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- PDB-6gbu: Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in c... -

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Basic information

Entry
Database: PDB / ID: 6gbu
TitleCrystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with the fourth SH3 domain of ITSN1 (SH3d)
Components
  • F-BAR and double SH3 domains protein 2
  • Intersectin-1
KeywordsENDOCYTOSIS / SH3-SH3 complex
Function / homology
Function and homology information


stereocilium shaft / clathrin-dependent synaptic vesicle endocytosis / positive regulation of Arp2/3 complex-mediated actin nucleation / neuromuscular synaptic transmission / regulation of actin filament polymerization / clathrin-dependent endocytosis / membrane organization / phosphatidylinositol-3,4-bisphosphate binding / proline-rich region binding / regulation of small GTPase mediated signal transduction ...stereocilium shaft / clathrin-dependent synaptic vesicle endocytosis / positive regulation of Arp2/3 complex-mediated actin nucleation / neuromuscular synaptic transmission / regulation of actin filament polymerization / clathrin-dependent endocytosis / membrane organization / phosphatidylinositol-3,4-bisphosphate binding / proline-rich region binding / regulation of small GTPase mediated signal transduction / anchoring junction / endosomal transport / intracellular vesicle / positive regulation of actin filament polymerization / NRAGE signals death through JNK / RHOQ GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / neuromuscular junction / recycling endosome / protein localization / G alpha (12/13) signalling events / protein transport / Cargo recognition for clathrin-mediated endocytosis / lamellipodium / nuclear envelope / Clathrin-mediated endocytosis / presynaptic membrane / molecular adaptor activity / intracellular signal transduction / neuron projection / calcium ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
F-BAR and double SH3 domains protein 2 / FCHSD, SH3 domain 1 / FCHSD2, SH3 domain 2 / 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 ...F-BAR and double SH3 domains protein 2 / FCHSD, SH3 domain 1 / FCHSD2, SH3 domain 2 / 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 / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / AH/BAR domain superfamily / 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. / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / SH3 type barrels. / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
F-BAR and double SH3 domains protein 2 / Intersectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å
AuthorsAlmeida-Souza, L. / Frank, R. / Garcia-Nafria, J. / Colussi, A. / Gunawardana, N. / Johnson, C.M. / Yu, M. / Howard, G. / Andrews, B. / Vallis, Y. / McMahon, H.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105178795 United Kingdom
European Molecular Biology Organization United Kingdom
CitationJournal: Cell / Year: 2018
Title: A Flat BAR Protein Promotes Actin Polymerization at the Base of Clathrin-Coated Pits.
Authors: Leonardo Almeida-Souza / Rene A W Frank / Javier García-Nafría / Adeline Colussi / Nushan Gunawardana / Christopher M Johnson / Minmin Yu / Gillian Howard / Byron Andrews / Yvonne Vallis / Harvey T McMahon /
Abstract: Multiple proteins act co-operatively in mammalian clathrin-mediated endocytosis (CME) to generate endocytic vesicles from the plasma membrane. The principles controlling the activation and ...Multiple proteins act co-operatively in mammalian clathrin-mediated endocytosis (CME) to generate endocytic vesicles from the plasma membrane. The principles controlling the activation and organization of the actin cytoskeleton during mammalian CME are, however, not fully understood. Here, we show that the protein FCHSD2 is a major activator of actin polymerization during CME. FCHSD2 deletion leads to decreased ligand uptake caused by slowed pit maturation. FCHSD2 is recruited to endocytic pits by the scaffold protein intersectin via an unusual SH3-SH3 interaction. Here, its flat F-BAR domain binds to the planar region of the plasma membrane surrounding the developing pit forming an annulus. When bound to the membrane, FCHSD2 activates actin polymerization by a mechanism that combines oligomerization and recruitment of N-WASP to PI(4,5)P, thus promoting pit maturation. Our data therefore describe a molecular mechanism for linking spatiotemporally the plasma membrane to a force-generating actin platform guiding endocytic vesicle maturation.
History
DepositionApr 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
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_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-BAR and double SH3 domains protein 2
B: Intersectin-1
C: F-BAR and double SH3 domains protein 2
D: Intersectin-1
F: Intersectin-1
H: Intersectin-1
E: F-BAR and double SH3 domains protein 2
G: F-BAR and double SH3 domains protein 2


