[English] 日本語
Yorodumi
- PDB-7oit: Crystal structure of AP2 Mu2 in complex with FCHO2 WxxPhi motif (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oit
TitleCrystal structure of AP2 Mu2 in complex with FCHO2 WxxPhi motif (P3221 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 / presynaptic endocytic zone membrane / clathrin adaptor complex / clathrin coat assembly / clathrin-dependent endocytosis / clathrin-coated vesicle / phosphatidylserine binding / synaptic vesicle endocytosis / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding ...membrane invagination / presynaptic endocytic zone membrane / clathrin adaptor complex / clathrin coat assembly / clathrin-dependent endocytosis / clathrin-coated vesicle / phosphatidylserine binding / synaptic vesicle endocytosis / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / protein localization to plasma membrane / intracellular protein transport / endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / lipid binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
F-BAR domain only protein 2 / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. ...F-BAR domain only protein 2 / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Fes/CIP4, and EFC/F-BAR homology domain / 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: 1.65 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: AP-2 complex subunit mu
BBB: F-BAR domain only protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0843
Polymers33,9922
Non-polymers921
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.364, 66.364, 161.556
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein AP-2 complex subunit mu


Mass: 32758.363 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: A0A140TAH5
#2: Protein/peptide F-BAR domain only protein 2


Mass: 1233.370 Da / Num. of mol.: 1
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20mM Sodium formate; 20mM Ammonium acetate; 20mM Sodium citrate tribasic dihydrate; 20mM Sodium potassium tartrate tetrahydrate; 20mM Sodium oxamate, 100mM Imidazole MES monohydrate pH6.5 , ...Details: 20mM Sodium formate; 20mM Ammonium acetate; 20mM Sodium citrate tribasic dihydrate; 20mM Sodium potassium tartrate tetrahydrate; 20mM Sodium oxamate, 100mM Imidazole MES monohydrate pH6.5 , 20% v/v Glycerol; 10% w/v PEG 4000

-
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: Jul 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→57.47 Å / Num. obs: 50587 / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.019 / Net I/σ(I): 19
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 17 % / Rmerge(I) obs: 2.696 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2463 / Rpim(I) all: 0.668 / Rrim(I) all: 2.779 / % possible all: 100

-
Processing

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

Resolution: 1.65→57.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.854 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.202 2538 5.026 %
Rwork0.1832 47957 -
all0.184 --
obs-50495 99.939 %
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: 32.847 Å2
Baniso -1Baniso -2Baniso -3
1--0.097 Å2-0.048 Å2-0 Å2
2---0.097 Å20 Å2
3---0.314 Å2
Refinement stepCycle: LAST / Resolution: 1.65→57.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 6 247 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132218
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172203
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.6462989
X-RAY DIFFRACTIONr_angle_other_deg1.3881.5845082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.935266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94820.796113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05215419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5931519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
X-RAY DIFFRACTIONr_nbd_refined0.1960.2290
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21926
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21025
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21231
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2197
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1520.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.22
X-RAY DIFFRACTIONr_nbd_other0.1270.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.213
X-RAY DIFFRACTIONr_mcbond_it3.0222.9871070
X-RAY DIFFRACTIONr_mcbond_other2.9692.9771068
X-RAY DIFFRACTIONr_mcangle_it4.1924.4531331
X-RAY DIFFRACTIONr_mcangle_other4.1544.4511331
X-RAY DIFFRACTIONr_scbond_it4.5113.621148
X-RAY DIFFRACTIONr_scbond_other4.513.6191148
X-RAY DIFFRACTIONr_scangle_it6.8495.1821657
X-RAY DIFFRACTIONr_scangle_other6.855.1811657
X-RAY DIFFRACTIONr_lrange_it9.04135.8752365
X-RAY DIFFRACTIONr_lrange_other8.90335.0672298
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
1.65-1.6930.3421670.31735120.31936820.7570.75899.91850.312
1.693-1.7390.2721790.28834270.28736070.8510.82799.97230.271
1.739-1.790.291940.26132670.26334670.8510.87999.82690.237
1.79-1.8450.2471980.24331820.24433870.9050.89599.79330.213
1.845-1.9050.2431600.20831210.2132870.9180.92599.81750.178
1.905-1.9720.211470.19530310.19631820.9410.9499.87430.167
1.972-2.0460.2311410.18729390.18930820.9290.94799.93510.163
2.046-2.130.2191380.19128570.19329960.9440.94799.96660.165
2.13-2.2240.2071300.17927100.18128400.9490.9531000.158
2.224-2.3330.2161500.17825760.1827260.9440.9571000.158
2.333-2.4590.1841410.1724830.17126240.9580.961000.151
2.459-2.6070.2021070.16823480.1724550.9520.9591000.151
2.607-2.7870.2141320.17422070.17623390.9480.9591000.156
2.787-3.010.1881110.17220690.17321800.9590.961000.159
3.01-3.2960.1881120.17219010.17320130.9590.9651000.164
3.296-3.6840.234780.17817530.1818310.9520.9631000.173
3.684-4.2510.178880.16815480.16816360.9640.9631000.169
4.251-5.1990.168810.14913170.1513980.9750.9761000.154
5.199-7.3220.193580.20610630.20511210.9740.9691000.207
7.322-57.4730.155260.1996450.1976720.970.95799.85120.2

+
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://pdbjlvh1.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