[English] 日本語
Yorodumi
- PDB-3sem: SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sem
TitleSEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR
Components
  • SEX MUSCLE ABNORMAL PROTEIN 5
  • SH3 PEPTOID INHIBITOR
KeywordsSIGNALING PROTEIN/INHIBITOR / SH3 DOMAIN / INHIBITORS / PEPTOIDS / PROTEIN-PROTEIN RECOGNITION / PROLINE-RICH MOTIFS / SIGNAL TRANSDUCTION / SIGNALING PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / SHC-mediated cascade:FGFR1 / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling ...Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / SHC-mediated cascade:FGFR1 / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / PI-3K cascade:FGFR4 / Insulin receptor signalling cascade / MET activates RAS signaling / MET activates PI3K/AKT signaling / RHOU GTPase cycle / FLT3 Signaling / PIP3 activates AKT signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / PI3K events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / EGFR Transactivation by Gastrin / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / regulation of nematode larval development / Negative regulation of MET activity / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / Regulation of signaling by CBL / regulation of vulval development / Clathrin-mediated endocytosis / regulation of cell projection organization / COP9 signalosome / male genitalia development / epidermal growth factor receptor binding / muscle organ development / regulation of MAPK cascade / phosphotyrosine residue binding / regulation of cell migration / epidermal growth factor receptor signaling pathway / signal transduction / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily ...Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Sex muscle abnormal protein 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNguyen, J.T. / Turck, C.W. / Cohen, F.E. / Zuckermann, R.N. / Lim, W.A.
CitationJournal: Science / Year: 1998
Title: Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors.
Authors: Nguyen, J.T. / Turck, C.W. / Cohen, F.E. / Zuckermann, R.N. / Lim, W.A.
History
DepositionNov 2, 1998Processing site: RCSB
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Sep 13, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SEX MUSCLE ABNORMAL PROTEIN 5
B: SEX MUSCLE ABNORMAL PROTEIN 5
C: SH3 PEPTOID INHIBITOR
D: SH3 PEPTOID INHIBITOR


Theoretical massNumber of molelcules
Total (without water)16,1784
Polymers16,1784
Non-polymers00
Water50428
1
A: SEX MUSCLE ABNORMAL PROTEIN 5
C: SH3 PEPTOID INHIBITOR


Theoretical massNumber of molelcules
Total (without water)8,0892
Polymers8,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area4370 Å2
MethodPISA
2
B: SEX MUSCLE ABNORMAL PROTEIN 5
D: SH3 PEPTOID INHIBITOR


Theoretical massNumber of molelcules
Total (without water)8,0892
Polymers8,0892
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-6 kcal/mol
Surface area4370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.050, 68.530, 35.020
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9816, 0.113, 0.1539), (0.1137, -0.9935, 0.004), (0.1534, 0.0135, -0.9881)
Vector: -10.9315, 80.6364, 84.6888)

-
Components

#1: Protein SEX MUSCLE ABNORMAL PROTEIN 5


Mass: 7000.690 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SH3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29355
#2: Protein/peptide SH3 PEPTOID INHIBITOR


Mass: 1088.328 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.49 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 50 %sat / Common name: ammonium phosphate

-
Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 61158 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.083
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rsym value: 0.434 / % possible all: 64.2
Reflection
*PLUS
Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 64.2 % / Rmerge(I) obs: 0.434

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SEM

1sem


Resolution: 2.2→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.31 655 10.4 %
Rwork0.248 --
obs0.248 6292 96 %
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 28 1084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.124
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
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.354 65 9.9 %
Rwork0.361 649 -

+
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