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- EMDB-65045: Cryo-EM Structure of Rc-o319 Ectodomain trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-65045
TitleCryo-EM Structure of Rc-o319 Ectodomain trimer
Map data
Sample
  • Complex: Cryo-EM structure of Rc-o319 Ectodomain trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCOMPLEX / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
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 ...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 speciesCoronaviridae (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsMatsumoto K / Shihoya W / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Cell Rep / Year: 2025
Title: Molecular basis of sarbecovirus evolution and receptor tropism in natural hosts, potential intermediate hosts, and humans.
Authors: Kosugi Y / Matsumoto K / Lytras S / Plianchaisuk A / Tolentino EJ / Fujita S / Yo SM / Luo C / Kim Y / Shihoya W / Ito J / Nureki O / Sato K
History
DepositionJun 13, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_65045.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1067 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.46921948 - 0.9064002
Average (Standard dev.)-0.0012442686 (±0.036354776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 265.60797 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of Rc-o319 Ectodomain trimer

EntireName: Cryo-EM structure of Rc-o319 Ectodomain trimer
Components
  • Complex: Cryo-EM structure of Rc-o319 Ectodomain trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of Rc-o319 Ectodomain trimer

SupramoleculeName: Cryo-EM structure of Rc-o319 Ectodomain trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Coronaviridae (virus)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Details: Cryo-EM structure of Rc-o319 Ectodomain trimer / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.563164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CVNITYGSHH LYVSSRTRGV YYPDDAFRSS TNVLHEGFFL PFDSNVTWYS FWNQKYSVAT SPFGDGVYFS TIDKSNVVRG WVFGTTLDN DTQSVLLYND GTHVRVEVCT FHFCPTPVFS ASSPHLYSSA FNCTLNYTLA SVRADFTEVD GSFKTIREFV F KLQDGSLN ...String:
CVNITYGSHH LYVSSRTRGV YYPDDAFRSS TNVLHEGFFL PFDSNVTWYS FWNQKYSVAT SPFGDGVYFS TIDKSNVVRG WVFGTTLDN DTQSVLLYND GTHVRVEVCT FHFCPTPVFS ASSPHLYSSA FNCTLNYTLA SVRADFTEVD GSFKTIREFV F KLQDGSLN VYYASTSYVL AIGATSQLPS GVTPLVPLWK IPIGLNITNF KTLVYLRSDN TPLQAAYVVG HLKRRTMMFK YD ENGTIVD AIDCALDPLS ETKCTLRSFI VEKGIYQTSN FRVQPQDTVV RFPNITNLCP FSEVFNATTF ASVYAWNRKR ISN CVADYS VLYNSTSFST FQCYGVSSTK LNDLCFTNVY ADSFVVRGDE VRQIAPGQTG VIADYNYKLP DDFTGCVLAW NSRN QDAST SGNFNYYYRI WRSEKLRPFE RDIAHYDYQV GTQFKSSLKN YGFYSSAGDS HQPYRVVVLS FELLNAPATV CGPKQ STEL IKNKCVNFNF NGLTGTGVLT DSNKKFQSFQ QFGRDVSDFT DSVKDPKTLE VLDITPCSYG GVSVITPGTN ASTQVA VLY QDVNCTDVPT AIHAEQLTPS WRVYSTGTNM FQTQAGCLIG AEHVNNSYDC DIPIGAGICA TYHTPSMLRS ANNNKRI VA YVMSLGAENS VAYSNNTIAI PTNFTISVTT EVMPVSMTKT SVDCTMYICG DSVECSTLLL QYGSFCTQLN RALTGIAV E QDKNTQEVFA QVKQIYKTPD IKDFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF VKQYGDCLGD IQARDLICA QKFNGLTVLP PLLTDEMIAA YTAALISGTA TAGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQESLTST PSALGKLQDV VNQNAQALNT LVKQLSSNFG AISSVLNDII SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ L IRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQAAPHGV VFLHVTYIPS QERNFTTAPA ICHEGKAHFP RE GVFVSNG THWFITQRNF YEPQIITTDN TFVSGTCDVV IGIVNNTVYD PLQPELESFK DELDKYFKNH TSPDIDLGDI SGI NASVVD IQKEIDILKD VAKNLNESLI NLQELGKYEQ YIGTKHHHHH H

UniProtKB: Spike glycoprotein

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 5.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2086299
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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