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- PDB-2jxc: Structure of the EPS15-EH2 Stonin2 Complex -

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Basic information

Entry
Database: PDB / ID: 2jxc
TitleStructure of the EPS15-EH2 Stonin2 Complex
Components
  • Epidermal growth factor receptor substrate 15
  • Stonin-2
KeywordsENDOCYTOSIS/PROTEIN BINDING / endocytosis / Membrane / Phosphorylation / Proto-oncogene / SH3-binding / ENDOCYTOSIS-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


Golgi to endosome transport / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / clathrin adaptor activity / membrane organization / endocytic recycling / aggresome / clathrin-coated vesicle ...Golgi to endosome transport / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / clathrin adaptor activity / membrane organization / endocytic recycling / aggresome / clathrin-coated vesicle / endosomal transport / positive regulation of receptor recycling / regulation of endocytosis / synaptic vesicle endocytosis / polyubiquitin modification-dependent protein binding / hematopoietic progenitor cell differentiation / clathrin-coated pit / vesicle-mediated transport / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / EGFR downregulation / Negative regulation of MET activity / SH3 domain binding / endocytosis / protein transport / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / Clathrin-mediated endocytosis / regulation of cell population proliferation / early endosome membrane / cytoplasmic vesicle / postsynapse / receptor-mediated endocytosis of virus by host cell / symbiont entry into host cell / cadherin binding / neuron projection / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / nucleolus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Stonin homology / Stonin / Stonin-2, N-terminal / Stonin-2 / Stonin 2 / Stonin homology domain (SHD) profile. / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain ...Stonin homology / Stonin / Stonin-2, N-terminal / Stonin-2 / Stonin 2 / Stonin homology domain (SHD) profile. / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Adaptor complexes medium subunit family / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Epidermal growth factor receptor substrate 15 / Stonin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsRumpf, J. / Simon, B. / Jung, N. / Maritzen, T. / Haucke, V. / Sattler, M. / Groemping, Y.
Citation
Journal: Embo J. / Year: 2008
Title: Structure of the Eps15-stonin2 complex provides a molecular explanation for EH-domain ligand specificity.
Authors: Rumpf, J. / Simon, B. / Jung, N. / Maritzen, T. / Haucke, V. / Sattler, M. / Groemping, Y.
#1: Journal: To be Published
Title: 1H, 13C, and 15N Chemical Shift Assignments for the Eps15-Stonin2 complex
Authors: Rumpf, J. / Simon, B. / Groemping, Y. / Sattler, M.
History
DepositionNov 12, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor receptor substrate 15
B: Stonin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0053
Polymers15,9652
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Epidermal growth factor receptor substrate 15 / Protein Eps15 / AF-1p protein


Mass: 10973.713 Da / Num. of mol.: 1 / Fragment: EH 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPS15, AF1P / Plasmid: pGEX6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE 3) / References: UniProt: P42566
#2: Protein/peptide Stonin-2 / Stoned B


Mass: 4991.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STON2, STN2, STNB / Plasmid: pGEX6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE 3) / References: UniProt: Q8WXE9
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CA)CB
1313D C(CO)NH
1413D CBCA(CO)NH
1513D 1H-15N NOESY
1633D 1H-13C NOESY
1713D (H)CCH-TOCSY
1813D H(CCO)NH
1952D 1H-1H NOESY
11023D HNCA
11123D HN(CA)CB
11223D CBCA(CO)NH
11323D C(CO)NH
11423D 1H-15N NOESY
11543D 1H-13C NOESY
11623D (H)CCH-TOCSY
11723D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-99% 13C; U-99% 15N] EH2, 0.5-1 mM Stonin peptide, 2 mM CA, 93% H2O/7% D2O93% H2O/7% D2O
20.5-1 mM EH2, 0.5-1 mM [U-99% 13C; U-99% 15N] Stonin peptide, 2 mM CA, 93% H2O/7% D2O93% H2O/7% D2O
30.5-1 mM [U-99% 13C; U-99% 15N] EH2, 0.5-1 mM Stonin peptide, 2 mM CA, 100% D2O100% D2O
40.5-1 mM EH2, 0.5-1 mM [U-99% 13C; U-99% 15N] Stonin peptide, 2 mM CA, 100% D2O100% D2O
50.6 mM EH2, 0.6 mM Stonin peptide, 2 mM CA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMEH2[U-99% 13C; U-99% 15N]1
0.5 mMStonin peptide1
2 mMCA1
0.5 mMEH22
0.5 mMStonin peptide[U-99% 13C; U-99% 15N]2
2 mMCA2
0.5 mMEH2[U-99% 13C; U-99% 15N]3
0.5 mMStonin peptide3
2 mMCA3
0.5 mMEH24
0.5 mMStonin peptide[U-99% 13C; U-99% 15N]4
2 mMCA4
0.6 mMEH25
0.6 mMStonin peptide5
2 mMCA5
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4Johnson, B.A. et al.chemical shift assignment
TopSpin1.3Bruker Biospincollection
NMRPipeDelaglio, F. et al.processing
CNS1.1Brunger, A.T. et al.refinement
ARIA1.2Linge, J.P. et al.structure solution
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 4320 / NOE intraresidue total count: 1718 / NOE long range total count: 688 / NOE medium range total count: 694 / NOE sequential total count: 820 / Hydrogen bond constraints total count: 32 / Protein chi angle constraints total count: 4 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 68 / Protein psi angle constraints total count: 68
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 4.58 ° / Maximum upper distance constraint violation: 0.44 Å
NMR ensemble rmsDistance rms dev: 0.0298 Å / Distance rms dev error: 0.0006 Å

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