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- EMDB-75725: 1332E5 Spike KP3.1.1 Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-75725
Title1332E5 Spike KP3.1.1 Complex
Map data
Sample
  • Complex: 1332E5 Fab / SARS-CoV-2 RBD KP3.1.1 Variant Complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: 1332E5 Heavy Chain
    • Protein or peptide: 1332E5 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFab / Complex / SARS-CoV-2 / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsKizziah JL / Walter MR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI161175 United States
CitationJournal: iScience / Year: 2026
Title: Emergence of neutralizing RBD antibodies following Omicron infection with limited activity against ancestral SARS-CoV-2.
Authors: Michael S Piepenbrink / Yao Ma / Simran Panjwani / Alexandra R Blake / Allison M Bell / James L Kizziah / Sara H Mahmoud / Gregory C Ippolito / Nathan B Erdmann / Paul A Goepfert / Luis ...Authors: Michael S Piepenbrink / Yao Ma / Simran Panjwani / Alexandra R Blake / Allison M Bell / James L Kizziah / Sara H Mahmoud / Gregory C Ippolito / Nathan B Erdmann / Paul A Goepfert / Luis Martinez-Sobrido / James J Kobie / Mark R Walter /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution reduces the efficacy of prophylactic vaccines and monoclonal antibody (mAb) therapies. To evaluate potency and breadth, receptor ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution reduces the efficacy of prophylactic vaccines and monoclonal antibody (mAb) therapies. To evaluate potency and breadth, receptor binding domain (RBD)-targeting neutralizing mAbs were identified from patient B cells using an Omicron KP3.1.1 Spike (S) protein bait. MAbs exhibiting the greatest neutralization potency (1332D4 and 1332E5) and binding breadth (1324A10 and 1316C10) were evaluated in greater detail. Cryo-electron microscopy (Cryo-EM) studies revealed 1332D4 and 1332E5 target RBD residue segments 439-446 and 498-506 of KP3.1.1 S, respectively. 1332E5 is a knob-targeting class-1/4 mAb that exhibits pan-Omicron specificity but does not bind or neutralize ancestral Wuhan-1. Further analysis suggests mAbs generically defined as class 1/4 mAbs may be separated into two classes. Class 1/4 mAbs, like 1332E5, and class 4/1 mAbs that make extensive interactions with the class-4 epitope and limited contacts with the class-1 knob. Despite these differences, the specificity of both mAb classes can be altered by mutations in knob.
History
DepositionFeb 26, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75725.png

Downloads & links

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Map

FileDownload / File: emd_75725.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.104 Å		0.72 Å/pix.
x 512 pix.
= 367.104 Å		0.72 Å/pix.
x 512 pix.
= 367.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.717 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.1645795 - 0.39485237
Average (Standard dev.)-0.0002747352 (±0.008486677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75725_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75725_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : 1332E5 Fab / SARS-CoV-2 RBD KP3.1.1 Variant Complex

EntireName: 1332E5 Fab / SARS-CoV-2 RBD KP3.1.1 Variant Complex
Components
  • Complex: 1332E5 Fab / SARS-CoV-2 RBD KP3.1.1 Variant Complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: 1332E5 Heavy Chain
    • Protein or peptide: 1332E5 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 1332E5 Fab / SARS-CoV-2 RBD KP3.1.1 Variant Complex

SupramoleculeName: 1332E5 Fab / SARS-CoV-2 RBD KP3.1.1 Variant Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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: 139.754953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSA YTNFTRGVYY PDKVFRSSVL HLTQDLFLPF FSNVTWFHAI SGTNGTKRFD NPVLPFNDGV YFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVFIK VCEFQFCNDP FLDVYHKNNK SWMESESGVY SSANNCTFEY V SQPFLMDL ...String:
MGWSCIILFL VATATGVHSA YTNFTRGVYY PDKVFRSSVL HLTQDLFLPF FSNVTWFHAI SGTNGTKRFD NPVLPFNDGV YFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVFIK VCEFQFCNDP FLDVYHKNNK SWMESESGVY SSANNCTFEY V SQPFLMDL EGKQGNFKNL REFVFKNIDG YFKIYSKHTP IIGRDFPQGF SALEPLVDLP IGINITRFQT LLALNRSYLT PG DSSSGWT AGAADYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQPTESIVRF PNV TNLCPF HEVFNATRFA SVYAWNRTRI SNCVADYSVL YNFAPFFAFK CYGVSPTKLN DLCFTNVYAD SFVIKGNEVS QIAP GQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKHSG NYDYWYRSLR KSKLKPFERD ISTEIYQAGN KPCKGKGPNC YFPLE SYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTKSNK KFLPFQQFGR DIVDTT DAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVSVAIHA DQLTPTWRVY STGSNVFQTR AGCLIGA EY VNNSYECDIP IGAGICASYQ TQTKSRGSAG SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTK T SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFSQ ILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGPA LQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLFSTP SALGKLQDVV NHNAQALNTL VKQLSSKFGA I SSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FP QSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFLTQRNFY EPQIITTDNT FVSGNCDVVI GIV NNTVYD PLQLELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQELGKYEQY IASS GYIPE APRDGQAYVR KDGEWVLLST FLEGTKHHHH HHHHGGSGGL NDIFEAQKIE WHE

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Macromolecule #2: 1332E5 Heavy Chain

MacromoleculeName: 1332E5 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.416613 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ VQLQQSGPGL VKPSETLSLT CTVSGGSISS YYWSWIRQPP GKGLEWIGYI YYSGLTNYNP SLKSRITLS VDTSKNQFSL KLNSVTAADT AVYYCATYVR LGGFWSGEAD AFDIWGPGTM VTVSSASTKG PSVFPLAPSS K STSGGTAA ...String:
MGWSCIILFL VATATGVHSQ VQLQQSGPGL VKPSETLSLT CTVSGGSISS YYWSWIRQPP GKGLEWIGYI YYSGLTNYNP SLKSRITLS VDTSKNQFSL KLNSVTAADT AVYYCATYVR LGGFWSGEAD AFDIWGPGTM VTVSSASTKG PSVFPLAPSS K STSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DK

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Macromolecule #3: 1332E5 Light Chain

MacromoleculeName: 1332E5 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.860705 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ SVLTQPASVS GSPGQSITIS CTGTSSDVGN YHLVSWYQQH PGKAPKLIIY EGSKRPSGVS NRFSGSKSG NTASLTISGL QAEDEADYYC CLYADSTTYV FGIGTKVTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT ...String:
MGWSCIILFL VATATGVHSQ SVLTQPASVS GSPGQSITIS CTGTSSDVGN YHLVSWYQQH PGKAPKLIIY EGSKRPSGVS NRFSGSKSG NTASLTISGL QAEDEADYYC CLYADSTTYV FGIGTKVTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT VAWKADSSPV KAGVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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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: 21 / 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

Concentration0.9 mg/mL
BufferpH: 7.2 / Details: 1x Phosphate buffered saline
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 91.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 8 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9eli

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 112091
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.5.3)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-11is:
1332E5 Spike KP3.1.1 Complex

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