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- EMDB-48348: Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M... -

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Entry
Database: EMDB / ID: EMD-48348
TitleStructure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-B8 Fab
Map data
Sample
  • Complex: SARS-CoV-2 Spike 6P in complex with M8b-B8 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2 spike glycoprotein
      • Protein or peptide: Spike glycoprotein
    • Complex: M8b-B8 Fab
      • Protein or peptide: M8b-B8 heavy chain
      • Protein or peptide: M8b-B8 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsimmune system / neutralizing antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFan C / Bjorkman PJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI165075 United States
Bill & Melinda Gates Foundation United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Authors: Chengcheng Fan / Jennifer R Keeffe / Kathryn E Malecek / Alexander A Cohen / Anthony P West / Viren A Baharani / Annie V Rorick / Han Gao / Priyanthi N P Gnanapragasam / Semi Rho / Jaasiel ...Authors: Chengcheng Fan / Jennifer R Keeffe / Kathryn E Malecek / Alexander A Cohen / Anthony P West / Viren A Baharani / Annie V Rorick / Han Gao / Priyanthi N P Gnanapragasam / Semi Rho / Jaasiel Alvarez / Luisa N Segovia / Theodora Hatziioannou / Paul D Bieniasz / Pamela J Bjorkman /
Abstract: Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) ...Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike-antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.
History
DepositionDec 18, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48348.png

Downloads & links

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Map

FileDownload / File: emd_48348.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 312.84 Å		0.87 Å/pix.
x 360 pix.
= 312.84 Å		0.87 Å/pix.
x 360 pix.
= 312.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.869 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6996045 - 1.070108
Average (Standard dev.)0.00015838529 (±0.026016926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 312.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_48348_additional_1.map
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Additional map: Map for local refinement

Fileemd_48348_additional_2.map
AnnotationMap for local refinement
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Half map: #2

Fileemd_48348_half_map_1.map
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Half map: #1

Fileemd_48348_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 Spike 6P in complex with M8b-B8 Fab

EntireName: SARS-CoV-2 Spike 6P in complex with M8b-B8 Fab
Components
  • Complex: SARS-CoV-2 Spike 6P in complex with M8b-B8 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2 spike glycoprotein
      • Protein or peptide: Spike glycoprotein
    • Complex: M8b-B8 Fab
      • Protein or peptide: M8b-B8 heavy chain
      • Protein or peptide: M8b-B8 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 Spike 6P in complex with M8b-B8 Fab

SupramoleculeName: SARS-CoV-2 Spike 6P in complex with M8b-B8 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 25 KDa

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Supramolecule #2: Severe acute respiratory syndrome coronavirus 2 spike glycoprotein

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 spike glycoprotein
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: stabilized with hexaproline
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: M8b-B8 Fab

SupramoleculeName: M8b-B8 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 139.344438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPA SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NQNAQALNTL V KQLSSNFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ YIKWPSGRLV PRGSPGSGYI PEAPRDGQAY VRKDGEWVLL STFLGHHHHH H

UniProtKB: Spike glycoprotein

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Macromolecule #2: M8b-B8 heavy chain

MacromoleculeName: M8b-B8 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 23.555324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QEQLEESGGG LVKPEGSLTL TCTASGFSFS SSYWICWVRQ APGKGLEWIG CIYTGDGSTY YATWAKGRFT ISKASSTTVT LQMTSLTAA DTATYFCTRE GGWYDLNLWG PGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QEQLEESGGG LVKPEGSLTL TCTASGFSFS SSYWICWVRQ APGKGLEWIG CIYTGDGSTY YATWAKGRFT ISKASSTTVT LQMTSLTAA DTATYFCTRE GGWYDLNLWG PGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDK

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Macromolecule #3: M8b-B8 light chain

MacromoleculeName: M8b-B8 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 23.683234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ADIVMTQTPA SVEAAVGGTV TINCQASESI SNYLSWYQQK PGQRPKLLIY YASTLASGVS SRFKGSRSGT EYTLTISDLE CADAATYYC QSAADSISDK RHAFGGGTEV LVKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
ADIVMTQTPA SVEAAVGGTV TINCQASESI SNYLSWYQQK PGQRPKLLIY YASTLASGVS SRFKGSRSGT EYTLTISDLE CADAATYYC QSAADSISDK RHAFGGGTEV LVKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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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: 31 / 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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMTrisTris
0.02 %NaN3Sodium azide
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 2634 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 576218
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7sc1

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 148375
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3)

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Atomic model buiding 1

Initial model
PDB IDChain

7uzd

source_name: PDB, initial_model_type: experimental model

7sc1

source_name: PDB, initial_model_type: experimental model
SoftwareName: UCSF Chimera (ver. 1.18)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 90
Output model

PDB-9ml5:
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-B8 Fab

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