein SHOC-2
L: cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6523
Polymers58,5602
Non-polymers921
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-5 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.764, 69.567, 200.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Leucine-rich repeat protein SHOC-2 / Protein soc-2 homolog / Protein sur-8 homolog


Mass: 56737.582 Da / Num. of mol.: 1 / Fragment: residues 80-582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHOC2, KIAA0862 / Plasmid: pFastbac1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UQ13
#2: Protein/peptide cyclic peptide


Mass: 1822.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M Hepes pH 7.5, 35% v/v pentaerythritol propoxylate 5/4 PO/OH (PP 5/4 PO/OH), 0.2M KCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.039→100.17 Å / Num. obs: 35606 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 31.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.153 / Net I/σ(I): 14.4
Reflection shellResolution: 2.039→2.046 Å / Redundancy: 13.4 % / Num. unique obs: 344 / Rsym value: 1.772 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata processing
PHENIXphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→34.78 Å / SU ML: 0.2498 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2521 1804 5.07 %
Rwork0.2035 33758 -
obs0.206 35562 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.53 Å2
Refinement stepCycle: LAST / Resolution: 2.04→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 135 209 4247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00174101
X-RAY DIFFRACTIONf_angle_d0.49445557
X-RAY DIFFRACTIONf_chiral_restr0.0385667
X-RAY DIFFRACTIONf_plane_restr0.0027708
X-RAY DIFFRACTIONf_dihedral_angle_d20.13681563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.36981280.30542513X-RAY DIFFRACTION99.92
2.09-2.160.33851300.29662586X-RAY DIFFRACTION99.63
2.16-2.230.31141330.26212519X-RAY DIFFRACTION99.77
2.23-2.30.29761470.23772551X-RAY DIFFRACTION99.85
2.3-2.40.31131310.22852578X-RAY DIFFRACTION99.85
2.4-2.510.30061380.21762538X-RAY DIFFRACTION99.85
2.51-2.640.2711360.21592575X-RAY DIFFRACTION99.96
2.64-2.80.27991370.2182598X-RAY DIFFRACTION99.96
2.8-3.020.29091550.23012585X-RAY DIFFRACTION99.96
3.02-3.320.27551520.21882605X-RAY DIFFRACTION99.93
3.32-3.80.23771160.20022643X-RAY DIFFRACTION100
3.8-4.790.18651470.14772661X-RAY DIFFRACTION99.96
4.79-34.780.2161540.18482806X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 4.42663522428 Å / Origin y: -7.22063981594 Å / Origin z: -32.0104244838 Å
111213212223313233
T0.352165908622 Å2-0.0182330229394 Å2-0.0192625146585 Å2-0.255605074504 Å2-0.0147770902375 Å2--0.267618378846 Å2
L0.248596450826 °20.0541746914774 °20.0184490527787 °2-0.328251729903 °2-0.151833326063 °2--0.761983637788 °2
S-0.00254204312716 Å °-0.00652683136449 Å °0.020745486151 Å °0.114691300425 Å °-0.0245937541707 Å °0.00976006229309 Å °-0.121177282352 Å °0.00506959039662 Å °2.08577942484E-6 Å °
Refinement TLS groupSelection details: all

+
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