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- PDB-7oho: Crystal structure of AP2 FCHO2 chimera -

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Basic information

Entry
Database: PDB / ID: 7oho
TitleCrystal structure of AP2 FCHO2 chimera
Components(AP-2 complex subunit ...) x 4
KeywordsENDOCYTOSIS / clathrin-mediated endocytosis (CME) / protein recycling / plasma membrane
Function / homology
Function and homology information


membrane invagination / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance ...membrane invagination / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance / Retrograde neurotrophin signalling / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / Recycling pathway of L1 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / Recycling pathway of L1 / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin coat assembly / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / LDL clearance / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / signal sequence binding / coronary vasculature development / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / endolysosome membrane / neurotransmitter secretion / clathrin-coated vesicle / aorta development / ventricular septum development / Neutrophil degranulation / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / positive regulation of endocytosis / positive regulation of receptor internalization / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / vesicle-mediated transport / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / MHC class II antigen presentation / protein serine/threonine kinase binding / VLDLR internalisation and degradation / protein localization to plasma membrane / intracellular protein transport / kidney development / clathrin-coated endocytic vesicle membrane / receptor internalization / kinase binding / cytoplasmic side of plasma membrane / terminal bouton / disordered domain specific binding / synaptic vesicle / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / transmembrane transporter binding / postsynapse / protein domain specific binding / synapse / lipid binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
F-BAR domain only protein 2 / : / GEM-interacting protein-like, FCH domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain ...F-BAR domain only protein 2 / : / GEM-interacting protein-like, FCH domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / AH/BAR domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu / F-BAR domain only protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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 1.1Jun 19, 2024Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: AP-2 complex subunit alpha-2
BBB: AP-2 complex subunit beta,F-BAR domain only protein 2
MMM: AP-2 complex subunit mu
SSS: AP-2 complex subunit sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,6259
Polymers209,5974
Non-polymers1,0285
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19170 Å2
ΔGint-74 kcal/mol
Surface area70340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.040, 122.040, 257.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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AP-2 complex subunit ... , 4 types, 4 molecules AAABBBMMMSSS

#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: 69656.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2a2, Adtab / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P18484
#2: Protein AP-2 complex subunit beta,F-BAR domain only protein 2 / AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta ...AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta / Beta-2-adaptin / Beta-adaptin / Clathrin assembly protein complex 2 beta large chain / Plasma membrane adaptor HA2/AP2 adaptin beta subunit


Mass: 71857.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP2B1, ADTB2, CLAPB1, FCHO2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63010, UniProt: Q0JRZ9
#3: Protein AP-2 complex subunit mu / AP-2 mu chain / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit ...AP-2 mu chain / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit mu / Clathrin assembly protein complex 2 mu medium chain / Clathrin coat assembly protein AP50 / Clathrin coat-associated protein AP50 / Mu2-adaptin / Plasma membrane adaptor AP-2 50 kDa protein


Mass: 51044.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P84092
#4: Protein AP-2 complex subunit sigma / Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / ...Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / Clathrin assembly protein 2 sigma small chain / Clathrin coat assembly protein AP17 / Clathrin coat-associated protein AP17 / Plasma membrane adaptor AP-2 17 kDa protein / Sigma-adaptin 3b / Sigma2-adaptin


Mass: 17038.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2s1, Ap17, Claps2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P62743

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Non-polymers , 2 types, 5 molecules

#5: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3

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Details

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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 18% PEG 12000 0.1M Na/K phosphate pH 6.2 0.2M NaCl 4mM DTT in the presence of 3-fold molar excess of IP6.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.88→66.61 Å / Num. obs: 51118 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 79.944 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.037 / Rrim(I) all: 0.115 / Net I/σ(I): 13.5
Reflection shellResolution: 2.88→2.95 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.803 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3710 / CC1/2: 0.529 / Rpim(I) all: 0.649 / Rrim(I) all: 2.019 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phaser

Resolution: 2.88→61.095 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.925 / SU B: 20.665 / SU ML: 0.379 / Cross valid method: FREE R-VALUE / ESU R Free: 0.425
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2734 2547 4.989 %
Rwork0.1819 48506 -
all0.187 --
obs-51053 99.978 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 96.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.539 Å20.269 Å2-0 Å2
2--0.539 Å20 Å2
3----1.747 Å2
Refinement stepCycle: LAST / Resolution: 2.88→61.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13621 0 60 0 13681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01313914
X-RAY DIFFRACTIONr_bond_other_d0.0020.01713686
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.63818832
X-RAY DIFFRACTIONr_angle_other_deg1.1831.57831475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76951697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39722.49715
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.251152571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1281592
X-RAY DIFFRACTIONr_chiral_restr0.0650.21842
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023111
X-RAY DIFFRACTIONr_nbd_refined0.2240.23342
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.213589
X-RAY DIFFRACTIONr_nbtor_refined0.1670.26552
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.27416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2328
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0810.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.218
X-RAY DIFFRACTIONr_nbd_other0.2570.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.23
X-RAY DIFFRACTIONr_mcbond_it9.07910.0856811
X-RAY DIFFRACTIONr_mcbond_other9.07910.0856810
X-RAY DIFFRACTIONr_mcangle_it13.1615.1198501
X-RAY DIFFRACTIONr_mcangle_other13.1615.128502
X-RAY DIFFRACTIONr_scbond_it8.67610.5047101
X-RAY DIFFRACTIONr_scbond_other8.67510.5047102
X-RAY DIFFRACTIONr_scangle_it12.8615.54710330
X-RAY DIFFRACTIONr_scangle_other12.85915.54810331
X-RAY DIFFRACTIONr_lrange_it16.976119.47415460
X-RAY DIFFRACTIONr_lrange_other16.976119.48115461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.9550.4031930.3353502X-RAY DIFFRACTION99.9729
2.955-3.0360.3541730.2913476X-RAY DIFFRACTION99.9726
3.036-3.1230.3591360.2593379X-RAY DIFFRACTION100
3.123-3.2190.3181610.2473258X-RAY DIFFRACTION100
3.219-3.3250.3211520.2253171X-RAY DIFFRACTION100
3.325-3.4410.3951650.2223062X-RAY DIFFRACTION100
3.441-3.5710.291540.1992948X-RAY DIFFRACTION100
3.571-3.7160.2951390.2052873X-RAY DIFFRACTION99.9668
3.716-3.8810.3141620.1962691X-RAY DIFFRACTION100
3.881-4.0690.3161570.1912659X-RAY DIFFRACTION100
4.069-4.2880.2641390.1692461X-RAY DIFFRACTION100
4.288-4.5470.2231420.1432368X-RAY DIFFRACTION100
4.547-4.860.2691160.1512241X-RAY DIFFRACTION100
4.86-5.2470.2611240.1532056X-RAY DIFFRACTION100
5.247-5.7440.2461100.1631944X-RAY DIFFRACTION100
5.744-6.4160.285690.1771784X-RAY DIFFRACTION100
6.416-7.3970.266940.1551551X-RAY DIFFRACTION100
7.397-9.0320.224740.1451346X-RAY DIFFRACTION100
9.032-12.6570.19530.1321072X-RAY DIFFRACTION100
12.657-61.0950.268340.264664X-RAY DIFFRACTION99.8569

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