[English] 日本語
Yorodumi
- EMDB-35079: BANAL-20-236 S1 in complex with R. Affinis ACE2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35079
TitleBANAL-20-236 S1 in complex with R. Affinis ACE2
Map data
Sample
  • Complex: BANAL-20-236 S1 in complex with R. Affinis ACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsBANAL-20-236 / Bat / Spike / S1 / R. Affinis / ACE2 / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / endocytosis involved in viral entry into host cell / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / endocytosis involved in viral entry into host cell / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular region / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus ...Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesunclassified Coronavirinae (virus) / Rhinolophus affinis (intermediate horseshoe bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang X / Xu G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The selective effect of fecal-oral transmission on the S proteins of bat SARS-CoV-2 related coronaviruses in favor of stability over infectivity
Authors: Wang X / Xu G
History
DepositionJan 4, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35079.png

Downloads & links

-
Map

FileDownload / File: emd_35079.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0102
Minimum - Maximum-0.027554005 - 0.063881755
Average (Standard dev.)-0.00000020929174 (±0.0020822436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions248248248
Spacing248248248
CellA=B=C: 262.87997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_35079_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35079_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BANAL-20-236 S1 in complex with R. Affinis ACE2

EntireName: BANAL-20-236 S1 in complex with R. Affinis ACE2
Components
  • Complex: BANAL-20-236 S1 in complex with R. Affinis ACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: BANAL-20-236 S1 in complex with R. Affinis ACE2

SupramoleculeName: BANAL-20-236 S1 in complex with R. Affinis ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: unclassified Coronavirinae (virus)

-
Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus affinis (intermediate horseshoe bat)
Molecular weightTheoretical: 76.340852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG KLSTTEDRAK IFLDNFNHEA EDLSYQSSLA SWEYNTNISD ENVQKMDEAG AKWSAFYEEQ SKLAKNYPL EEIQTVPVKL QLQILQQSGS PVLSEDKSKR LNSILNAMST IYSTGKVCKP NNPQECFLLE PGLDNIMGTS K DYNERLWA ...String:
METDTLLLWV LLLWVPGSTG KLSTTEDRAK IFLDNFNHEA EDLSYQSSLA SWEYNTNISD ENVQKMDEAG AKWSAFYEEQ SKLAKNYPL EEIQTVPVKL QLQILQQSGS PVLSEDKSKR LNSILNAMST IYSTGKVCKP NNPQECFLLE PGLDNIMGTS K DYNERLWA WEGWRAEVGK QLRPLYEEYV ALKNEMARGY HYEDYGDYWR RDYETEESSG SGYSRDQLMK DVDRIFTEIK PL YEHLHAY VRTKLMDTYP FHISPTGCLP AHLLGDMWGR FWTNLYPLTV PFGQKPNIDV TDAMVNQGWD ANRIFKEAEK FFV SVGLPN MTEGFWNNSM LTEPGDGRKV VCHPTAWDLG KGDFRIKMCT KVTMEDFLTA HHEMGHIQYD MAYATQPYLL RNGA NEGFH EAVGEVMSLS VATPKHLKTM GLLSPDFLED NETEINFLLK QALNIVGTLP FTYMLEKWRW MVFRGEIPKE EWMKK WWEM KRDLVGVVEP VPHDETYCDP ASLFHVANDY SFIRYYTRTI FEFQFHEALC RIAQHDGPLH KCDISNSTDA GKKLHQ MLS VGKSQPWTVT LKDIVDSRNM DVGPLLRYFE PLYTWLQEQN RKSYVGWNTD WSPYSDSRGS GLEVLFQGPG SWSHPQF EK GGGSGGGSGG SAWSHPQFEK

UniProtKB: Angiotensin-converting enzyme

-
Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unclassified Coronavirinae (virus)
Molecular weightTheoretical: 141.914672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLFFFFLCFA SVNSQCVNLT GRATIQPSFT NSSHRGVYYP DTIFRSNSLV LSQGYFLPFY SNISWYYALT KTNGAEKRVD NPILDFKDG IYFAATEKSN IVRGWIFGTT LDNTSQSLLI VNNATNVIIK VCNFQFCYDP YLSGYFHNNK TWSTREFAVY S SYANCTFE ...String:
MLFFFFLCFA SVNSQCVNLT GRATIQPSFT NSSHRGVYYP DTIFRSNSLV LSQGYFLPFY SNISWYYALT KTNGAEKRVD NPILDFKDG IYFAATEKSN IVRGWIFGTT LDNTSQSLLI VNNATNVIIK VCNFQFCYDP YLSGYFHNNK TWSTREFAVY S SYANCTFE YVSKPFMLDI SGKSGLFDTL REFVFRNVDG YFKIYSKYSP VNVNSNLPSG FSALEPLVEL PAGINITRFR TL LTIHRGD PMPNNGWTVF SAAYYVGYLA PRTFMLKYNE NGTITDAVDC SLDPLSEAKC TLKSFTVEKG IYQTSNFRVQ PTD SIVRFP NITNLCPFGE VFNATTFASV YAWNRKRISN CVADYSVLYN STSFSTFKCY GVSPTKLNDL CFTNVYADSF VVRG DEVRQ IAPGQTGKIA DYNYKLPDDF TGCVIAWNSN NLDSKVGGNY NYLYRLFRKS NLKPFERDIS TEIYQAGSTP CNGVE GFNC YFPLKSYGFH PTNGVGYQPY RVVVLSFELL NAPATVCGPK KSTNLIKNKC VNFNFNGLTG TGVLTESNKK FLPFQQ FGR DIADTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNASNQ VAVLYQDVNC TEVPVAIHAD QLTPTWRVYS TGSNVFQ TR AGCLIGAEHV NNSYECDIPI GAGICASYQT QTNSRSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILP V SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY KTPQIKDFGG FNFSQILPD PSKPSKRSFI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNQNAQ ALNTLVKQLS S NFGAISSV LNDILSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YH LMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDV VIGIVN NTVYDPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQQLG KYEQ LEGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGGGSGGSAW SHPQF EK

UniProtKB: Spike glycoprotein

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 5.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156892

+
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