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- PDB-6dee: Crystal structure of the C-terminus of Homo sapiens SPIN90 (SH3-p... -

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Basic information

Entry
Database: PDB / ID: 6dee
TitleCrystal structure of the C-terminus of Homo sapiens SPIN90 (SH3-protein interacting with Nck), residues 306-722
ComponentsNCK-interacting protein with SH3 domain
KeywordsENDOCYTOSIS / partially active form / N-terminally truncated SPIN90 / 6 and half armadillo repeats / part of middle segment / activates Arp2-3 complex / not full activity
Function / homology
Function and homology information


Arp2/3 complex binding / intermediate filament / regulation of postsynapse assembly / RHO GTPases Activate WASPs and WAVEs / cytoskeletal protein binding / cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of neuron projection development / SH3 domain binding / Regulation of actin dynamics for phagocytic cup formation ...Arp2/3 complex binding / intermediate filament / regulation of postsynapse assembly / RHO GTPases Activate WASPs and WAVEs / cytoskeletal protein binding / cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of neuron projection development / SH3 domain binding / Regulation of actin dynamics for phagocytic cup formation / endocytosis / postsynapse / glutamatergic synapse / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
NCK-interacting protein with SH3 domain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsNolen, B.J. / Luan, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)R01GM092917 United States
CitationJournal: EMBO J. / Year: 2018
Title: Structure of the nucleation-promoting factor SPIN90 bound to the actin filament nucleator Arp2/3 complex.
Authors: Luan, Q. / Liu, S.L. / Helgeson, L.A. / Nolen, B.J.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NCK-interacting protein with SH3 domain


Theoretical massNumber of molelcules
Total (without water)46,9741
Polymers46,9741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18500 Å2
Unit cell
Length a, b, c (Å)98.504, 98.504, 81.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NCK-interacting protein with SH3 domain / 54 kDa VacA-interacting protein / 54 kDa vimentin-interacting protein / VIP54 / 90 kDa SH3 protein ...54 kDa VacA-interacting protein / 54 kDa vimentin-interacting protein / VIP54 / 90 kDa SH3 protein interacting with Nck / AF3p21 / Dia-interacting protein 1 / DIP-1 / Diaphanous protein-interacting protein / SH3 adapter protein SPIN90 / WASP-interacting SH3-domain protein / WISH / Wiskott-Aldrich syndrome protein-interacting protein


Mass: 46973.594 Da / Num. of mol.: 1 / Fragment: UNP residues 306-722
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCKIPSD, AF3P21, SPIN90 / Plasmid: pGv67
Details (production host): N-terminal GST-fusion with TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9NZQ3

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, pH 6, 100 mM magnesium sulfate, 1.5% PEG6000
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791829 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2014 / Details: Sagittal focusing 2nd crystal horizontal focusing
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. obs: 8213 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.122 / Rsym value: 0.113 / Χ2: 1.489 / Net I/σ(I): 22.5
Reflection shellResolution: 3.04→3.09 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 405 / CC1/2: 0.764 / Rpim(I) all: 0.609 / Χ2: 0.978 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-30002.3.6data reduction
HKL-30002.3.6data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6DED

6ded


Resolution: 3.04→42.196 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.16
RfactorNum. reflection% reflectionSelection details
Rfree0.3081 822 10.01 %random selection
Rwork0.2593 ---
obs0.2642 8212 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.04→42.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 0 0 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022603
X-RAY DIFFRACTIONf_angle_d0.5133555
X-RAY DIFFRACTIONf_dihedral_angle_d10.469829
X-RAY DIFFRACTIONf_chiral_restr0.018455
X-RAY DIFFRACTIONf_plane_restr0.002460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0269-3.21650.42381310.33491175X-RAY DIFFRACTION98
3.2165-3.46470.42571350.311217X-RAY DIFFRACTION100
3.4647-3.81320.3461350.27871212X-RAY DIFFRACTION100
3.8132-4.36440.32871370.25351234X-RAY DIFFRACTION100
4.3644-5.49680.28391390.27061250X-RAY DIFFRACTION100
5.4968-42.19980.26111450.231302X-RAY DIFFRACTION98

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