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- EMDB-44666: Cryo-EM of RBD(EG5.1)/1301B7 Fab Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44666
TitleCryo-EM of RBD(EG5.1)/1301B7 Fab Complex
Map datalocal refined map
Sample
  • Complex: Complex of RBDeg5.1 with Fab 1301B7
    • Protein or peptide: 1301B7 Heavy Chain
    • Protein or peptide: 1301B7 Light Chain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFab / RBD / Complex / PROTEIN BINDING / 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 speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWalter MR / Green TJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI161175 United States
CitationJournal: Npj Viruses / Year: 2024
Title: Potent neutralization by a RBD antibody with broad specificity for SARS-CoV-2 JN.1 and other variants.
Authors: Michael S Piepenbrink / Ahmed Magdy Khalil / Ana Chang / Ahmed Mostafa / Madhubanti Basu / Sanghita Sarkar / Simran Panjwani / Yaelyn H Ha / Yao Ma / Chengjin Ye / Qian Wang / Todd J Green / ...Authors: Michael S Piepenbrink / Ahmed Magdy Khalil / Ana Chang / Ahmed Mostafa / Madhubanti Basu / Sanghita Sarkar / Simran Panjwani / Yaelyn H Ha / Yao Ma / Chengjin Ye / Qian Wang / Todd J Green / James L Kizziah / Nathaniel B Erdmann / Paul A Goepfert / Lihong Liu / David D Ho / Luis Martinez-Sobrido / Mark R Walter / James J Kobie /
Abstract: SARS-CoV-2 continues to be a public health burden, driven in-part by its continued antigenic diversification and resulting emergence of new variants. By increasing herd immunity, current vaccines ...SARS-CoV-2 continues to be a public health burden, driven in-part by its continued antigenic diversification and resulting emergence of new variants. By increasing herd immunity, current vaccines have improved infection outcomes for many. However, prophylactic and treatment interventions that are not compromised by viral evolution of the Spike protein are still needed. Using a differential staining strategy with a rationally designed SARS-CoV-2 Receptor Binding Domain (RBD) - ACE2 fusion protein and a native Omicron RBD protein, we developed a recombinant human monoclonal antibody (hmAb) from a convalescent individual following SARS-CoV-2 Omicron infection. The resulting hmAb, 1301B7 potently neutralized a wide range of SARS-CoV-2 variants including the original Wuhan-1, the more recent Omicron JN.1 strain, and SARS-CoV. 1301B7 contacts the ACE2 binding site of RBD exclusively through its VH1-69 heavy chain. Broad specificity is achieved through 1301B7 binding to many conserved residues of Omicron variants including Y501 and H505. Consistent with its extensive binding epitope, 1301B7 is able to potently diminish viral burden in the upper and lower respiratory tract and protect mice from challenge with Omicron XBB1.5 and Omicron JN.1 viruses. These results suggest 1301B7 has broad potential to prevent or treat clinical SARS-CoV-2 infections and to guide development of RBD-based universal SARS-CoV-2 prophylactic vaccines and therapeutic approaches.
History
DepositionApr 30, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44666.png

Downloads & links

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Map

FileDownload / File: emd_44666.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 357.7 Å		0.89 Å/pix.
x 400 pix.
= 357.7 Å		0.89 Å/pix.
x 400 pix.
= 357.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89425 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.048
Minimum - Maximum-0.44283277 - 0.62834966
Average (Standard dev.)-0.0000948364 (±0.008568853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 357.69998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map-A

Fileemd_44666_half_map_1.map
Annotationhalf-map-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halp-map-B

Fileemd_44666_half_map_2.map
Annotationhalp-map-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of RBDeg5.1 with Fab 1301B7

EntireName: Complex of RBDeg5.1 with Fab 1301B7
Components
  • Complex: Complex of RBDeg5.1 with Fab 1301B7
    • Protein or peptide: 1301B7 Heavy Chain
    • Protein or peptide: 1301B7 Light Chain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of RBDeg5.1 with Fab 1301B7

