[English] 日本語
Yorodumi
- EMDB-53923: Structure of the Human Peptide-Loading Complex Arrested by HCMV US6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53923
TitleStructure of the Human Peptide-Loading Complex Arrested by HCMV US6
Map data
Sample
  • Complex: Human peptide-loading complex arrested by HCMV US6
    • Protein or peptide: x 6 types
  • Ligand: x 5 types
Keywordsantigen processing / adaptive immunity / cryo-EM / ER chaperones / MHC class I / transporter associated with antigen processing / IMMUNE SYSTEM
Function / homology
Function and homology information


MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / tapasin binding / ABC-type peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / ABC-type peptide transporter activity ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / tapasin binding / ABC-type peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / ABC-type peptide transporter activity / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / TAP2 binding / TAP1 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / peptide transport / peptide transmembrane transporter activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / MHC class I protein binding / molecular sequestering activity / antigen processing and presentation of peptide antigen via MHC class I / endoplasmic reticulum-Golgi intermediate compartment membrane / protein folding chaperone / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / defense response / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / transmembrane transport / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / centriolar satellite / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / unfolded protein binding / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / protein transport / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / regulation of gene expression / protein-containing complex assembly / early endosome membrane / molecular adaptor activity / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / nuclear speck / immune response / host cell endoplasmic reticulum membrane / endoplasmic reticulum lumen / Amyloid fiber formation
Similarity search - Function
Viral unique short region 6 / Viral unique short region 6 / Tapasin / Antigen peptide transporter 2 / ABC transporter Tap-like / Type 1 protein exporter / : / ABC transporter transmembrane region / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Viral unique short region 6 / Viral unique short region 6 / Tapasin / Antigen peptide transporter 2 / ABC transporter Tap-like / Type 1 protein exporter / : / ABC transporter transmembrane region / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / MHC classes I/II-like antigen recognition protein / ABC transporter / : / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MHC class I antigen / Tapasin / Unique short US6 glycoprotein / Beta-2-microglobulin / Antigen peptide transporter 1 / Antigen peptide transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsStolz M / Susac L / Trowitzsch S / Tampe R
Funding supportEuropean Union, Germany, United States, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)789121European Union
European Research Council (ERC)101141396European Union
German Research Foundation (DFG)TA157/12-1 Germany
German Research Foundation (DFG)CRC1507/P18 Germany
Other privateUR013222 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 29, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53923.png

Downloads & links

-
Map

FileDownload / File: emd_53923.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.042457413 - 0.92385787
Average (Standard dev.)0.008457146 (±0.017306233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Human peptide-loading complex arrested by HCMV US6

EntireName: Human peptide-loading complex arrested by HCMV US6
Components
  • Complex: Human peptide-loading complex arrested by HCMV US6
    • Protein or peptide: Antigen peptide transporter 1
    • Protein or peptide: Tapasin
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Antigen peptide transporter 2
    • Protein or peptide: Unique short US6 glycoprotein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water

+
Supramolecule #1: Human peptide-loading complex arrested by HCMV US6

SupramoleculeName: Human peptide-loading complex arrested by HCMV US6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Antigen peptide transporter 1

