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- EMDB-46691: Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nat... -

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Basic information

Entry
Database: EMDB / ID: EMD-46691
TitleMerbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2
Map data
Sample
  • Complex: Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2
    • Protein or peptide: ACE2
    • Protein or peptide: Spike glycoprotein receptor binding domain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water
KeywordsMerbecovirus / Spike glycoprotein / fusion protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / inhibitor / VIRAL PROTEIN
Biological speciesMerbecovirus / Pipistrellus nathusii (Nathusius's pipistrelle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsPark YJ / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: Cell / Year: 2025
Title: Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses.
Authors: Cheng-Bao Ma / Chen Liu / Young-Jun Park / Jingjing Tang / Jing Chen / Qing Xiong / Jimin Lee / Cameron Stewart / Daniel Asarnow / Jack Brown / M Alejandra Tortorici / Xiao Yang / Ye-Hui Sun ...Authors: Cheng-Bao Ma / Chen Liu / Young-Jun Park / Jingjing Tang / Jing Chen / Qing Xiong / Jimin Lee / Cameron Stewart / Daniel Asarnow / Jack Brown / M Alejandra Tortorici / Xiao Yang / Ye-Hui Sun / Yuan-Mei Chen / Xiao Yu / Jun-Yu Si / Peng Liu / Fei Tong / Mei-Ling Huang / Jing Li / Zheng-Li Shi / Zengqin Deng / David Veesler / Huan Yan /
Abstract: The angiotensin-converting enzyme 2 (ACE2) receptor is shared by various coronaviruses with distinct receptor-binding domain (RBD) architectures, yet our understanding of these convergent acquisition ...The angiotensin-converting enzyme 2 (ACE2) receptor is shared by various coronaviruses with distinct receptor-binding domain (RBD) architectures, yet our understanding of these convergent acquisition events remains elusive. Here, we report that two bat MERS-related coronaviruses (MERSr-CoVs) infecting Pipistrellus nathusii (P.nat)-MOW15-22 and PnNL2018B-use ACE2 as their receptor, with narrow ortholog specificity. Cryoelectron microscopy structures of the MOW15-22/PnNL2018B RBD-ACE2 complexes unveil an unexpected and entirely distinct binding mode, mapping >45 Å away from that of any other known ACE2-using coronaviruses. Functional profiling of ACE2 orthologs from 105 mammalian species led to the identification of host tropism determinants, including an ACE2 N432-glycosylation restricting viral recognition, and the design of a soluble P.nat ACE2 mutant with potent viral neutralizing activity. Our findings reveal convergent acquisition of ACE2 usage for merbecoviruses found in European bats, underscoring the extraordinary diversity of ACE2 recognition modes among coronaviruses and the promiscuity of this receptor.
History
DepositionAug 22, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46691.png

Downloads & links

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Map

FileDownload / File: emd_46691.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 320 pix.
= 320.352 Å		1 Å/pix.
x 320 pix.
= 320.352 Å		1 Å/pix.
x 320 pix.
= 320.352 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0011 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.7472872 - 3.3089924
Average (Standard dev.)0.0006914455 (±0.047204092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 320.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_46691_additional_1.map
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Half map: #1

Fileemd_46691_half_map_1.map
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Half map: #2

Fileemd_46691_half_map_2.map
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Sample components

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Entire : Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nat...

EntireName: Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2
Components
  • Complex: Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2
    • Protein or peptide: ACE2
    • Protein or peptide: Spike glycoprotein receptor binding domain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nat...

SupramoleculeName: Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Merbecovirus

