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- PDB-1sem: STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQ... -

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Basic information

Entry
Database: PDB / ID: 1sem
TitleSTRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS
Components
  • 10-RESIDUE PROLINE-RICH PEPTIDE FROM MSOS (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG)
  • SEM-5
KeywordsSIGNAL TRANSDUCTION PROTEIN / SRC-HOMOLOGY 3 (SH3) DOMAIN / PEPTIDE-BINDING PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR
Function / homology
Function and homology information


Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / : / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling ...Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / : / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / PI-3K cascade:FGFR4 / RHO GTPases Activate WASPs and WAVEs / Negative regulation of MET activity / 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 / EGFR downregulation / PI3K events in ERBB2 signaling / EGFR Transactivation by Gastrin / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Cargo recognition for clathrin-mediated endocytosis / regulation of cell projection organization / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / regulation of nematode larval development / Clathrin-mediated endocytosis / regulation of vulval development / male genitalia development / COP9 signalosome / muscle organ development / epidermal growth factor receptor binding / regulation of MAPK cascade / regulation of cell migration / phosphotyrosine residue binding / 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 / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily ...Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLim, W.A. / Richards, F.M. / Fox, R.O.
Citation
Journal: Nature / Year: 1994
Title: Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains.
Authors: Lim, W.A. / Richards, F.M. / Fox, R.O.
#1: Journal: Nature / Year: 1993
Title: The Sh2 and SH3 Domains of Mammalian Grb2 Couple the Egf Receptor to the Ras Activator Msos1
Authors: Rozakis-Adcock, M. / Fernley, R. / Wade, J. / Pawson, T. / Bowtell, D.
#2: Journal: Nature / Year: 1992
Title: C. Elegans Cell-Signalling Gene Sem-5 Encodes a Protein with Sh2 and SH3 Domains
Authors: Clark, S.G. / Stern, M.J. / Horvitz, H.R.
History
DepositionMar 28, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SEM-5
B: SEM-5
C: 10-RESIDUE PROLINE-RICH PEPTIDE FROM MSOS (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG)
D: 10-RESIDUE PROLINE-RICH PEPTIDE FROM MSOS (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG)


Theoretical massNumber of molelcules
Total (without water)15,8004
Polymers15,8004
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-15 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.912, 68.410, 35.029
Angle α, β, γ (deg.)90.00, 94.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SEM-5


Mass: 6799.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: GRB2 / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: P29355
#2: Protein/peptide 10-RESIDUE PROLINE-RICH PEPTIDE FROM MSOS (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG)


Mass: 1100.339 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Source detailsMOLECULE_NAME: MSOS, 10-RESIDUE PEPTIDE (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG). PEPTIDE IS FROM ...MOLECULE_NAME: MSOS, 10-RESIDUE PEPTIDE (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG). PEPTIDE IS FROM BIOLOGICAL SEQUENCE, BUT IS CHEMICALLY SYNTHESIZED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
215 mMsodium acetate1drop
352.5 %satammonium sulfate1reservoir
4100 mMTris-HCl1reservoir
55 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 24, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 6912 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→7 Å / σ(F): 2
Details: SSBOND CRYSTALS GROWN IN THE PRESENCE OF DTT; DISULFIDE BOND THOUGHT TO FORM AFTER INITIAL EXPOSURE TO X-RAYS; CAUSED STABLE SHIFT IN UNIT CELL DIMENSIONS.
RfactorNum. reflection
Rwork0.189 -
obs0.189 6912
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 0 67 1128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.54
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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