MacromoleculeName: Antigen peptide transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type antigen peptide transporter
Source (natural)Organism: Homo sapiens (human) / Tissue: Burkitt lymphoma
Molecular weightTheoretical: 81.080383 KDa
SequenceString: MASSRCPAPR GCRCLPGASL AWLGTVLLLL ADWVLLRTAL PRIFSLLVPT ALPLLRVWAV GLSRWAVLWL GACGVLRATV GSKSENAGA QGWLAALKPL AAALGLALPG LALFRELISW GAPGSADSTR LLHWGSHPTA FVVSYAAALP AAALWHKLGS L WVPGGQGG ...String:
MASSRCPAPR GCRCLPGASL AWLGTVLLLL ADWVLLRTAL PRIFSLLVPT ALPLLRVWAV GLSRWAVLWL GACGVLRATV GSKSENAGA QGWLAALKPL AAALGLALPG LALFRELISW GAPGSADSTR LLHWGSHPTA FVVSYAAALP AAALWHKLGS L WVPGGQGG SGNPVRRLLG CLGSETRRLS LFLVLVVLSS LGEMAIPFFT GRLTDWILQD GSADTFTRNL TLMSILTIAS AV LEFVGDG IYNNTMGHVH SHLQGEVFGA VLRQETEFFQ QNQTGNIMSR VTEDTSTLSD SLSENLSLFL WYLVRGLCLL GIM LWGSVS LTMVTLITLP LLFLLPKKVG KWYQLLEVQV RESLAKSSQV AIEALSAMPT VRSFANEEGE AQKFREKLQE IKTL NQKEA VAYAVNSWTT SISCMLLKVG ILYIGGQLVT SGAVSSGNLV TFVLYQMQFT QAVEVLLSIY PRVQKAVGSS EKIFE YLDR TPRCPPSGLL TPLHLEGLVQ FQDVSFAYPN RPDVLVLQGL TFTLRPGEVT ALVGPNGSGK STVAALLQNL YQPTGG QLL LDGKPLPQYE HRYLHRQVAA VGQEPQVFGR SLQENIAYGL TQKPTMEEIT AAAVKSGAHS FISGLPQGYD TEVDEAG SQ LSGGQRQAVA LARALIRKPC VLILDDATSA LDANSQLQVE QLLYESPERY SRSVLLITQH LSLVEQADHI LFLEGGAI R EGGTHQQLME KKGCYWAMVQ APADAPE

UniProtKB: Antigen peptide transporter 1

+
Macromolecule #2: Tapasin

MacromoleculeName: Tapasin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Burkitt lymphoma
Molecular weightTheoretical: 47.673539 KDa
SequenceString: MKSLSLLLAV ALGLATAVSA GPAVIECWFV EDASGKGLAK RPGALLLRQG PGEPPPRPDL DPELYLSVHD PAGALQAAFR RYPRGAPAP HCEMSRFVPL PASAKWASGL TPAQNCPRAL DGAWLMVSIS SPVLSLSSLL RPQPEPQQEP VLITMATVVL T VLTHTPAP ...String:
MKSLSLLLAV ALGLATAVSA GPAVIECWFV EDASGKGLAK RPGALLLRQG PGEPPPRPDL DPELYLSVHD PAGALQAAFR RYPRGAPAP HCEMSRFVPL PASAKWASGL TPAQNCPRAL DGAWLMVSIS SPVLSLSSLL RPQPEPQQEP VLITMATVVL T VLTHTPAP RVRLGQDALL DLSFAYMPPT SEAASSLAPG PPPFGLEWRR QHLGKGHLLL AATPGLNGQM PAAQEGAVAF AA WDDDEPW GPWTGNGTFW LPRVQPFQEG TYLATIHLPY LQGQVTLELA VYKPPKVSLM PATLARAAPG EAPPELLCLV SHF YPSGGL EVEWELRGGP GGRSQKAEGQ RWLSALRHHS DGSVSLSGHL QPPPVTTEQH GARYACRIHH PSLPASGRSA EVTL EVAGL SGPSLEDSVG LFLSAFLLLG LFKALGWAAV YLSTCKDSKK KAE

UniProtKB: Tapasin

+
Macromolecule #3: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 3 / Details: HLA-B*15:10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Burkitt lymphoma
Molecular weightTheoretical: 40.480973 KDa
SequenceString: MLVMAPRTVL LLLSAALALT ETWAGSHSMR YFYTSVSRPG RGEPRFISVG YVDDTQFVRF DSDAASPREE PRAPWIEQEG PEYWDRNTQ IYKAQAQTDR ESLRNLRGYY NQSEAGSHTL QSMYGCDVGP DGRLLRGHDQ YAYDGKDYIA LNEDLRSWTA A DTAAQITQ ...String:
MLVMAPRTVL LLLSAALALT ETWAGSHSMR YFYTSVSRPG RGEPRFISVG YVDDTQFVRF DSDAASPREE PRAPWIEQEG PEYWDRNTQ IYKAQAQTDR ESLRNLRGYY NQSEAGSHTL QSMYGCDVGP DGRLLRGHDQ YAYDGKDYIA LNEDLRSWTA A DTAAQITQ RKWEAAREAE QRRAYLEGEC VEWLRRYLEN GKDKLERADP PKTHVTHHPI SDHEATLRCW ALGFYPAEIT LT WQRDGED QTQDTELVET RPAGDRTFQK WAAVVVPSGE EQRYTCHVQH EGLPKPLTLR WEPSSQSTVP IVGIVAGLAV LAV VVIGAV VAAVMCRKKS SGGKGGSYSQ AACSDSAQGS DVSLTA

