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- PDB-7oiq: Crystal structure of AP2 Mu2 in complex with FCHO2 WxxPhi motif (... -

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Basic information

Entry
Database: PDB / ID: 7oiq
TitleCrystal structure of AP2 Mu2 in complex with FCHO2 WxxPhi motif (C2 crystal form)
Components
  • AP-2 complex subunit mu
  • F-BAR domain only protein 2
KeywordsENDOCYTOSIS / clathrin-mediated endocytosis (CME) / protein recycling / plasma membrane
Function / homology
Function and homology information


membrane invagination / Gap junction degradation / Formation of annular gap junctions / presynaptic endocytic zone membrane / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane ...membrane invagination / Gap junction degradation / Formation of annular gap junctions / presynaptic endocytic zone membrane / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / positive regulation of synaptic vesicle endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / phosphatidylserine binding / positive regulation of receptor internalization / Trafficking of GluR2-containing AMPA receptors / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / protein localization to plasma membrane / intracellular protein transport / terminal bouton / receptor internalization / disordered domain specific binding / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / Clathrin-mediated endocytosis / cytoplasmic vesicle / protein-containing complex assembly / postsynapse / transmembrane transporter binding / lipid binding / glutamatergic synapse / synapse / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
F-BAR domain only protein 2 / GEM-interacting protein-like, FCH domain / Muniscin C-terminal / Muniscin C-terminal mu homology 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. ...F-BAR domain only protein 2 / GEM-interacting protein-like, FCH domain / Muniscin C-terminal / Muniscin C-terminal mu homology 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 complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / AH/BAR domain superfamily
Similarity search - Domain/homology
AP-2 complex subunit mu / F-BAR domain only protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 12, 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 mu
BBB: AP-2 complex subunit mu
CCC: F-BAR domain only protein 2
DDD: F-BAR domain only protein 2


Theoretical massNumber of molelcules
Total (without water)67,9834
Polymers67,9834
Non-polymers00
Water6,305350
1
AAA: AP-2 complex subunit mu
DDD: F-BAR domain only protein 2


  • defined by author&software
  • Evidence: homology
  • 34 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)33,9922
Polymers33,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-6 kcal/mol
Surface area14990 Å2
MethodPISA
2
BBB: AP-2 complex subunit mu
CCC: F-BAR domain only protein 2


  • defined by author&software
  • 34 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)33,9922
Polymers33,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-7 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.888, 64.539, 108.439
Angle α, β, γ (deg.)90.000, 111.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-551-

HOH

21AAA-637-

HOH

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Components

#1: 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: 32758.363 Da / Num. of mol.: 2
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
#2: Protein/peptide F-BAR domain only protein 2


Mass: 1233.370 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCHO2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q0JRZ9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30mM Magnesium chloride hexahydrate, 30mM Calcium chloride dihydrate, 100mM Sodium HEPES MOPS (acid) pH 7.5, 20% v/v Ethylene glycol; 10 % w/v PEG 8000

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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 EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→55.7 Å / Num. obs: 58302 / % possible obs: 89.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 32.287 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.039 / Rrim(I) all: 0.099 / Net I/σ(I): 9.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4 % / Rmerge(I) obs: 1.064 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1599 / Rpim(I) all: 0.577 / Rrim(I) all: 1.221 / % possible all: 49.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19rc1_4016refinement
DIALSdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phaser

Resolution: 1.85→55.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.189 / SU ML: 0.091 / Cross valid method: FREE R-VALUE / ESU R: 0.128 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2087 2932 5.03 %
Rwork0.1859 55363 -
all0.187 --
obs-58295 89.401 %
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: 38.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.632 Å20 Å20.678 Å2
2---1.099 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 0 350 4604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134343
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174344
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.6455847
X-RAY DIFFRACTIONr_angle_other_deg1.2551.58410017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3825520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97420.461217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46915829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8191538
X-RAY DIFFRACTIONr_chiral_restr0.0750.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02989
X-RAY DIFFRACTIONr_nbd_refined0.1690.2552
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23846
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21950
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1560.212
X-RAY DIFFRACTIONr_nbd_other0.1120.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.214
X-RAY DIFFRACTIONr_mcbond_it3.4933.5862104
X-RAY DIFFRACTIONr_mcbond_other3.4663.5822102
X-RAY DIFFRACTIONr_mcangle_it4.9375.3382616
X-RAY DIFFRACTIONr_mcangle_other4.9415.3382616
X-RAY DIFFRACTIONr_scbond_it4.6934.1982239
X-RAY DIFFRACTIONr_scbond_other4.6934.22240
X-RAY DIFFRACTIONr_scangle_it7.0946.0383231
X-RAY DIFFRACTIONr_scangle_other7.0936.043232
X-RAY DIFFRACTIONr_lrange_it9.13640.4084473
X-RAY DIFFRACTIONr_lrange_other9.10439.9734397
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.2721340.29322330.29147670.8190.77849.65390.286
1.898-1.950.2931470.26525970.26646960.8140.82758.43270.251
1.95-2.0060.2471350.24229050.24245130.8780.87267.3610.22
2.006-2.0680.2461610.23534940.23544320.8780.87982.46840.215
2.068-2.1360.2722030.21939830.22142930.8790.89697.50760.197
2.136-2.2110.2551820.20638880.20941100.9030.91399.02680.185
2.211-2.2940.2372050.18937710.19240100.9180.93199.15210.17
2.294-2.3870.2321870.18636550.18938700.9290.94199.27650.168
2.387-2.4930.2491820.18634830.18936870.9240.93799.40330.169
2.493-2.6150.2471850.18133210.18435280.9210.94599.37640.167
2.615-2.7560.2371780.18231610.18533550.9310.94499.52310.171
2.756-2.9220.2141710.18830290.1932130.9430.94599.59540.182
2.922-3.1240.2171530.18328240.18529850.9330.94699.7320.183
3.124-3.3730.2231380.19126700.19228180.9460.95299.64510.198
3.373-3.6940.1931320.19124300.19125650.9550.95499.8830.203
3.694-4.1270.1671140.1722200.1723350.9590.96299.95720.188
4.127-4.7620.1381210.13419550.13420760.9790.9761000.159
4.762-5.8210.171930.15816650.15817580.9710.9761000.184
5.821-8.1880.228740.18813100.1913840.9570.9621000.215
8.188-55.70.244370.2417680.2428080.970.94899.62870.307

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