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- EMDB-63603: Cryo-EM structure of Rc-o319 RBD/R. cornutus ACE2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63603
TitleCryo-EM structure of Rc-o319 RBD/R. cornutus ACE2 complex
Map data
Sample
  • Complex: Rc-o319 RBD and R. cornutus ACE2 complex
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
KeywordsRhinolophus cornutus / Coronavirinae / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / 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 / proteolysis / extracellular space / metal ion binding / membrane / 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. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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
Spike glycoprotein / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesRhinolophus cornutus (Little Japanese Horseshoe Bat) / Sarbecovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 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: Yusuke Kosugi / Kanata Matsumoto / Spyros Lytras / Arnon Plianchaisuk / Jarel Elgin Tolentino / Shigeru Fujita / Maximilian Stanley Yo / Chen Luo / Yoonjin Kim / Wataru Shihoya / Jumpei Ito ...Authors: Yusuke Kosugi / Kanata Matsumoto / Spyros Lytras / Arnon Plianchaisuk / Jarel Elgin Tolentino / Shigeru Fujita / Maximilian Stanley Yo / Chen Luo / Yoonjin Kim / Wataru Shihoya / Jumpei Ito / Osamu Nureki / Kei Sato /
Abstract: The spike protein of many sarbecoviruses binds to the angiotensin-converting enzyme 2 (ACE2) receptor and facilitates viral entry. The diversification of the sarbecovirus spike gene and the mammalian ...The spike protein of many sarbecoviruses binds to the angiotensin-converting enzyme 2 (ACE2) receptor and facilitates viral entry. The diversification of the sarbecovirus spike gene and the mammalian ACE2 gene suggests that sarbecoviruses and their hosts have co-evolved, and the genetic diversity in these genes affects the host tropism of sarbecoviruses. Better comprehending the evolutionary potential of sarbecoviruses can lead to preparedness for the next pandemic. However, the host tropism of sarbecoviruses is not fully understood. Here, we performed pseudovirus infection assays using 53 sarbecoviruses and ACE2s from 17 mammals to elucidate the ACE2 tropism of sarbecoviruses in natural hosts, potential intermediate hosts, and humans. We determined the factors responsible for the ACE2 tropism of sarbecoviruses through structural and phylogenetic analyses and infection experiments, revealing which substitutions can expand the host range of sarbecoviruses. These results highlight the mechanisms modulating host tropism throughout sarbecovirus evolution.
History
DepositionMar 2, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63603.png

Downloads & links

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Map

FileDownload / File: emd_63603.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 210 pix.
= 232.407 Å		1.11 Å/pix.
x 210 pix.
= 232.407 Å		1.11 Å/pix.
x 210 pix.
= 232.407 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.40912214 - 0.8656296
Average (Standard dev.)-0.000027447308 (±0.022901697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 232.40698 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63603_msk_1.map
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Half map: #1

Fileemd_63603_half_map_1.map
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Half map: #2

Fileemd_63603_half_map_2.map
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Sample components

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Entire : Rc-o319 RBD and R. cornutus ACE2 complex

EntireName: Rc-o319 RBD and R. cornutus ACE2 complex
Components
  • Complex: Rc-o319 RBD and R. cornutus ACE2 complex
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: Rc-o319 RBD and R. cornutus ACE2 complex

SupramoleculeName: Rc-o319 RBD and R. cornutus ACE2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhinolophus cornutus (Little Japanese Horseshoe Bat)
Molecular weightTheoretical: 99.73 kDa/nm