Theoretical massNumber of molelcules
Total (without water)57,2088
Polymers57,2088
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.984, 186.984, 186.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32H
42F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A3 - 63
2113C3 - 63
3113E3 - 63
4113G3 - 63
1123B3 - 65
2123D3 - 65
3123H3 - 65
4123F3 - 65

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.65904, 0.304883, -0.687541), (-0.252169, 0.771666, 0.583902), (0.708574, 0.558192, -0.431677)32.13382, -32.72882, 60.4436
3given(0.879275, 0.359092, -0.312935), (0.219548, -0.888582, -0.402766), (-0.422699, 0.285438, -0.860146)30.79948, -29.98079, 63.72425
4given(-0.182501, -0.188873, 0.964894), (-0.086061, -0.97454, -0.207038), (0.979432, -0.120824, 0.1616)-28.13025, -46.24257, 17.17419

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Components

#1: Protein
F-BAR and double SH3 domains protein 2 / Carom / SH3 multiple domains protein 3


Mass: 7048.674 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCHSD2, KIAA0769, SH3MD3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: O94868
#2: Protein
Intersectin-1 / SH3 domain-containing protein 1A / SH3P17


Mass: 7253.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITSN1, ITSN, SH3D1A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q15811
Has protein modificationY

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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: 4.76 Å3/Da / Density % sol: 74.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.5M ammonium sulfate, 10% Glycerol, Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.44→132.2 Å / Num. obs: 13008 / % possible obs: 99.4 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 27.1
Reflection shellResolution: 3.44→3.53 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DL7, 1UE9

2dl7

1ue9


Resolution: 3.44→132.2 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24673 1437 9.9 %RANDOM
Rwork0.20788 ---
obs0.2118 13008 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 142.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.44→132.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 0 0 3581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023672
X-RAY DIFFRACTIONr_bond_other_d00.023262
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9575009
X-RAY DIFFRACTIONr_angle_other_deg3.85837553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2145464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31625.366164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26215524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.8831512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214165
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02743
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.70515.0141882
X-RAY DIFFRACTIONr_mcbond_other11.715.0141882
X-RAY DIFFRACTIONr_mcangle_it17.37922.4722338
X-RAY DIFFRACTIONr_mcangle_other17.37822.4752339
X-RAY DIFFRACTIONr_scbond_it11.63214.9071789
X-RAY DIFFRACTIONr_scbond_other11.63314.9031787
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other17.31722.2522671
X-RAY DIFFRACTIONr_long_range_B_refined20.9783831
X-RAY DIFFRACTIONr_long_range_B_other20.9793832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A276loose positional0.165
11C276loose positional0.195
11E276loose positional0.295
11G276loose positional0.175
22B518loose positional0.135
22D518loose positional0.085
22H518loose positional0.095
22F518loose positional0.155
11A245tight thermal53.590.5
11C245tight thermal43.080.5
11E245tight thermal49.780.5
11G245tight thermal48.490.5
22B365tight thermal24.610.5
22D365tight thermal13.990.5
22H365tight thermal22.690.5
22F365tight thermal17.170.5
11A276loose thermal46.1810
11C276loose thermal34.6410
11E276loose thermal38.1710
11G276loose thermal43.6210
22B518loose thermal21.910
22D518loose thermal13.6810
22H518loose thermal21.1510
22F518loose thermal15.4910
LS refinement shellResolution: 3.445→3.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 98 -
Rwork0.337 884 -
obs--93.79 %

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