SupramoleculeName: Complex of RBDeg5.1 with Fab 1301B7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Fab generated by proteolytic cleavage
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 1301B7 Heavy Chain

MacromoleculeName: 1301B7 Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.768365 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGAE VKNPGSSVKV SCKASEGTFG SYPIIWVRQA PGQGLEWVGG IIPILGTVIY AQKFQGRVTI TGDTYAGSAH MELSGLRSE DTAVFYCARG SYDYGDRLLN YTYYAMDVWG PGTTVTVSS

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Macromolecule #2: 1301B7 Light Chain

MacromoleculeName: 1301B7 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.517782 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QPGLTQPPSV SGAPGQRVTI SCTGSRSNIG AVYAVHWYQH VPGAAPKLLI YENNNRPSGI PDRFSGSKSG TSASLVITGL QAEDEADYL CQSYDRSVGV VFGGGTRLTV L

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Macromolecule #3: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 137.934078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPTLLWSLL LLLGVFAAAA AAYTNSFTRG VYYPDKVFRS SVLHSTHDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPALP FNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY QKNNKSWMES EFRVYSSANN C TFEYVSQP ...String:
MRPTLLWSLL LLLGVFAAAA AAYTNSFTRG VYYPDKVFRS SVLHSTHDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPALP FNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY QKNNKSWMES EFRVYSSANN C TFEYVSQP FLMDLEGKEG NFKNLREFVF KNIDGYFKIY SKHTPINLER DLPQGFSALE PLVDLPIGIN ITRFQTLLAL HR SYLTPVD SSSGWTAGAA AYYVGYLQPR TFLLKYNENG TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESI VRFPNI TNLCPFHEVF NATTFASVYA WNRKRISNCV ADYSVIYNFA PFFAFKCYGV SPTKLNDLCF TNVYADSFVI RGNE VSQIA PGQTGNIADY NYKLPDDFTG CVIAWNSNNL DSKPSGNYNY LYRLLRKSKL KPFERDISTE IYQAGNKPCN GVAGP NCYS PLQSYGFRPT YGVGHQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFG RDI ADTTDAVRDP QTLEILDITP CSFGGVSVIT PGTNTSNQVA VLYQGVNCTE VPVAIHADQL TPTWRVYSTG SNVFQTR AG CLIGAEYVNN SYECDIPIGA GICASYQTQT KSHGSAGSVA SQSIIAYTMS LGAENSVAYS NNSIAIPTNF TISVTTEI L PVSMTKTSVD CTMYICGDST ECSNLLLQYG SFCTQLKRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPIKYF GGFNFSQIL PDPSKPSKRS PIEDLLFNKV TLADAGFIKQ YGDCLGDIAA RDLICAQKFN GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGPALQ IPFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTPSAL GKLQDVVNHN AQALNTLVKQ L SSKFGAIS SVLNDILSRL DPPEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KG YHLMSFP QSAPHGVVFL HVTYVPAQEK NFTTAPAICH DGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GNC DVVIGI VNNTVYDPLQ PELDSFKEEL DKYFKNHTSP DVDLGDISGI NASVVNIQKE IDRLNEVAKN LNESLIDLQE LGKY EQYIA SSGYIPEAPR DGQAYVRKDG EWVLLSTFLE GTKHHHHHH

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: 1 / 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

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMhepes
50.0 mMsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm

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Image processing

Particle selectionNumber selected: 1113228
Startup modelType of model: OTHER / Details: InSilico model for Fab PDB entry for RBD
Final reconstructionNumber classes used: 5 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88411
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.41)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.41) / Details: local refinement
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC (ver. 4.41)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8iou

chain_id: A, residue_range: 330-532, source_name: PDB, initial_model_type: experimental model
chain_id: H, source_name: Other, initial_model_type: in silico modelIgFold
chain_id: L, source_name: Other, initial_model_type: in silico modelIgFold
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9bll:
Cryo-EM of RBD(EG5.1)/1301B7 Fab Complex

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