[English] 日本語
Yorodumi
- EMDB-38773: Cryo-EM structure of BANAL-20-52 spike protein (6P) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38773
TitleCryo-EM structure of BANAL-20-52 spike protein (6P)
Map dataCryo-EM structure of BANAL-20-52 spike protein (6P)
Sample
  • Complex: BANAL-20-52 spike protein (6P)
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
KeywordsBANAL-20-52 / spike protein / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesCoronavirinae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsXu ZP / Li LJ / Gu YH / Qi JX / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: J Virol / Year: 2025
Title: CX1/BtSY2 and BANAL-20-52 exhibit broader receptor binding and higher affinities to multiple animal ACE2 orthologs than SARS-CoV-2 prototype.
Authors: Zepeng Xu / Linjie Li / Yuhang Gu / Dedong Li / Jianxun Qi / Kefang Liu / Chu-Xia Deng / George Fu Gao /
Abstract: Animal coronaviruses (CoVs) CX1 (formerly named BtSY2) and BANAL-20-52 are phylogenetically closely related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and CX1 is the first ...Animal coronaviruses (CoVs) CX1 (formerly named BtSY2) and BANAL-20-52 are phylogenetically closely related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and CX1 is the first observed animal betaCoV carrying naturally occurring Y501 in its receptor-binding domain (RBD) of the spike (S) protein, a residue related to human adaptation and broader host range. We evaluated the ACE2 usage of CX1 and BANAL-20-52 and observed broader receptor binding spectra and higher affinities to most of the tested animal ACE2 orthologs than the SARS-CoV-2 prototype. Determination of the cryo-EM structures of their S proteins and RBD/hACE2 complexes reveals that Y501 is inter-replaceable with H498 substitution while synergetic with R498 for human ACE2 binding. These results provide further structural insights into SARS-CoV-2 receptor recognition and address the importance of surveillance on potential emerging CoVs.IMPORTANCESince the outbreak of COVID-19, forewarning and prevention of the next pandemic have been widely discussed. Coronaviruses (CoVs) CX1 (formerly named BtSY2) and BANAL-20-52 are phylogenetically closely related to SARS-CoV-2. Particularly, CX1 is the first SARS-CoV-2-related CoV containing Y501 in its receptor-binding domain (RBD) of the spike (S) protein. This study evaluated the interspecies transmission potential of the two CoVs and structurally elucidated the interplay between two RBD residues 498 and 501 on ACE2 binding, further highlighting the importance of surveillance on zoonotic CoVs.
History
DepositionJan 19, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_38773.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of BANAL-20-52 spike protein (6P)
Voxel sizeX=Y=Z: 0.69 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.4346747 - 0.9872575
Average (Standard dev.)-0.000092776914 (±0.03142237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : BANAL-20-52 spike protein (6P)

EntireName: BANAL-20-52 spike protein (6P)
Components
  • Complex: BANAL-20-52 spike protein (6P)
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID

-
Supramolecule #1: BANAL-20-52 spike protein (6P)

SupramoleculeName: BANAL-20-52 spike protein (6P) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Coronavirinae (virus)

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Coronavirinae (virus)
Molecular weightTheoretical: 141.729734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SSTRGVYYPD KVFRSSVLHL TQDLFLPFFS NVTWFHAIHV SGTNGIKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHRNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SSTRGVYYPD KVFRSSVLHL TQDLFLPFFS NVTWFHAIHV SGTNGIKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHRNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPP GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCSLDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATT FASVYAWNRK RISNCVADYS VLYNSTSFST FKCYGVSPTK LNDLCFTNVY ADSF VVRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFHPTNGVG YQPYRVVVLS FELLNAPATV CGPKKSTNLI KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN ASNQVAVLYQ DVNCTEVPVA IHANQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSRS VASQSIIAYT MSLGAENSVA YSNNSIAIPT NFTISVTT E ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLNR ALTGIAVEQD KNTQEVFAQV KQIYKTPQIK DFGGFNFSQ ILPDPSKPSK RSPIEDLLFN KVTLADAGFI KQYGDCLGDI AARDLICAQK FNGLTVLPPL LTDEMIAQYT SALLAGTITS GWTFGAGPA LQIPFPMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLSSTPS ALGKLQDVVN QNAQALNTLV K QLSSNFGA ISSVLNDILS RLDPPEAEVQ IDRLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC VLGQSKRVDF CG KGYHLMS FPQSAPHGVV FLHVTYVPAQ EKNFTTAPAI CHDGKAHFPR EGVFVSNGTH WFVTQRNFYE PQIITTDNTF VSG NCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLSDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELG KYEQY IKWPWYIWGG GSGGGSGYIP EAPRDGQAYV RKDGEWVLLS TFLGGGSAWS HPQFEKGGGS GGGSGGSSAW SHPQF EK

UniProtKB: Spike glycoprotein

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 45 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #4: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 4 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 253926
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: RANDOM ASSIGNMENT

+
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