[English] 日本語
Yorodumi
- EMDB-45213: AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nano... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45213
TitleAP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map
Map datadeepEMhancer sharpened map
Sample
  • Complex: AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: AP-3 complex subunit delta-1
    • Protein or peptide: AP-3 complex subunit mu-1
    • Protein or peptide: AP-3 complex subunit sigma-1
    • Protein or peptide: Lysosome-associated membrane glycoprotein 1
    • Protein or peptide: AP-3 complex subunit beta-1
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsAdaptor Protein complex / AP-3 / Lysosomal transport / Endosomal transport / Protein trafficking / TRANSPORT PROTEIN
Function / homology
Function and homology information


synaptic vesicle coating / synaptic vesicle budding from endosome / establishment of protein localization to mitochondrial membrane involved in mitochondrial fission / clathrin-coated vesicle cargo loading, AP-3-mediated / skin epidermis development / AP-type membrane coat adaptor complex / synaptic vesicle membrane organization / zinc ion import into lysosome / AP-3 adaptor complex / neurotransmitter receptor transport, postsynaptic endosome to lysosome ...synaptic vesicle coating / synaptic vesicle budding from endosome / establishment of protein localization to mitochondrial membrane involved in mitochondrial fission / clathrin-coated vesicle cargo loading, AP-3-mediated / skin epidermis development / AP-type membrane coat adaptor complex / synaptic vesicle membrane organization / zinc ion import into lysosome / AP-3 adaptor complex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / anterograde synaptic vesicle transport / microvesicle / endosome to melanosome transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Golgi to vacuole transport / synaptic vesicle recycling / postsynaptic recycling endosome / clathrin adaptor complex / platelet dense granule organization / Glycosphingolipid transport / regulation of receptor internalization / melanosome assembly / Intra-Golgi traffic / presynaptic endosome / regulation of Arp2/3 complex-mediated actin nucleation / postsynaptic neurotransmitter receptor internalization / granulocyte differentiation / positive regulation of NK T cell differentiation / Synthesis of PIPs at the Golgi membrane / clathrin-coated vesicle membrane / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / protein targeting to vacuole / GTP-dependent protein binding / protein targeting to lysosome / melanosome organization / respiratory system process / anterograde axonal transport / Nef Mediated CD4 Down-regulation / dendritic spine organization / intracellular zinc ion homeostasis / protein localization to membrane / long-term synaptic depression / protein localization to cell surface / COPI-dependent Golgi-to-ER retrograde traffic / lysosome organization / toll-like receptor signaling pathway / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / cell leading edge / lung morphogenesis / Synthesis of PIPs at the plasma membrane / Association of TriC/CCT with target proteins during biosynthesis / homeostasis of number of cells / intracellular copper ion homeostasis / single fertilization / intracellular transport / hematopoietic progenitor cell differentiation / transport vesicle / COPI-mediated anterograde transport / vesicle-mediated transport / axon cytoplasm / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoplasmic vesicle membrane / sarcomere / small monomeric GTPase / intracellular protein transport / mRNA transcription by RNA polymerase II / protein modification process / cell morphogenesis / cellular response to virus / small GTPase binding / terminal bouton / endocytosis / blood coagulation / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / large ribosomal subunit / presynapse / cytoplasmic vesicle / protein phosphatase binding / spermatogenesis / early endosome / lysosome / neuron projection / endosome membrane / postsynapse / postsynaptic density / structural constituent of ribosome / inflammatory response / translation / protein domain specific binding / Golgi membrane / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / GTP binding / glutamatergic synapse
