[English] 日本語
Yorodumi
- EMDB-10754: Clathrin with bound beta2 appendage of AP2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10754
TitleClathrin with bound beta2 appendage of AP2
Map dataSharpened map of hexagon bounding clathrin leg enriched in beta-appendage
Sample
  • Complex: Clathrin/AP2 coat assembled on membrane.
    • Complex: Clathrin
      • Protein or peptide: Clathrin heavy chain
      • Protein or peptide: Clathrin heavy chain
      • Protein or peptide: Clathrin light chain
    • Complex: beta2 appendage of AP2 adaptor
      • Protein or peptide: AP-2 complex subunit beta
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / clathrin coat of coated pit / AP-2 adaptor complex ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / clathrin coat of coated pit / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance / clathrin-dependent endocytosis / coronary vasculature development / signal sequence binding / endolysosome membrane / Nef Mediated CD4 Down-regulation / aorta development / clathrin-coated vesicle / ventricular septum development / clathrin binding / Recycling pathway of L1 / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / kidney development / clathrin-coated endocytic vesicle membrane / intracellular protein transport / cytoplasmic side of plasma membrane / endocytic vesicle membrane / disordered domain specific binding / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / postsynapse / Potential therapeutics for SARS / glutamatergic synapse / structural molecule activity / nucleolus / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat ...Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / 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 / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin light chain / Clathrin heavy chain / Nucleolar protein 16 / Clathrin heavy chain / AP-2 complex subunit beta
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human) / Pig (pig)
Methodsubtomogram averaging / cryo EM / Resolution: 9.2 Å
AuthorsKovtun O / Kane Dickson V / Kelly BT / Owen D / Briggs JAG
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust207455/Z/17/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Sci Adv / Year: 2020
Title: Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles.
Authors: Oleksiy Kovtun / Veronica Kane Dickson / Bernard T Kelly / David J Owen / John A G Briggs /
Abstract: Clathrin-mediated endocytosis (CME) is crucial for modulating the protein composition of a cell's plasma membrane. Clathrin forms a cage-like, polyhedral outer scaffold around a vesicle, to which ...Clathrin-mediated endocytosis (CME) is crucial for modulating the protein composition of a cell's plasma membrane. Clathrin forms a cage-like, polyhedral outer scaffold around a vesicle, to which cargo-selecting clathrin adaptors are attached. Adaptor protein complex (AP2) is the key adaptor in CME. Crystallography has shown AP2 to adopt a range of conformations. Here, we used cryo-electron microscopy, tomography, and subtomogram averaging to determine structures, interactions, and arrangements of clathrin and AP2 at the key steps of coat assembly, from AP2 in solution to membrane-assembled clathrin-coated vesicles (CCVs). AP2 binds cargo and PtdIns(4,5) (phosphatidylinositol 4,5-bisphosphate)-containing membranes via multiple interfaces, undergoing conformational rearrangement from its cytosolic state. The binding mode of AP2 β2 appendage into the clathrin lattice in CCVs and buds implies how the adaptor structurally modulates coat curvature and coat disassembly.
History
DepositionMar 12, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateAug 19, 2020-
Current statusAug 19, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6yai
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yai
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10754.png

Downloads & links

-
Map

FileDownload / File: emd_10754.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of hexagon bounding clathrin leg enriched in beta-appendage
Voxel sizeX=Y=Z: 1.78 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.44512126 - 0.6409551
Average (Standard dev.)-0.0000633295 (±0.055856194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 284.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z284.800284.800284.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.4450.641-0.000

-
Supplemental data

-
Mask #1

Fileemd_10754_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unsharpened half-map of hexagon bounding clathrin leg enriched...

Fileemd_10754_half_map_1.map
AnnotationUnsharpened half-map of hexagon bounding clathrin leg enriched in beta2-appendage
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unsharpened half-map of hexagon bounding clathrin leg enriched...

Fileemd_10754_half_map_2.map
AnnotationUnsharpened half-map of hexagon bounding clathrin leg enriched in beta-appendage
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Clathrin/AP2 coat assembled on membrane.

EntireName: Clathrin/AP2 coat assembled on membrane.
Components
  • Complex: Clathrin/AP2 coat assembled on membrane.
    • Complex: Clathrin
      • Protein or peptide: Clathrin heavy chain
      • Protein or peptide: Clathrin heavy chain
      • Protein or peptide: Clathrin light chain
    • Complex: beta2 appendage of AP2 adaptor
      • Protein or peptide: AP-2 complex subunit beta

-
Supramolecule #1: Clathrin/AP2 coat assembled on membrane.

