[English] 日本語
Yorodumi
- EMDB-38866: BA.2.86-V483 RBD in complex with bACE2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38866
TitleBA.2.86-V483 RBD in complex with bACE2
Map data
Sample
  • Complex: BA.2.86-V483 RBD in complex with bACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike protein S1 RBD
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / complex / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / cilium / apical plasma membrane / proteolysis / extracellular region / metal ion binding / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile.
Similarity search - Domain/homology
Angiotensin-converting enzyme
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.13 Å
AuthorsYue C / Liu P
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: BA.2.86-V483 RBD in complex with bACE2
Authors: Yue C / Liu P
History
DepositionJan 28, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_38866.png

Downloads & links

-
Map

FileDownload / File: emd_38866.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.0097625 - 4.0515385
Average (Standard dev.)0.0013069354 (±0.069926396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_38866_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38866_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BA.2.86-V483 RBD in complex with bACE2

EntireName: BA.2.86-V483 RBD in complex with bACE2
Components
  • Complex: BA.2.86-V483 RBD in complex with bACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike protein S1 RBD
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: BA.2.86-V483 RBD in complex with bACE2

SupramoleculeName: BA.2.86-V483 RBD in complex with bACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron/BA.2.86

-
Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 91.310852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STTEEQAKTF LEKFNHEAED LSYQSSLASW NYNTNITDEN VQKMNEARAK WSAFYEEQSR MAKTYSLEEI QNLTLKRQLK ALQHSGTSA LSAEKSKRLN TILNKMSTIY STGKVLDPNT QECLALEPGL DDIMENSRDY NRRLWAWEGW RAEVGKQLRP L YEEYVVLE ...String:
STTEEQAKTF LEKFNHEAED LSYQSSLASW NYNTNITDEN VQKMNEARAK WSAFYEEQSR MAKTYSLEEI QNLTLKRQLK ALQHSGTSA LSAEKSKRLN TILNKMSTIY STGKVLDPNT QECLALEPGL DDIMENSRDY NRRLWAWEGW RAEVGKQLRP L YEEYVVLE NEMARANNYE DYGDYWRGDY EVTGAGDYDY SRDQLMKDVE RTFAEIKPLY EQLHAYVRAK LMHTYPSYIS PT GCLPAHL LGDMWGRFWT NLYSLTVPFE HKPSIDVTEK MENQSWDAER IFKEAEKFFV SISLPYMTQG FWDNSMLTEP GDG RKVVCH PTAWDLGKGD FRIKMCTKVT MDDFLTAHHE MGHIQYDMAY AAQPYLLRNG ANEGFHEAVG EIMSLSAATP HYLK ALGLL APDFHEDNET EINFLLKQAL TIVGTLPFTY MLEKWRWMVF KGEIPKQQWM EKWWEMKREI VGVVEPLPHD ETYCD PACL FHVAEDYSFI RYYTRTIYQF QFHEALCKTA KHEGALFKCD ISNSTEAGQR LLQMLRLGKS EPWTLALENI VGIKTM DVK PLLNYFEPLF TWLKEQNRNS FVGWSTEWTP YSDQSIKVRI SLKSALGENA YEWNDNEMYL FQSSVAYAMR KYFSEAR NE TVLFGEDNVW VSDKKPRISF KFFVTSPNNV SDIIPRTEVE NAIRLSRDRF NDVFQLDDNS LEFLGIQPTL GPPYEPPV T IWLIIFGVVM GVVVIGIVVL IFTGIRNRRK KNQASSEENP YGSVDLNKGE NNSGFQNIDD VQTSL

UniProtKB: Angiotensin-converting enzyme

-
Macromolecule #2: Spike protein S1 RBD

MacromoleculeName: Spike protein S1 RBD / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron/BA.2.86
Molecular weightTheoretical: 23.981236 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NVTNLCPFHE VFNATRFASV YAWNRTRISN CVADYSVLYN FAPFFAFKCY GVSPTKLNDL CFTNVYADSF VIKGNEVSQI APGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKHSGNY DYWYRLFRKS KLKPFERDIS TEIYQAGNKP CKGVKGPNCY F PLQSYGFR ...String:
NVTNLCPFHE VFNATRFASV YAWNRTRISN CVADYSVLYN FAPFFAFKCY GVSPTKLNDL CFTNVYADSF VIKGNEVSQI APGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKHSGNY DYWYRLFRKS KLKPFERDIS TEIYQAGNKP CKGVKGPNCY F PLQSYGFR PTYGVGHQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNF

-
Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 597508
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