[English] 日本語
Yorodumi
- PDB-6gbu: Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in c... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of caveolin-mediated endocytosis / postsynaptic endocytic zone / positive regulation of growth hormone secretion / regulation of actin filament polymerization / regulation of modification of postsynaptic actin cytoskeleton / neuromuscular synaptic transmission / clathrin-dependent endocytosis ...stereocilium shaft / clathrin-dependent synaptic vesicle endocytosis / positive regulation of Arp2/3 complex-mediated actin nucleation / positive regulation of caveolin-mediated endocytosis / postsynaptic endocytic zone / positive regulation of growth hormone secretion / regulation of actin filament polymerization / regulation of modification of postsynaptic actin cytoskeleton / neuromuscular synaptic transmission / clathrin-dependent endocytosis / membrane organization / apical dendrite / postsynaptic actin cytoskeleton / phosphatidylinositol-3,4-bisphosphate binding / proline-rich region binding / regulation of postsynapse organization / regulation of small GTPase mediated signal transduction / anchoring junction / endosomal transport / NRAGE signals death through JNK / intracellular vesicle / positive regulation of dendritic spine development / RHOQ GTPase cycle / positive regulation of actin filament polymerization / exocytosis / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / neuromuscular junction / recycling endosome / intracellular protein localization / nuclear envelope / Cargo recognition for clathrin-mediated endocytosis / G alpha (12/13) signalling events / lamellipodium / protein transport / Clathrin-mediated endocytosis / presynaptic membrane / dendritic spine / molecular adaptor activity / intracellular signal transduction / neuronal cell body / calcium ion binding / glutamatergic synapse / 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 / : / EH domain / 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 / : / EH domain / 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 / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more