SupramoleculeName: Clathrin/AP2 coat assembled on membrane. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Clathrin/AP coat was formed on the membrane containing cargo signal peptides. The AP2 adaptor lacked hinge and appendage regions in its alpha subunit.

-
Supramolecule #2: Clathrin

SupramoleculeName: Clathrin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3-#4
Details: Clathrin in the clathrin/AP2 coat formed on the membrane
Source (natural)Organism: Sus scrofa (pig) / Organ: brain

-
Supramolecule #3: beta2 appendage of AP2 adaptor

SupramoleculeName: beta2 appendage of AP2 adaptor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: beta2 appendage of the AP2 bound to clathrin to clathrin/AP2 coat formed on the membrane
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Macromolecule #1: Clathrin heavy chain

MacromoleculeName: Clathrin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 187.145125 KDa
SequenceString: MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISADS AIMNPASKVI ALKAGKTLQ IFNIEMKSKM KAHTMTDDVT FWKWISLNTV ALVTDNAVYH WSMEGESQPV KMFDRHSSLA GCQIINYRTD A KQKWLLLT ...String:
MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISADS AIMNPASKVI ALKAGKTLQ IFNIEMKSKM KAHTMTDDVT FWKWISLNTV ALVTDNAVYH WSMEGESQPV KMFDRHSSLA GCQIINYRTD A KQKWLLLT GISAQQNRVV GAMQLYSVDR KVSQPIEGHA ASFAQFKMEG NAEESTLFCF AVRGQAGGKL HIIEVGTPPT GN QPFPKKA VDVFFPPEAQ NDFPVAMQIS EKHDVVFLIT KYGYIHLYDL ETGTCIYMNR ISGETIFVTA PHEATAGIIG VNR KGQVLS VCVEEENIIP YITNVLQNPD LALRMAVRNN LAGAEELFAR KFNALFAQGN YSEAAKVAAN APKGILRTPD TIRR FQSVP AQPGQTSPLL QYFGILLDQG QLNKYESLEL CRPVLQQGRK QLLEKWLKED KLECSEELGD LVKSVDPTLA LSVYL RANV PNKVIQCFAE TGQVQKIVLY AKKVGYTPDW IFLLRNVMRI SPDQGQQFAQ MLVQDEEPLA DITQIVDVFM EYNLIQ QCT AFLLDALKNN RPSEGPLQTR LLEMNLMHAP QVADAILGNQ MFTHYDRAHI AQLCEKAGLL QRALEHFTDL YDIKRAV VH THLLNPEWLV NYFGSLSVED SLECLRAMLS ANIRQNLQIC VQVASKYHEQ LSTQSLIELF ESFKSFEGLF YFLGSIVN F SQDPDVHFKY IQAACKTGQI KEVERICRES NCYDPERVKN FLKEAKLTDQ LPLIIVCDRF DFVHDLVLYL YRNNLQKYI EIYVQKVNPS RLPVVIGGLL DVDCSEDVIK NLILVVRGQF STDELVAEVE KRNRLKLLLP WLEARIHEGC EEPATHNALA KIYIDSNNN PERFLRENPY YDSRVVGKYC EKRDPHLACV AYERGQCDLE LINVCNENSL FKSLSRYLVR RKDPELWGSV L LESNPYRR PLIDQVVQTA LSETQDPEEV SVTVKAFMTA DLPNELIELL EKIVLDNSVF SEHRNLQNLL ILTAIKADRT RV MEYINRL DNYDAPDIAN IAISNELFEE AFAIFRKFDV NTSAVQVLIE HIGNLDRAYE FAERCNEPAV WSQLAKAQLQ KGM VKEAID SYIKADDPSS YMEVVQAANT SGNWEELVKY LQMARKKARE SYVETELIFA LAKTNRLAEL EEFINGPNNA HIQQ VGDRC YDEKMYDAAK LLYNNVSNFG RLASTLVHLG EYQAAVDGAR KANSTRTWKE VCFACVDGKE FRLAQMCGLH IVVHA DELE ELINYYQDRG YFEELITMLE AALGLERAHM GMFTELAILY SKFKPQKMRE HLELFWSRVN IPKVLRAAEQ AHLWAE LVF LYDKYEEYDN AIITMMNHPT DAWKEGQFKD IITKVANVEL YYRAIQFYLE FKPLLLNDLL MVLSPRLDHT RAVNYFS KV KQLPLVKPYL RSVQNHNNKS VNESLNNLFI TEEDYQALRT SIDAYDNFDN ISLAQRLEKH ELIEFRRIAA YLFKGNNR W KQSVELCKKD SLYKDAMQYA SESKDTELAE ELLQWFLQEE KRECFGACLF TCYDLLRPDV VLETAWRHNI MDFAMPYFI QVMKEYLTKV DKLDASESLR KEEEQATETQ