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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: Rhinolophus cornutus (Little Japanese Horseshoe Bat)
Molecular weightTheoretical: 69.564234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STTEDEAKKF LNDFNSEAEN LTYQSSLASW DYNTNISDEN VQKMDEAGAK WSAFYEEQSK IAKNYPLEEI QTDIVKRQLQ ILQQSGSPV LSEDKSKRLN SILNAMSTIY STGKVCKPNN PQECLLLEPG LDNIMGTSKD YHERLWAWEG WRAEVGKQLR P LYEEYVVL ...String:
STTEDEAKKF LNDFNSEAEN LTYQSSLASW DYNTNISDEN VQKMDEAGAK WSAFYEEQSK IAKNYPLEEI QTDIVKRQLQ ILQQSGSPV LSEDKSKRLN SILNAMSTIY STGKVCKPNN PQECLLLEPG LDNIMGTSKD YHERLWAWEG WRAEVGKQLR P LYEEYVVL KNEMARGYHY EDYGDYWRRD YETEESSGPG YSRDQLMKDV DRIFTEIKPL YEHLHAYVRA KLMDTYPLHI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPNIDVTD EMVKQGWDAN RIFKEAEKFF VSVGLPNMTE GFWNNSMLTE PGD GRKVVC HPTAWDLGKG DFRIKMCTKV TMEDFLTAHH EMGHIQYDMA YASQPYLLRN GANEGFHEAV GEVMSLSVAT PKHL KTMGL LSPDFREDDE TEINFLLKQA LNIVGTLPFT YMLEKWRWMV FKGEIPKEEW MKKWWEMRRE IVGVVEPVPH DETYC DPAS LFHVANDYSF IRYYTRTIFE FQFHEALCRI AQHNGPLHKC DISNSTDAGK KLHQMLSVGK SQAWTKTLED IVGSRN MDV GPLLRYFEPL YTWLQEQNRK SYVGWNTDWS PYSD

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus
Molecular weightTheoretical: 133.626016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EFKLATMGIL PSPGMPALLS LVSLLSVLLM GCVAETGVYG CVNITYGSHH LYVSSRTRGV YYPDDAFRSS TNVLHEGFFL PFDSNVTWY SFWNQKYSVA TSPFGDGVYF STIDKSNVVR GWVFGTTLDN DTQSVLLYND GTHVRVEVCT FHFCPTPVFS A SSPHLYSS ...String:
EFKLATMGIL PSPGMPALLS LVSLLSVLLM GCVAETGVYG CVNITYGSHH LYVSSRTRGV YYPDDAFRSS TNVLHEGFFL PFDSNVTWY SFWNQKYSVA TSPFGDGVYF STIDKSNVVR GWVFGTTLDN DTQSVLLYND GTHVRVEVCT FHFCPTPVFS A SSPHLYSS AFNCTLNYTL ASVRADFTEV DGSFKTIREF VFKLQDGSLN VYYASTSYVL AIGATSQLPS GVTPLVPLWK IP IGLNITN FKTLVYLRSD NTPLQAAYVV GHLKRRTMMF KYDENGTIVD AIDCALDPLS ETKCTLRSFI VEKGIYQTSN FRV QPQDTV VRFPNITNLC PFSEVFNATT FASVYAWNRK RISNCVADYS VLYNSTSFST FQCYGVSSTK LNDLCFTNVY ADSF VVRGD EVRQIAPGQT GVIADYNYKL PDDFTGCVLA WNSRNQDAST SGNFNYYYRI WRSEKLRPFE RDIAHYDYQV GTQFK SSLK NYGFYSSAGD SHQPYRVVVL SFELLNAPAT VCGPKQSTEL IKNKCVNFNF NGLTGTGVLT DSNKKFQSFQ QFGRDV SDF TDSVKDPKTL EVLDITPCSY GGVSVITPGT NASTQVAVLY QDVNCTDVPT AIHAEQLTPS WRVYSTGTNM FQTQAGC LI GAEHVNNSYD CDIPIGAGIC ATYHTPSMLR SANNNKRIVA YVMSLGAENS VAYSNNTIAI PTNFTISVTT EVMPVSMT K TSVDCTMYIC GDSVECSTLL LQYGSFCTQL NRALTGIAVE QDKNTQEVFA QVKQIYKTPD IKDFGGFNFS QILPDPSKP SKRSPIEDLL FNKVTLADAG FVKQYGDCLG DIQARDLICA QKFNGLTVLP PLLTDEMIAA YTAALISGTA TAGWTFGAGP ALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQESLTST PSALGKLQDV VNQNAQALNT LVKQLSSNFG A ISSVLNDI ISRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SF PQAAPHG VVFLHVTYIP SQERNFTTAP AICHEGKAHF PREGVFVSNG THWFITQRNF YEPQIITTDN TFVSGTCDVV IGI VNNTVY DPLQPELESF KDELDKYFKN HTSPDIDLGD ISGINASVVD IQKEIDILKD VAKNLNESLI NLQELGKYEQ YIGT KHHHH HH

UniProtKB: Spike glycoprotein

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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: 7.5
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1330941
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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