Similarity search - Function
AP-3 complex subunit sigma / AP-3 complex subunit delta domain, metazoa / AP-3 complex subunit delta-1 / Bovine leukaemia virus receptor (BLVR) / AP-3 complex subunit beta, C-terminal domain / AP-3 complex subunit beta 1, serine-rich domain / : / Clathrin-adaptor complex-3 beta-1 subunit C-terminal / Serine-rich region of AP3B1, clathrin-adaptor complex / AP-3 complex subunit beta-1, C-terminal domain ...AP-3 complex subunit sigma / AP-3 complex subunit delta domain, metazoa / AP-3 complex subunit delta-1 / Bovine leukaemia virus receptor (BLVR) / AP-3 complex subunit beta, C-terminal domain / AP-3 complex subunit beta 1, serine-rich domain / : / Clathrin-adaptor complex-3 beta-1 subunit C-terminal / Serine-rich region of AP3B1, clathrin-adaptor complex / AP-3 complex subunit beta-1, C-terminal domain / Clathrin-adaptor complex-3 beta-1 subunit C-terminal / Adaptor protein complex AP-3, delta subunit / AP-3 complex subunit beta / Adaptor protein complex, sigma subunit / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / ADP-ribosylation factor 1-5 / 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. / : / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Mu homology domain / Mu homology domain (MHD) profile. / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / : / Armadillo-like helical / Small GTP-binding protein domain / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AP-3 complex subunit beta-1 / AP-3 complex subunit delta-1 / Ribosomal protein L22p/L17e / ADP-ribosylation factor 1 / AP-3 complex subunit sigma-1 / AP-3 complex subunit mu-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBegley MC / Baker RW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM150960 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: A structure-based mechanism for initiation of AP-3 coated vesicle formation.
Authors: Matthew Begley / Mahira Aragon / Richard W Baker /
Abstract: Adaptor protein complex-3 (AP-3) mediates cargo sorting from endosomes to lysosomes and lysosome-related organelles. Recently, it was shown that AP-3 adopts a constitutively open conformation ...Adaptor protein complex-3 (AP-3) mediates cargo sorting from endosomes to lysosomes and lysosome-related organelles. Recently, it was shown that AP-3 adopts a constitutively open conformation compared to the related AP-1 and AP-2 coat complexes, which are inactive until undergoing large conformational changes upon membrane recruitment. How AP-3 is regulated is therefore an open question. To understand the mechanism of AP-3 membrane recruitment and activation, we reconstituted human AP-3 and determined multiple structures in the soluble and membrane-bound states using electron cryo-microscopy. Similar to yeast AP-3, human AP-3 is in a constitutively open conformation. To reconstitute AP-3 activation by adenosine di-phosphate (ADP)-ribosylation factor 1 (Arf1), a small guanosine tri-phosphate (GTP)ase, we used lipid nanodiscs to build Arf1-AP-3 complexes on membranes and determined three structures showing the stepwise conformational changes required for formation of AP-3 coated vesicles. First, membrane recruitment is driven by one of two predicted Arf1 binding sites, which flexibly tethers AP-3 to the membrane. Second, cargo binding causes AP-3 to adopt a fixed position and rigidifies the complex, which stabilizes binding for a second Arf1 molecule. Finally, binding of the second Arf1 molecule provides the template for AP-3 dimerization, providing a glimpse into the first step of coat polymerization. We propose coat polymerization only occurs after cargo engagement, thereby linking cargo sorting with assembly of higher-order coat structures. Additionally, we provide evidence for two amphipathic helices in AP-3, suggesting that AP-3 contributes to membrane deformation during coat assembly. In total, these data provide evidence for the first stages of AP-3-mediated vesicle coat assembly.
History
DepositionJun 6, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45213.png