UniProtKB: MHC class I antigen

+
Macromolecule #4: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Burkitt lymphoma
Molecular weightTheoretical: 13.732547 KDa
SequenceString:
MSRSVALAVL ALLSLSGLEA IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTE FTPTEKDEYA CRVNHVTLSQ PKIVKWDRDM

UniProtKB: Beta-2-microglobulin

+
Macromolecule #5: Antigen peptide transporter 2

MacromoleculeName: Antigen peptide transporter 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type antigen peptide transporter
Source (natural)Organism: Homo sapiens (human) / Tissue: Burkitt lymphoma
Molecular weightTheoretical: 74.697242 KDa
SequenceString: RPWTSLLLVD AALLWLLQGP LGTLLPQGLP GLWLEGTLRL GGLWGLLKLR GLLGFVGTLL LPLCLATPLT VSLRALVAGA SRAPPARVA SAPWSWLLVG YGAAGLSWSL WAVLSPPGAQ EKEQDQVNNK VLMWRLLKLS RPDLPLLVAA FFFLVLAVLG E TLIPHYSG ...String:
RPWTSLLLVD AALLWLLQGP LGTLLPQGLP GLWLEGTLRL GGLWGLLKLR GLLGFVGTLL LPLCLATPLT VSLRALVAGA SRAPPARVA SAPWSWLLVG YGAAGLSWSL WAVLSPPGAQ EKEQDQVNNK VLMWRLLKLS RPDLPLLVAA FFFLVLAVLG E TLIPHYSG RVIDILGGDF DPHAFASAIF FMCLFSFGSS LSAGCRGGCF TYTMSRINLR IREQLFSSLL RQDLGFFQET KT GELNSRL SSDTTLMSNW LPLNANVLLR SLVKVVGLYG FMLSISPRLT LLSLLHMPFT IAAEKVYNTR HQEVLREIQD AVA RAGQVV REAVGGLQTV RSFGAEEHEV CRYKEALEQC RQLYWRRDLE RALYLLVRRV LHLGVQMLML SCGLQQMQDG ELTQ GSLLS FMIYQESVGS YVQTLVYIYG DMLSNVGAAE KVFSYMDRQP NLPSPGTLAP TTLQGVVKFQ DVSFAYPNRP DRPVL KGLT FTLRPGEVTA LVGPNGSGKS TVAALLQNLY QPTGGQVLLD EKPISQYEHC YLHSQVVSVG QEPVLFSGSV RNNIAY GLQ SCEDDKVMAA AQAAHADDFI QEMEHGIYTD VGEKGSQLAA GQKQRLAIAR ALVRDPRVLI LDEATSALDV QCEQALQ DW NSRGDRTVLV IAHRLQTVQR AHQILVLQEG KLQKL

UniProtKB: Antigen peptide transporter 2

+
Macromolecule #6: Unique short US6 glycoprotein

MacromoleculeName: Unique short US6 glycoprotein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.671127 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDLLIRLGFL LMCALPTPGE RSSRDPKTLL SLSPRQQACV PRTKSHRPVC YNDTGDCTDA DDSWKQLGED FAHQCLQAAK KRPKTHKSR PNDRNLEGRL TCQRVRRLLP CDLDIHPSHR LLTLMNNCVC DGAVWNAFRL IERHGFFAVT LYLCCGITLL V VILALLCS ITYESTGRGI RRCGS

UniProtKB: Unique short US6 glycoprotein

+
Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

+
Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

+
Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.5 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4S-NaOHHEPES-sodium hydroxide
150.0 mMNaClsodium chloride
10.0 mMMgCl2magnesium chloride
0.05 %C56H92O25glycodiosgenin
2.5 mMC10H16N2O3Sbiotin

Details: 20 mM HEPES-NaOH pH 6.5, 150 mM NaCl, 10 mM MgCl2, 2.5 mM biotin, 0.05% (w/v) glycodiosgenin
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 5, Blot time 5 s.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 25454 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60241 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
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 selectionNumber selected: 726723
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: OTHER
Details: Composite map generated from 4 focus maps ranging 2.59 - 2.88 A
Number images used: 269213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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