-
Macromolecule #2: AP-2 complex subunit beta

MacromoleculeName: AP-2 complex subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.429457 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: GGYVAPKAVW LPAVKAKGLE ISGTFTHRQG HIYMEMNFTN KALQHMTDFA IQFNKNSFGV IPSTPLAIHT PLMPNQSIDV SLPLNTLGP VMKMEPLNNL QVAVKNNIDV FYFSCLIPLN VLFVEDGKME RQVFLATWKD IPNENELQFQ IKECHLNADT V SSKLQNNN ...String:
GGYVAPKAVW LPAVKAKGLE ISGTFTHRQG HIYMEMNFTN KALQHMTDFA IQFNKNSFGV IPSTPLAIHT PLMPNQSIDV SLPLNTLGP VMKMEPLNNL QVAVKNNIDV FYFSCLIPLN VLFVEDGKME RQVFLATWKD IPNENELQFQ IKECHLNADT V SSKLQNNN VYTIAKRNVE GQDMLYQSLK LTNGIWILAE LRIQPGNPNY TLSLKCRAPE VSQYIYQVYD SILKN

-
Macromolecule #3: Clathrin heavy chain

MacromoleculeName: Clathrin heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 187.117094 KDa
SequenceString: MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISADS AIMNPASKVI ALKAGKTLQ IFNIEMKSKM KAHTMTDDVT FWKWISLNTV ALVTDNAVYH WSMEGESQPV KMFDRHSSLA GCQIINYRTD A KQKWLLLT ...String:
MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISADS AIMNPASKVI ALKAGKTLQ IFNIEMKSKM KAHTMTDDVT FWKWISLNTV ALVTDNAVYH WSMEGESQPV KMFDRHSSLA GCQIINYRTD A KQKWLLLT GISAQQNRVV GAMQLYSVDR KVSQPIEGHA ASFAQFKMEG NAEESTLFCF AVRGQAGGKL HIIEVGTPPT GN QPFPKKA VDVFFPPEAQ NDFPVAMQIS EKHDVVFLIT KYGYIHLYDL ETGTCIYMNR ISGETIFVTA PHEATAGIIG VNR KGQVLS VCVEEENIIP YITNVLQNPD LALRMAVRNN LAGAEELFAR KFNALFAQGN YSEAAKVAAN APKGILRTPD TIRR FQSVP AQPGQTSPLL QYFGILLDQG QLNKYESLEL CRPVLQQGRK QLLEKWLKED KLECSEELGD LVKSVDPTLA LSVYL RANV PNKVIQCFAE TGQVQKIVLY AKKVGYTPDW IFLLRNVMRI SPDQGQQFAQ MLVQDEEPLA DITQIVDVFM EYNLIQ QCT AFLLDALKNN RPSEGPLQTR LLEMNLMHAP QVADAILGNQ MFTHYDRAHI AQLCEKAGLL QRALEHFTDL YDIKRAV VH THLLNPEWLV NYFGSLSVED SLECLRAMLS ANIRQNLQIC VQVASKYHEQ LSTQSLIELF ESFKSFEGLF YFLGSIVN F SQDPDVHFKY IQAACKTGQI KEVERICRES NCYDPERVKN FLKEAKLTDQ LPLIIVCDRF DFVHDLVLYL YRNNLQKYI EIYVQKVNPS RLPVVIGGLL DVDCSEDVIK NLILVVRGQF STDELVAEVE KRNRLKLLLP WLEARIHEGC TEPATHNALA KIYIDSNNN PERFLRENPY YDSRVVGKYC EKRDPHLACV AYERGQCDLE LINVCNENSL FKSLSRYLVR RKDPELWGSV L LESNPYRR PLIDQVVQTA LSETQDPEEV SVTVKAFMTA DLPNELIELL EKIVLDNSVF SEHRNLQNLL ILTAIKADRT RV MEYINRL DNYDAPDIAN IAISNELFEE AFAIFRKFDV NTSAVQVLIE HIGNLDRAYE FAERCNEPAV WSQLAKAQLQ KGM VKEAID SYIKADDPSS YMEVVQAANT SGNWEELVKY LQMARKKARE SYVETELIFA LAKTNRLAEL EEFINGPNNA HIQQ VGDRC YDEKMYDAAK LLYNNVSNFG RLASTLVHLG EYQAAVDGAR KANSTRTWKE VCFACVDGKE FRLAQMCGLH IVVHA DELE ELINYYQDRG YFEELITMLE AALGLERAHM GMFTELAILY SKFKPQKMRE HLELFWSRVN IPKVLRAAEQ AHLWAE LVF LYDKYEEYDN AIITMMNHPT DAWKEGQFKD IITKVANVEL YYRAIQFYLE FKPLLLNDLL MVLSPRLDHT RAVNYFS KV KQLPLVKPYL RSVQNHNNKS VNESLNNLFI TEEDYQALRT SIDAYDNFDN ISLAQRLEKH ELIEFRRIAA YLFKGNNR W KQSVELCKKD SLYKDAMQYA SESKDTELAE ELLQWFLQEE KRECFGACLF TCYDLLRPDV VLETAWRHNI MDFAMPYFI QVMKEYLTKV DKLDASESLR KEEEQATETQ