Downloads & links

-
Map

FileDownload / File: emd_45213.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 423.2 Å		1.06 Å/pix.
x 400 pix.
= 423.2 Å		1.06 Å/pix.
x 400 pix.
= 423.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017917362 - 2.148494
Average (Standard dev.)0.00061385497 (±0.01930322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Composite full map

Fileemd_45213_additional_1.map
AnnotationComposite full map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Composite half map 1

Fileemd_45213_half_map_1.map
AnnotationComposite half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Composite half map 2

Fileemd_45213_half_map_2.map
AnnotationComposite half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nano...

EntireName: AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map
Components
  • Complex: AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: AP-3 complex subunit delta-1
    • Protein or peptide: AP-3 complex subunit mu-1
    • Protein or peptide: AP-3 complex subunit sigma-1
    • Protein or peptide: Lysosome-associated membrane glycoprotein 1
    • Protein or peptide: AP-3 complex subunit beta-1
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nano...

SupramoleculeName: AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightTheoretical: 215 KDa

-
Macromolecule #1: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 1 / Details: Q to L mutation at position 71 / Number of copies: 2 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.775812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GNIFANLFKG LFGKKEMRIL MVGLDAAGKT TILYKLKLGE IVTTIPTIGF NVETVEYKNI SFTVWDVGGL DKIRPLWRHY FQNTQGLIF VVDSNDRERV NEAREELMRM LAEDELRDAV LLVFANKQDL PNAMNAAEIT DKLGLHSLRH RNWYIQATCA T SGDGLYEG LDWLSNQLRN QKSL

UniProtKB: ADP-ribosylation factor 1

-
Macromolecule #2: AP-3 complex subunit delta-1

MacromoleculeName: AP-3 complex subunit delta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.381977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALKMVKGSI DRMFDKNLQD LVRGIRNHKE DEAKYISQCI DEIKQELKQD NIAVKANAVC KLTYLQMLGY DISWAAFNII EVMSASKFT FKRIGYLAAS QSFHEGTDVI MLTTNQIRKD LSSPSQYDTG VALTGLSCFV TPDLARDLAN DIMTLMSHTK P YIRKKAVL ...String:
MALKMVKGSI DRMFDKNLQD LVRGIRNHKE DEAKYISQCI DEIKQELKQD NIAVKANAVC KLTYLQMLGY DISWAAFNII EVMSASKFT FKRIGYLAAS QSFHEGTDVI MLTTNQIRKD LSSPSQYDTG VALTGLSCFV TPDLARDLAN DIMTLMSHTK P YIRKKAVL IMYKVFLKYP ESLRPAFPRL KEKLEDPDPG VQSAAVNVIC ELARRNPKNY LSLAPLFFKL MTSSTNNWVL IK IIKLFGA LTPLEPRLGK KLIEPLTNLI HSTSAMSLLY ECVNTVIAVL ISLSSGMPNH SASIQLCVQK LRILIEDSDQ NLK YLGLLA MSKILKTHPK SVQSHKDLIL QCLDDKDESI RLRALDLLYG MVSKKNLMEI VKKLMTHVDK AEGTTYRDEL LTKI IDICS QSNYQYITNF EWYISILVEL TRLEGTRHGH LIAAQMLDVA IRVKAIRKFA VSQMSALLDS AHLLASSTQR NGICE VLYA AAWICGEFSE HLQEPHHTLE AMLRPRVTTL PGHIQAVYVQ NVVKLYASIL QQKEQAGEAE GAQAVTQLMV DRLPQF VQS ADLEVQERAS CILQLVKHIQ KLQAKDVPVA EEVSALFAGE LNPVAPKAQK KVPV

UniProtKB: AP-3 complex subunit delta-1

-
Macromolecule #3: AP-3 complex subunit mu-1

MacromoleculeName: AP-3 complex subunit mu-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.989965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIHSLFLINC SGDIFLEKHW KSVVSQSVCD YFFEAQEKAA DVENVPPVIS TPHHYLISIY RDKLFFVSVI QTEVPPLFVI EFLHRVADT FQDYFGECSE AAIKDNVVIV YELLEEMLDN GFPLATESNI LKELIKPPTI LRSVVNSITG SSNVGDTLPT G QLSNIPWR ...String:
MIHSLFLINC SGDIFLEKHW KSVVSQSVCD YFFEAQEKAA DVENVPPVIS TPHHYLISIY RDKLFFVSVI QTEVPPLFVI EFLHRVADT FQDYFGECSE AAIKDNVVIV YELLEEMLDN GFPLATESNI LKELIKPPTI LRSVVNSITG SSNVGDTLPT G QLSNIPWR RAGVKYTNNE AYFDVVEEID AIIDKSGSTV FAEIQGVIDA CIKLSGMPDL SLSFMNPRLL DDVSFHPCIR FK RWESERV LSFIPPDGNF RLISYRVSSQ NLVAIPVYVK HSISFKENSS CGRFDITIGP KQNMGKTIEG ITVTVHMPKV VLN MNLTPT QGSYTFDPVT KVLTWDVGKI TPQKLPSLKG LVNLQSGAPK PEENPSLNIQ FKIQQLAISG LKVNRLDMYG EKYK PFKGV KYVTKAGKFQ VRT

