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- EMDB-63852: Cryo-EM Structure of Human ACE2 Complexed with RacCS20637 RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-63852
TitleCryo-EM Structure of Human ACE2 Complexed with RacCS20637 RBD
Map data
Sample
  • Complex: RacCS20637 RBD and R. cornutus ACE2 complex
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCOMPLEX / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of systemic arterial blood pressure by renin-angiotensin / maternal process involved in female pregnancy / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of systemic arterial blood pressure by renin-angiotensin / maternal process involved in female pregnancy / regulation of cardiac conduction / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / viral life cycle / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / apical plasma membrane / cilium / endocytosis involved in viral entry into host cell / membrane raft / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / cell surface / negative regulation of transcription by RNA polymerase II / : / extracellular exosome / extracellular region / zinc ion binding / membrane / identical protein binding / plasma membrane
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. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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 2
Similarity search - Component
Biological speciesCoronaviridae (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsMatsumoto K / Akasaka H / Shihoya W / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Cell / Year: 2026
Title: Virological characteristics of SARS-CoV-2-related coronaviruses dynamically circulating in Southeast Asia.
Authors: Supaporn Wacharapluesadee / Wilaiporn Saikruang / Spyros Lytras / Kanata Matsumoto / Keiya Uriu / Alfredo Hinay / Ziyi Guo / Khwankamon Rattanatumhi / Ananporn Supataragul / Sasiprapa ...Authors: Supaporn Wacharapluesadee / Wilaiporn Saikruang / Spyros Lytras / Kanata Matsumoto / Keiya Uriu / Alfredo Hinay / Ziyi Guo / Khwankamon Rattanatumhi / Ananporn Supataragul / Sasiprapa Ninwattana / Nattakarn Thippamom / Tanawut Srisuk / Patarapol Maneeorn / Kirana Noradechanon / Prateep Duengkae / Nutthinee Sirichan / Yusuke Kosugi / Shigeru Fujita / Maximilian Stanley Yo / Ryo Matsunaga / Bingjie Hu / Lianzhao Du / Lei Wang / Masumi Tsuda / Yoshitaka Oda / Hesham Nasser / Kanako Terakado Kimura / Hiroaki Akasaka / Hiroyuki Asakura / Mami Nagashima / Kenji Sadamasu / Kazuhisa Yoshimura / Yuki Yamamoto / Tetsuharu Nagamoto / Takanori Asakura / Wataru Shihoya / Takao Hashiguchi / Terumasa Ikeda / Shinya Tanaka / Hin Chu / Kouhei Tsumoto / Osamu Nureki / / / Arnon Plianchaisuk / Opass Putcharoen / Kei Sato /
Abstract: By sampling horseshoe bats-the reservoir hosts of SARS-CoV-2-related coronaviruses (SC2r-CoVs)-in Thailand, we present two clades of SC2r-CoVs co-circulating in the same bat population. Through a ...By sampling horseshoe bats-the reservoir hosts of SARS-CoV-2-related coronaviruses (SC2r-CoVs)-in Thailand, we present two clades of SC2r-CoVs co-circulating in the same bat population. Through a comprehensive set of experimental approaches, including cryo-electron microscopy (cryo-EM), pseudovirus and live virus assays, and hamster experiments, we characterize the virological properties of these new viruses. We show that one of the two clades discovered in this study is able to bind the human angiotensin converting enzyme 2 (ACE2) receptor; however, it exhibits reduced fusogenicity and replication in vitro and lower pathogenicity and transmissibility compared with SARS-CoV-2. Phylogeography and recombination analyses reveal a complex evolutionary history for these viruses characterized by extensive, recent geographic movement and recombination with co-circulating virus lineages. Our findings provide new insights into the diversity of SC2r-CoVs dynamically co-circulating in Southeast Asia as well as the virological characteristics of these viruses relative to SARS-CoV-2.
History
DepositionMar 19, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63852.png

Downloads & links

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Map

FileDownload / File: emd_63852.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 265.608 Å		1.11 Å/pix.
x 240 pix.
= 265.608 Å		1.11 Å/pix.
x 240 pix.
= 265.608 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1067 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.4317134 - 0.8588572
Average (Standard dev.)-0.0009278159 (±0.018617969)
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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Mask #1

Fileemd_63852_msk_1.map
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Half map: #2

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Half map: #1

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Sample components

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Entire : RacCS20637 RBD and R. cornutus ACE2 complex

EntireName: RacCS20637 RBD and R. cornutus ACE2 complex
Components
  • Complex: RacCS20637 RBD and R. cornutus ACE2 complex
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: RacCS20637 RBD and R. cornutus ACE2 complex

SupramoleculeName: RacCS20637 RBD and R. cornutus ACE2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Coronaviridae (virus)

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Macromolecule #1: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.322711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GSTIEEQAKT FLDKFNHEAE DLFYQSSLAS WNYNTNITEE NVQNMNNAGD KWSAFLKEQ STLAQMYPLQ EIQNLTVKLQ LQALQQNGSS VLSEDKSKRL NTILNTMSTI YSTGKVCNPD NPQECLLLEP G LNEIMANS ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GSTIEEQAKT FLDKFNHEAE DLFYQSSLAS WNYNTNITEE NVQNMNNAGD KWSAFLKEQ STLAQMYPLQ EIQNLTVKLQ LQALQQNGSS VLSEDKSKRL NTILNTMSTI YSTGKVCNPD NPQECLLLEP G LNEIMANS LDYNERLWAW ESWRSEVGKQ LRPLYEEYVV LKNEMARANH YEDYGDYWRG DYEVNGVDGY DYSRGQLIED VE HTFEEIK PLYEHLHAYV RAKLMNAYPS YISPIGCLPA HLLGDMWGRF WTNLYSLTVP FGQKPNIDVT DAMVDQAWDA QRI FKEAEK FFVSVGLPNM TQGFWENSML TDPGNVQKAV CHPTAWDLGK GDFRILMCTK VTMDDFLTAH HEMGHIQYDM AYAA QPFLL RNGANEGFHE AVGEIMSLSA ATPKHLKSIG LLSPDFQEDN ETEINFLLKQ ALTIVGTLPF TYMLEKWRWM VFKGE IPKD QWMKKWWEMK REIVGVVEPV PHDETYCDPA SLFHVSNDYS FIRYYTRTLY QFQFQEALCQ AAKHEGPLHK CDISNS TEA GQKLFNMLRL GKSEPWTLAL ENVVGAKNMN VRPLLNYFEP LFTWLKDQNK NSFVGWSTDW SPYADGTKHH HHHH

UniProtKB: Angiotensin-converting enzyme 2

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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: Coronaviridae (virus)
Molecular weightTheoretical: 28.079803 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METGLRWLLL VAVLKGVQCR VQPTDSIVRF PNITNLCPFG EVFNATTFAS VYAWNRKRIS NCVADYSVLY NSTSFSTFKC YGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK S NLKPFERD ...String:
METGLRWLLL VAVLKGVQCR VQPTDSIVRF PNITNLCPFG EVFNATTFAS VYAWNRKRIS NCVADYSVLY NSTSFSTFKC YGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK S NLKPFERD ISTEIYQAGN EPCNGVEGFN CYFPLQSYGF HPTNGVGYQP YRVVVLSFEL LNAPATVCGP KKSTNLIKNK CV NFHHHHH H

UniProtKB: Spike glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / 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: 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: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110912
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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