-
Macromolecule #4: Clathrin light chain

MacromoleculeName: Clathrin light chain / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 25.2185 KDa
SequenceString: MADDFGFFSS SESGAPEVAE EDPAAAFLAQ QESEIAGIEN DEGFGAPAGS QAALAQPGPA SGAGPEDMGT TVNGDVFQDA NGPADGYAA IAQADRLTQE PESIRKWREE QRKRLQELDA ASKVTEQEWR EKAKKDLEEW NQRQSEQVEK NKINNRIADK A FYQQPDAD ...String:
MADDFGFFSS SESGAPEVAE EDPAAAFLAQ QESEIAGIEN DEGFGAPAGS QAALAQPGPA SGAGPEDMGT TVNGDVFQDA NGPADGYAA IAQADRLTQE PESIRKWREE QRKRLQELDA ASKVTEQEWR EKAKKDLEEW NQRQSEQVEK NKINNRIADK A FYQQPDAD IIGYVASEEA FVKESKEETP GTEWEKVAQL CDFNPKSSKQ CKDVSRLRSV LMSLKQTPLS R

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.2
Component:
ConcentrationName
10.0 mMHepes KOH
120.0 mMPotassium Acetate
2.0 mMMagnesium chloride
5.0 mM2-Mercaptoethanol
GridModel: C-flat-2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 291 K / Instrument: LEICA EM GP
Details: The sample was supplemented with 10 nm nanogold fiducials, and 3 ul of the mixture was backside blotted for 3 seconds..
DetailsThe sample (in vitro budding reaction) contained AP2, clathrin and 400 nm extruded liposomes

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 6.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-10 / Number grids imaged: 2 / Average exposure time: 0.2 sec. / Average electron dose: 3.2 e/Å2
Details: The images were collected in movie mode at 10 frames per second
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 58121 / Number images used: 198871 / Reference model: reference-free / Method: geometrically defined initial positions / Software - Name: TOM
Details: To define initial positions of subtomograms, centres and radii of coated vesicles, buds were manually marked in bin4 tomograms. These measurements were used to define spheres. Subtomogram ...Details: To define initial positions of subtomograms, centres and radii of coated vesicles, buds were manually marked in bin4 tomograms. These measurements were used to define spheres. Subtomogram positions were then defined on the surface of these spheres with uniform sampling. The orientations were calculated to be normal to the surfaces of the spheres with random in-plane rotation.
CTF correctionSoftware - Name: NOVACTF (ver. 1.0) / Details: CTF correction in novaCTF with by multiplication
Final 3D classificationNumber classes: 10 / Avg.num./class: 1200 / Software: (Name: PEET, Dynamo)
Details: Principal component analysis (PCA) to sort subtomograms by beta-appendage occupancy. The PCA was performed on wedge-masked difference maps with calculations implemented in MATLAB using code ...Details: Principal component analysis (PCA) to sort subtomograms by beta-appendage occupancy. The PCA was performed on wedge-masked difference maps with calculations implemented in MATLAB using code adapted from PEET and Dynamo packages.
Final angle assignmentType: OTHER / Software: (Name: TOM, AV3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: TOM, AV3) / Number subtomograms used: 12076
DetailsThe images were low pass filtered according to the cumulative radiation dose.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

1xi4


6sct


1e42

chain_id: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: correlation coefficient
Output model

PDB-6yai:
Clathrin with bound beta2 appendage of AP2

+
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