UniProtKB: AP-3 complex subunit mu-1

-
Macromolecule #4: AP-3 complex subunit sigma-1

MacromoleculeName: AP-3 complex subunit sigma-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.755061 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKAILIFNN HGKPRLSKFY QPYSEDTQQQ IIRETFHLVS KRDENVCNFL EGGLLIGGSD NKLIYRHYAT LYFVFCVDSS ESELGILDL IQVFVETLDK CFENVCELDL IFHVDKVHNI LAEMVMGGMV LETNMNEIVT QIDAQNKLEK SEAGLAGAPA R AVSAVKNM ...String:
MIKAILIFNN HGKPRLSKFY QPYSEDTQQQ IIRETFHLVS KRDENVCNFL EGGLLIGGSD NKLIYRHYAT LYFVFCVDSS ESELGILDL IQVFVETLDK CFENVCELDL IFHVDKVHNI LAEMVMGGMV LETNMNEIVT QIDAQNKLEK SEAGLAGAPA R AVSAVKNM NLPEIPRNIN IGDISIKVPN LPSFK

UniProtKB: AP-3 complex subunit sigma-1

-
Macromolecule #5: Lysosome-associated membrane glycoprotein 1

MacromoleculeName: Lysosome-associated membrane glycoprotein 1 / type: protein_or_peptide / ID: 5 / Details: Synthetic peptide with an oleic acid conjugation / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.377553 KDa
SequenceString:
GRKRSHAGYQ TI

UniProtKB: Ribosomal protein L22p/L17e

-
Macromolecule #6: AP-3 complex subunit beta-1

MacromoleculeName: AP-3 complex subunit beta-1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.499609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSNSFPYNE QSGGGEATEL GQEATSTISP SGAFGLFSSD LKKNEDLKQM LESNKDSAKL DAMKRIVGMI AKGKNASELF PAVVKNVAS KNIEIKKLVY VYLVRYAEEQ QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP IMMLAIKEAS A DLSPYVRK ...String:
MSSNSFPYNE QSGGGEATEL GQEATSTISP SGAFGLFSSD LKKNEDLKQM LESNKDSAKL DAMKRIVGMI AKGKNASELF PAVVKNVAS KNIEIKKLVY VYLVRYAEEQ QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP IMMLAIKEAS A DLSPYVRK NAAHAIQKLY SLDPEQKEML IEVIEKLLKD KSTLVAGSVV MAFEEVCPDR IDLIHKNYRK LCNLLVDVEE WG QVVIIHM LTRYARTQFV SPWKEGDELE DNGKNFYESD DDQKEKTDKK KKPYTMDPDH RLLIRNTKPL LQSRNAAVVM AVA QLYWHI SPKSEAGIIS KSLVRLLRSN REVQYIVLQN IATMSIQRKG MFEPYLKSFY VRSTDPTMIK TLKLEILTNL ANEA NISTL LREFQTYVKS QDKQFAAATI QTIGRCATNI LEVTDTCLNG LVCLLSNRDE IVVAESVVVI KKLLQMQPAQ HGEII KHMA KLLDSITVPV ARASILWLIG ENCERVPKIA PDVLRKMAKS FTSEDDLVKL QILNLGAKLY LTNSKQTKLL TQYILN LGK YDQNYDIRDR TRFIRQLIVP NVKSGALSKY AKKIFLAQKP APLLESPFKD RDHFQLGTLS HTLNIKATGY LELSNWP EV APDPSVRNVE VIELAKEWTP AGKAKQENSA KKFYS

UniProtKB: AP-3 complex subunit beta-1

-
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #8: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
2.7 mMKClPotassium Chloride
10.0 mMNa2HPO4Sodium Phosphate (Dibasic)
1.8 mMKH2PO4Potassium Phosphate (Monobasic)
300.0 mMNaClSodium Chloride
1.0 mMC9H15O6PTCEP

Details: 1x PBS (pH 7.4), 300mM NaCl, 1mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
Details: Used Quantifoil Active grids - backside gold coated before plasma cleaning. 12 mA used for plasma cleaning.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: SPOTITON / Details: Commercialized version - chameleon.
DetailsSpecimen appeared as a monodisperse peak via size exclusion chromatography (SEC)

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 53.4 e/Å2
Details: 2 datasets collected, processed independently, and merged.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionDetails: Mixture of blob picker, template picker, crYOLO, and Topaz
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1)
Details: Non-Uniform refinement in cryoSPARC. Map is a composite map of two focused refinements, combined using phenix.combine_focused_maps.
Number images used: 176749
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9c5b:
AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map

+
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