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- PDB-6h5t: Intersectin SH3A short isoform -

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Basic information

Entry
Database: PDB / ID: 6h5t
TitleIntersectin SH3A short isoform
ComponentsIntersectin-1
KeywordsENDOCYTOSIS / SH3 domain / intersectin 1 / splice isoform
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. / SH3 Domains / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / EF-hand, calcium binding motif / Src homology 3 domains / SH3 type barrels. / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / ACETATE ION / Intersectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.689 Å
AuthorsDriller, J.H. / Gerth, F. / Freund, C. / Wahl, M.C. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB958 Germany
CitationJournal: Structure / Year: 2019
Title: Exon Inclusion Modulates Conformational Plasticity and Autoinhibition of the Intersectin 1 SH3A Domain.
Authors: Gerth, F. / Japel, M. / Sticht, J. / Kuropka, B. / Schmitt, X.J. / Driller, J.H. / Loll, B. / Wahl, M.C. / Pagel, K. / Haucke, V. / Freund, C.
History
DepositionJul 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2019Group: Data collection / Category: pdbx_database_proc
Revision 1.3Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Aug 21, 2019Group: Data collection / Database references / Category: pdbx_related_exp_data_set

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intersectin-1
B: Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5269
Polymers21,4662
Non-polymers1,0607
Water3,045169
1
A: Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2845
Polymers10,7331
Non-polymers5514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2424
Polymers10,7331
Non-polymers5093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.792, 86.792, 141.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-902-

CL

21B-1029-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 10733.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITSN1, ITSN, SH3D1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q15811

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H36O9
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (v/v) polyethylene glycol 550 mono-methyl ether, 100 mM MES-NaOH at pH 6.5, and 10 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.689→50 Å / Num. obs: 30662 / % possible obs: 99.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 28.6 Å2 / Rrim(I) all: 0.083 / Net I/σ(I): 17
Reflection shellResolution: 1.689→1.79 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4848 / Rrim(I) all: 0.96 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.689→30.692 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.09
RfactorNum. reflection% reflection
Rfree0.1908 1533 5 %
Rwork0.1756 --
obs0.1763 30640 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.689→30.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 25 169 1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141177
X-RAY DIFFRACTIONf_angle_d1.2451600
X-RAY DIFFRACTIONf_dihedral_angle_d20.101716
X-RAY DIFFRACTIONf_chiral_restr0.086156
X-RAY DIFFRACTIONf_plane_restr0.009211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6886-1.74310.28051370.27922589X-RAY DIFFRACTION99
1.7431-1.80540.28881380.23832620X-RAY DIFFRACTION100
1.8054-1.87770.24631370.21482600X-RAY DIFFRACTION100
1.8777-1.96310.21351360.18812579X-RAY DIFFRACTION100
1.9631-2.06660.19711380.18262626X-RAY DIFFRACTION100
2.0666-2.1960.19341390.18312630X-RAY DIFFRACTION100
2.196-2.36550.19081380.16712638X-RAY DIFFRACTION100
2.3655-2.60350.181410.16982665X-RAY DIFFRACTION100
2.6035-2.97990.17681390.17972648X-RAY DIFFRACTION100
2.9799-3.75340.20031420.16562703X-RAY DIFFRACTION100
3.7534-30.69670.16131480.15762809X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.76391.1807-0.31592.70150.11182.6513-0.1061-0.0478-0.3527-0.0347-0.0009-0.05910.4008-0.10390.09030.256-0.01630.04870.1527-0.00350.167139.648325.910658.1821
22.45751.1064-0.1013.45080.03492.00090.02630.1003-0.0267-0.064-0.00410.38220.0371-0.0872-0.03330.1354-0.0134-0.01140.1332-0.03140.210929.871631.529835.4267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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