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Macromolecule #1: ACE2

MacromoleculeName: ACE2 / type: protein_or_peptide / ID: 1
Details: N-terminal tag: MGGEGLRASPRRRPLLPLQPRGCPRGDGCLRGGRGRAGFGFWRVTGGSRASANHVHAFFFFLQLLGNVLVIVLSHHFGKEFATMPMGSLQPLATLYLLGMLVASVLA C-terminal tag: ...Details: N-terminal tag: MGGEGLRASPRRRPLLPLQPRGCPRGDGCLRGGRGRAGFGFWRVTGGSRASANHVHAFFFFLQLLGNVLVIVLSHHFGKEFATMPMGSLQPLATLYLLGMLVASVLA C-terminal tag: PTLGPPYQPPVTGTGGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGGGSDYKDHDGDYKDHDIDYKDDDDKL
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pipistrellus nathusii (Nathusius's pipistrelle)
Molecular weightTheoretical: 102.102375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSRA SANHVHAFFF FLQLLGNVLV IVLSHHFGKE FATMPMGSL QPLATLYLLG MLVASVLAQS LTTEEKAREF LDKFNSEAEN WSHESALASW DYNTNINDKN AQKMNEADSK W SAFYKEHS ...String:
MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSRA SANHVHAFFF FLQLLGNVLV IVLSHHFGKE FATMPMGSL QPLATLYLLG MLVASVLAQS LTTEEKAREF LDKFNSEAEN WSHESALASW DYNTNINDKN AQKMNEADSK W SAFYKEHS KLAQGFPLQE IQNSTIKLQL QILQQNGSSV LTAEKSKRLS TILTTMSTIY STGKVCNPNN PQQCFTLSGL ED IMEKSKD YHQRLWIWEG WRSEVGKQLR PLYEEYVALK NEMARGNNYK DYGDYWRGDY ETEGGDGYNY SRNHLIEDVD RIF LEIKPL YEQLHAYVRA KLMNAYPSRI SPTGCLPAHL LGDMWGRFWT NLYNLTVPFE KKQNIDVTDT MKKQSWDAEK IFKE AEKFY LSVGLHNMTP EFWNNSMLTE PSDGRQVVCH PTAWDLGKND FRIKMCTKVT MDDFLTAHHE MGHIQYDMAY AKQPY LLRN GANEGFHEAV GEIMSLSAAT PKHLKDLGLL AQNYPEDYET EINFLLKQAL NIVGTLPFTY MLEKWRWMVF EGKIPK EQW MEKWWEMKRE IVGVVEPLPH DETYCDPASL FHVANDYSFI RYFTRTILEF QFQEALCQIA NHTGPLHKCD ISNSTEA GK QLKNMLELGK SKPWTFALEQ IARTKEMDAK PLLNYFKPLF SWLKELNGNS VGWSADWSPY SEQSIKVRIS LKSALGEK A YEWNDNEMYL FRSSVAYAMR VYFLKVKNET IPFRAEDVWV SDEKIRVSFK FFVTSPTNVS DIIPRSEVED AIRMSRGRI NDAFRLDDKT LEFLGIQPTL GPPYQPPVTG TGGGSWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGGGGSDY KDHDGDYKDH DIDYKDDDD KL

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Macromolecule #2: Spike glycoprotein receptor binding domain

MacromoleculeName: Spike glycoprotein receptor binding domain / type: protein_or_peptide / ID: 2
Details: N-terminal tag: MGILPSPGMPALLSLVSLLSVLLMGCVAETGT C-terminal tag: LVPRGSSSGGSGLNDIFEAQKIEWHEGGSHHHHHHHH
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Merbecovirus / Strain: PnNL2018B
Molecular weightTheoretical: 34.357488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTYSVSSFEA RPQGSFVESV YEGNECDFTK LFRGPVPQPY EFGRLVFTNC NYNFTKLLS YFQVDAFECK KVTPESIATG CYSSLTVDWF AYRVADKSDL LPGSSSDLQR FNYKPTYAHP TCLISAYTDL S ALGGSNPT ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTYSVSSFEA RPQGSFVESV YEGNECDFTK LFRGPVPQPY EFGRLVFTNC NYNFTKLLS YFQVDAFECK KVTPESIATG CYSSLTVDWF AYRVADKSDL LPGSSSDLQR FNYKPTYAHP TCLISAYTDL S ALGGSNPT NYTLLTNCYG CVGQPPKRTC LEEFPSFVEA GYRPKPSCAR IGMQGHASGN ETYTAVVTNN ELDSVGDPIW RM GVAQTKE PSVTDKAELA FFVSVQIDSQ SSSVCPLGSP KLVPRGSSSG GSGLNDIFEA QKIEWHEGGS HHHHHHHH

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 144 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
VitrificationCryogen name: ETHANE

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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: 3.5 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1555546
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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