[English] 日本語
Yorodumi
- PDB-7oi5: Crystal structure of AP2 Mu2 - FCHO2 chimera (GST cleaved) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oi5
TitleCrystal structure of AP2 Mu2 - FCHO2 chimera (GST cleaved)
ComponentsAP-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: 2.61 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 / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: AP-2 complex subunit mu,F-BAR domain only protein 2
D: AP-2 complex subunit mu,F-BAR domain only protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0265
Polymers78,7502
Non-polymers2763
Water28816
1
B: AP-2 complex subunit mu,F-BAR domain only protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5593
Polymers39,3751
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: AP-2 complex subunit mu,F-BAR domain only protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4672
Polymers39,3751
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.046, 55.380, 167.735
Angle α, β, γ (deg.)90.000, 109.050, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein AP-2 complex subunit mu,F-BAR domain only protein 2 / 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: 39374.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Homo sapiens (human)
Gene: Ap2m1, FCHO2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P84092, UniProt: Q0JRZ9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: 20% w/v PEG 3350, 0.2 M Sodium phosphate dibasic dehydrate pH 9.1. The crystal was cryo-protected by soaking in mother liquor supplemented with 25% glycerol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2019
RadiationMonochromator: 0.91589 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.61→79.27 Å / Num. obs: 31089 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 49.031 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.068 / Rrim(I) all: 0.177 / Net I/σ(I): 6.6
Reflection shellResolution: 2.61→2.65 Å / Rmerge(I) obs: 1.576 / Mean I/σ(I) obs: 1 / Num. unique obs: 1543 / CC1/2: 0.374 / Rpim(I) all: 0.693 / Rrim(I) all: 1.725 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PHENIX1.19rc1_4016refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phaser

Resolution: 2.61→79.27 Å / SU ML: 0.402 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 37.3155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2972 3014 5.04 %
Rwork0.2384 56774 -
obs0.2414 29463 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.33 Å2
Refinement stepCycle: LAST / Resolution: 2.61→79.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4635 0 18 16 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394746
X-RAY DIFFRACTIONf_angle_d0.72776373
X-RAY DIFFRACTIONf_chiral_restr0.0507694
X-RAY DIFFRACTIONf_plane_restr0.0096801
X-RAY DIFFRACTIONf_dihedral_angle_d6.9433629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.650.39721150.39492589X-RAY DIFFRACTION98.87
2.65-2.690.42131620.37092570X-RAY DIFFRACTION99.24
2.69-2.740.43491580.3672555X-RAY DIFFRACTION98.73
2.74-2.790.45831580.37122558X-RAY DIFFRACTION99.05
2.79-2.840.4666990.35492597X-RAY DIFFRACTION99.7
2.84-2.90.39481290.3512634X-RAY DIFFRACTION99.5
2.9-2.960.39781310.32862508X-RAY DIFFRACTION99.66
2.97-3.030.43861570.31092629X-RAY DIFFRACTION99.61
3.03-3.110.31961290.28632535X-RAY DIFFRACTION99.48
3.11-3.190.38141070.27862610X-RAY DIFFRACTION98.91
3.19-3.290.34211550.29542551X-RAY DIFFRACTION99.34
3.29-3.390.31771470.27592606X-RAY DIFFRACTION99.57
3.39-3.520.29361650.23782529X-RAY DIFFRACTION99.67
3.52-3.660.29561170.22022606X-RAY DIFFRACTION99.6
3.66-3.820.29821220.22482582X-RAY DIFFRACTION99.82
3.82-4.020.31061280.22452655X-RAY DIFFRACTION99.82
4.02-4.280.26751450.19532573X-RAY DIFFRACTION99.82
4.28-4.610.25341420.1812606X-RAY DIFFRACTION99.78
4.61-5.070.21861340.15822537X-RAY DIFFRACTION99.85
5.07-5.80.25551500.18812588X-RAY DIFFRACTION99.74
5.8-7.310.27841440.21872559X-RAY DIFFRACTION99.82
7.31-79.270.21081200.21912597X-RAY DIFFRACTION99.31

+
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