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- PDB-2khn: NMR solution structure of the EH 1 domain from human intersectin-... -

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Basic information

Entry
Database: PDB / ID: 2khn
TitleNMR solution structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646E.
ComponentsIntersectin-1
KeywordsSIGNALING PROTEIN / GFT NMR / high throughput / NESGC / human intersectin-1 / Alternative splicing / Calcium / Cell junction / Cell projection / Coiled coil / Endocytosis / Membrane / Phosphoprotein / SH3 domain / Synapse / Synaptosome / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


clathrin-dependent synaptic vesicle endocytosis / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle ...clathrin-dependent synaptic vesicle endocytosis / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / protein localization / recycling endosome / G alpha (12/13) signalling events / protein transport / Cargo recognition for clathrin-mediated endocytosis / lamellipodium / presynaptic membrane / Clathrin-mediated endocytosis / nuclear envelope / molecular adaptor activity / neuron projection / intracellular signal transduction / calcium ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain ...Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Variant SH3 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. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / EF-hand / Recoverin; domain 1 / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsMills, J.L. / Ghosh, A. / Garcia, E. / Zhang, Q. / Shastry, R. / Foote, E.L. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Mills, J.L. / Ghosh, A. / Garcia, E. / Zhang, Q. / Shastry, R. / Foote, E.L. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646E.
Authors: Mills, J.L. / Ghosh, A. / Garcia, E. / Zhang, Q. / Shastry, R. / Foote, E.L. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionApr 9, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intersectin-1


Theoretical massNumber of molelcules
Total (without water)13,6151
Polymers13,6151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Intersectin-1 / SH3 domain-containing protein 1A / SH3P17


Mass: 13614.548 Da / Num. of mol.: 1 / Fragment: UNP residues 1-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITSN1, ITSN, SH3D1A / Plasmid: pET14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q15811
Sequence detailsAUTHORS STATE THAT THE SEQUENCE DIFFERENCE AT POSITION 14 IS DUE TO STRAIN VARIATION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1413D sim. 15N,13C NOESY
1513D HNCO
161GFT (4,3)D HNCABCA
171GFT (4,3)D CABCA(CO)NH
181GFT (4,3)D arom. (H)CCH
191GFT (4,3)D aliph. (H)CCH
1101GFT (4,3)D HABCAB(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.87 mM [U-98% 13C; U-98% 15N] HR3646E-1, 20 mM MES-2, 200 mM sodium chloride-3, 5 mM calcium chloride-4, 10 mM DTT-5, 0.02 % sodium azide-6, 90% H2O/10% D2O90% H2O/10% D2O
20.81 mM [U-5% 13C; U-98% 15N] HR3646E-7, 20 mM MES-8, 200 mM sodium chloride-9, 5 mM calcium chloride-10, 10 mM DTT-11, 0.02 % sodium azide-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.87 mMHR3646E-1[U-98% 13C; U-98% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
0.81 mMHR3646E-7[U-5% 13C; U-98% 15N]2
20 mMMES-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
Sample conditionsIonic strength: 430 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPSCANGlaserprocessing
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionestructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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