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- EMDB-73426: Local refinement of hACE2/SARS-CoV-2 BA.3.2.1 spike, conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-73426
TitleLocal refinement of hACE2/SARS-CoV-2 BA.3.2.1 spike, conformation 1
Map dataSharpen Local-refinement map
Sample
  • Complex: hACE2/SARS-CoV-2 BA.3.2.1 spike, conformation 1
    • Protein or peptide: Angiotensin-converting enzyme 2
    • Protein or peptide: SARS-CoV-2 BA.3.2.1 spike RBD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / VIRAL PROTEIN / VIRAL PROTEIN-Hydrolase complex
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 / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / apical plasma membrane / cilium / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / 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.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsWang Y / Hu Y / Chen Z / Liang B / Xie X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural characteristics of the SARS-CoV-2 Omicron subvariant BA.3.2 and LP.8.1 spike protein
Authors: Wang Y / Hu Y / Chen Z / Liang B / Xie X
History
DepositionOct 19, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73426.png

Downloads & links

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Map

FileDownload / File: emd_73426.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpen Local-refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 399.36 Å		0.83 Å/pix.
x 480 pix.
= 399.36 Å		0.83 Å/pix.
x 480 pix.
= 399.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.0018572266 - 1.8430359
Average (Standard dev.)0.00027346093 (±0.011935076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 399.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local-refinement map

Fileemd_73426_additional_1.map
AnnotationLocal-refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_73426_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_73426_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hACE2/SARS-CoV-2 BA.3.2.1 spike, conformation 1

EntireName: hACE2/SARS-CoV-2 BA.3.2.1 spike, conformation 1
Components
  • Complex: hACE2/SARS-CoV-2 BA.3.2.1 spike, conformation 1
    • Protein or peptide: Angiotensin-converting enzyme 2
    • Protein or peptide: SARS-CoV-2 BA.3.2.1 spike RBD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: hACE2/SARS-CoV-2 BA.3.2.1 spike, conformation 1

SupramoleculeName: hACE2/SARS-CoV-2 BA.3.2.1 spike, conformation 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.972852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSSSWLLLS LVAVTAAQST IEEQAKTFLD KFNHEAEDLF YQSSLASWNY NTNITEENVQ NMNNAGDKWS AFLKEQSTLA QMYPLQEIQ NLTVKLQLQA LQQNGSSVLS EDKSKRLNTI LNTMSTIYST GKVCNPDNPQ ECLLLEPGLN EIMANSLDYN E RLWAWESW ...String:
MSSSSWLLLS LVAVTAAQST IEEQAKTFLD KFNHEAEDLF YQSSLASWNY NTNITEENVQ NMNNAGDKWS AFLKEQSTLA QMYPLQEIQ NLTVKLQLQA LQQNGSSVLS EDKSKRLNTI LNTMSTIYST GKVCNPDNPQ ECLLLEPGLN EIMANSLDYN E RLWAWESW RSEVGKQLRP LYEEYVVLKN EMARANHYED YGDYWRGDYE VNGVDGYDYS RGQLIEDVEH TFEEIKPLYE HL HAYVRAK LMNAYPSYIS PIGCLPAHLL GDMWGRFWTN LYSLTVPFGQ KPNIDVTDAM VDQAWDAQRI FKEAEKFFVS VGL PNMTQG FWENSMLTDP GNVQKAVCHP TAWDLGKGDF RILMCTKVTM DDFLTAHHEM GHIQYDMAYA AQPFLLRNGA NEGF HEAVG EIMSLSAATP KHLKSIGLLS PDFQEDNETE INFLLKQALT IVGTLPFTYM LEKWRWMVFK GEIPKDQWMK KWWEM KREI VGVVEPVPHD ETYCDPASLF HVSNDYSFIR YYTRTLYQFQ FQEALCQAAK HEGPLHKCDI SNSTEAGQKL FNMLRL GKS EPWTLALENV VGAKNMNVRP LLNYFEPLFT WLKDQNKNSF VGWSTDWSPY ADGSHHHHHH

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #2: SARS-CoV-2 BA.3.2.1 spike RBD

MacromoleculeName: SARS-CoV-2 BA.3.2.1 spike RBD / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 141.2345 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLLL VSSQCVNLTT TTQLPLAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNIT RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFNNKSWM ESESRVYSSA KNCTFEYVFQ P FLMDLEGK ...String:
MFVFLVLLLL VSSQCVNLTT TTQLPLAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNIT RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFNNKSWM ESESRVYSSA KNCTFEYVFQ P FLMDLEGK QGNFTNLREF VFKNIDGYFK IYSKHTPIIV RDLPQGFSAL EPLVDLPIGI NITRFQTLLH RSYLTSGDSS SG WTAGAAA YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSNFRVQPTE SVVRFPNITN LCP FYEVFN ATRFPSVYAW NRKRISNCVA DYSVLYNFAP FFTFKCYGVS PTKLNDLCFT NVYADSFVIK GNEVSQIAPG QTGN IADYN YKLPDDFTGC VISWNSNRLD SKADGNYNYW YRLFRKSKLK PFERDISTEI YQAGNNPCNG VKGFNCYFPL QSYSF RPTY GVGYQPYRVV VLSFELLHAP ATVCGPKNST NLVKNKCVNF NFNGLTGTGV LTDSNKKFLP FQQFGRDIAD TTDAVR DPQ TLDILDITPC SFGGVSVITP GTNTSNQVAV LYQGVNCTEV PVAIRADQLT PTWRVYSTGS KGFQTRAGCL IGAKYVN NS YECDIPIGAG ICASYQTQTR SRGSASSVDS QSIIAYTMSL GAENLVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVD C TMYICGDSTE CSNLLLQYGS FCTQLKRALT GIAVEQDKNT QEVFAQVKQI YKTPPITYFG GFNFSQILPD PSKPSKRSP IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICKQKFNG LTVLPPLLTD EMIAQYTSAL LAGTITSGWT FGAGPALQIP FPMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLFSTPSALG KLQDVVNHNA QALNTLVKQL SSKFGAISSV L NDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS AP HGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRNFYEPQI ITTDNTFVSG NCDVVIGIVN NTV YDPLQP ELDSFKEELD KYFKNHTSRD VDLGDISGIN ASVVNIQKEI ERLNEVAKNL NESLIDLQEL GKYEQGSGYI PEAP RDGQA YVRKDGEWVL LSTFLGRSLE VLFQGPGHHH HHHHHSAWSH PQFEKGGGSG GGGSGGSAWS HPQFEK

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / 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

Concentration1.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTristris (hydroxymethyl) aminomethane
200.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 10500
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 278738
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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