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- PDB-7ohi: FCHO1-peptide-AP2 alpha ear complex -

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Basic information

Entry
Database: PDB / ID: 7ohi
TitleFCHO1-peptide-AP2 alpha ear complex
Components
  • AP-2 complex subunit alpha-2
  • F-BAR domain only protein 1
KeywordsENDOCYTOSIS / clathrin-mediated endocytosis (CME) / protein recycling / plasma membrane
Function / homology
Function and homology information


LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / AP-2 adaptor complex binding / VLDLR internalisation and degradation / Recycling pathway of L1 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization ...LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / AP-2 adaptor complex binding / VLDLR internalisation and degradation / Recycling pathway of L1 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / regulation of hematopoietic stem cell differentiation / protein serine/threonine kinase binding / clathrin-coated pit / vesicle-mediated transport / Neutrophil degranulation / phosphatidylinositol binding / secretory granule / intracellular protein transport / cytoplasmic side of plasma membrane / kinase binding / disordered domain specific binding / positive regulation of T cell activation / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / T cell receptor signaling pathway / cytoplasmic vesicle / postsynapse / protein domain specific binding / protein-containing complex binding / protein kinase binding / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
F-BAR domain only protein 1 / FCHo1, F-BAR domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain ...F-BAR domain only protein 1 / FCHo1, F-BAR domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / AH/BAR domain superfamily / TBP domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
F-BAR domain only protein 1 / AP-2 complex subunit alpha-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsZaccai, N.R. / Kelly, B.T. / Evans, P.R. / Owen, D.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust207455/Z/17/Z United Kingdom
Citation
Journal: Sci Adv / Year: 2022
Title: FCHO controls AP2's initiating role in endocytosis through a PtdIns(4,5)P-dependent switch.
Authors: Nathan R Zaccai / Zuzana Kadlecova / Veronica Kane Dickson / Kseniya Korobchevskaya / Jan Kamenicky / Oleksiy Kovtun / Perunthottathu K Umasankar / Antoni G Wrobel / Jonathan G G Kaufman / ...Authors: Nathan R Zaccai / Zuzana Kadlecova / Veronica Kane Dickson / Kseniya Korobchevskaya / Jan Kamenicky / Oleksiy Kovtun / Perunthottathu K Umasankar / Antoni G Wrobel / Jonathan G G Kaufman / Sally R Gray / Kun Qu / Philip R Evans / Marco Fritzsche / Filip Sroubek / Stefan Höning / John A G Briggs / Bernard T Kelly / David J Owen / Linton M Traub /
Abstract: Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo adaptor AP2 requires membrane- ...Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo adaptor AP2 requires membrane-localized Fer/Cip4 homology domain-only proteins (FCHO). Here, live-cell enhanced total internal reflection fluorescence-structured illumination microscopy shows that FCHO marks sites of clathrin-coated pit (CCP) initiation, which mature into uniform-sized CCPs comprising a central patch of AP2 and clathrin corralled by an FCHO/Epidermal growth factor potential receptor substrate number 15 (Eps15) ring. We dissect the network of interactions between the FCHO interdomain linker and AP2, which concentrates, orients, tethers, and partially destabilizes closed AP2 at the plasma membrane. AP2's subsequent membrane deposition drives its opening, which triggers FCHO displacement through steric competition with phosphatidylinositol 4,5-bisphosphate, clathrin, cargo, and CME accessory factors. FCHO can now relocate toward a CCP's outer edge to engage and activate further AP2s to drive CCP growth/maturation.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP-2 complex subunit alpha-2
B: F-BAR domain only protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3298
Polymers30,6542
Non-polymers6766
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-67 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.168, 145.487, 88.808
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1004-

SO4

21A-1004-

SO4

31A-1171-

HOH

41A-1293-

HOH

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Components

#1: Protein AP-2 complex subunit alpha-2 / 100 kDa coated vesicle protein C / Adaptor protein complex AP-2 subunit alpha-2 / Adaptor-related ...100 kDa coated vesicle protein C / Adaptor protein complex AP-2 subunit alpha-2 / Adaptor-related protein complex 2 subunit alpha-2 / Alpha-adaptin C / Alpha2-adaptin / Clathrin assembly protein complex 2 alpha-C large chain / Plasma membrane adaptor HA2/AP2 adaptin alpha C subunit


Mass: 28048.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2a2, Adtab / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (plysS) / References: UniProt: P17427
#2: Protein/peptide F-BAR domain only protein 1


Mass: 2605.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14526
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Magnesium sulfate heptahydrate 0.1M MES pH 6.5. The crystal were subsequently cryo-protected with ~20% glycerol final.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.41→47.6 Å / Num. obs: 73320 / % possible obs: 95.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 18.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.062 / Net I/σ(I): 17
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.81 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 2558 / CC1/2: 0.253 / Rpim(I) all: 1.157 / Rrim(I) all: 3.054 / % possible all: 63.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PHENIX1.19rc1_4016refinement
DIALS2.2.4data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b9k

1b9k


Resolution: 1.41→44.4 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9259
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2154 3608 5.06 %
Rwork0.1965 67757 -
obs0.1975 71365 93.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.78 Å2
Refinement stepCycle: LAST / Resolution: 1.41→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 37 202 2323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612180
X-RAY DIFFRACTIONf_angle_d0.90532959
X-RAY DIFFRACTIONf_chiral_restr0.0732328
X-RAY DIFFRACTIONf_plane_restr0.0064388
X-RAY DIFFRACTIONf_dihedral_angle_d13.47290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.4299570.48231079X-RAY DIFFRACTION39
1.43-1.450.4311660.49651441X-RAY DIFFRACTION52.11
1.45-1.470.44611060.44471897X-RAY DIFFRACTION69.19
1.47-1.490.4541290.44892201X-RAY DIFFRACTION79.9
1.49-1.510.38551660.38612464X-RAY DIFFRACTION90.66
1.51-1.540.35891540.34392642X-RAY DIFFRACTION95.43
1.54-1.570.30361440.31412752X-RAY DIFFRACTION99.01
1.57-1.590.29911390.27042743X-RAY DIFFRACTION99.65
1.59-1.620.26761440.24222779X-RAY DIFFRACTION99.9
1.62-1.660.24621400.2352767X-RAY DIFFRACTION100
1.66-1.690.26161640.23042776X-RAY DIFFRACTION100
1.69-1.730.22881460.22182755X-RAY DIFFRACTION100
1.73-1.780.26411300.21982812X-RAY DIFFRACTION99.9
1.78-1.820.25081550.23072757X-RAY DIFFRACTION100
1.82-1.880.25231590.2272762X-RAY DIFFRACTION100
1.88-1.940.23071540.21762779X-RAY DIFFRACTION99.97
1.94-2.010.18451410.18962794X-RAY DIFFRACTION100
2.01-2.090.21681480.18972802X-RAY DIFFRACTION100
2.09-2.180.19021390.18782804X-RAY DIFFRACTION100
2.18-2.30.20261320.1962813X-RAY DIFFRACTION100
2.3-2.440.24351590.19682805X-RAY DIFFRACTION100
2.44-2.630.19491610.19112804X-RAY DIFFRACTION100
2.63-2.90.19971530.18822819X-RAY DIFFRACTION100
2.9-3.310.24231160.19392860X-RAY DIFFRACTION100
3.32-4.180.16241370.15482893X-RAY DIFFRACTION100
4.18-44.40.19051690.17142957X-RAY DIFFRACTION99.52

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