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- EMDB-75696: 1332D4-RBD KP3.1.1 Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-75696
Title1332D4-RBD KP3.1.1 Complex
Map data
Sample
  • Complex: 1332D4-SARS-CoV-2 KP3.1.1 RBD Complex
    • Protein or peptide: SARS-CoV-2 KP3.1.1
    • Protein or peptide: 1332D4 Heavy Chain
    • Protein or peptide: 1332D4 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / KP3.1.1 / Antibody / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 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) 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 24, 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_75696.png

Downloads & links

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Map

FileDownload / File: emd_75696.map.gz / Format: CCP4 / Size: 824 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 600 pix.
= 430.2 Å		0.72 Å/pix.
x 600 pix.
= 430.2 Å		0.72 Å/pix.
x 600 pix.
= 430.2 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: 0.08
Minimum - Maximum-2.201472 - 2.2476168
Average (Standard dev.)-0.00007605575 (±0.013864078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 430.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75696_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_75696_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 1332D4-SARS-CoV-2 KP3.1.1 RBD Complex

EntireName: 1332D4-SARS-CoV-2 KP3.1.1 RBD Complex
Components
  • Complex: 1332D4-SARS-CoV-2 KP3.1.1 RBD Complex
    • Protein or peptide: SARS-CoV-2 KP3.1.1
    • Protein or peptide: 1332D4 Heavy Chain
    • Protein or peptide: 1332D4 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 1332D4-SARS-CoV-2 KP3.1.1 RBD Complex

SupramoleculeName: 1332D4-SARS-CoV-2 KP3.1.1 RBD Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SARS-CoV-2 KP3.1.1

MacromoleculeName: SARS-CoV-2 KP3.1.1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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: 1332D4 Heavy Chain

MacromoleculeName: 1332D4 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.708041 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ VQLVQSGAEV KKPGESLRIS CKTSGYIFTN FWIGWARQMP GKGLEWMGII YPDDSDTRYS PSFQGQVTI SADKSISTAY LQWSTLKASD TAMYYCVRPD GVNDWFGVDP WGQGTLVTVS SASTKGPSVF PLAPCSKSTS G GTAALGCL ...String:
MGWSCIILFL VATATGVHSQ VQLVQSGAEV KKPGESLRIS CKTSGYIFTN FWIGWARQMP GKGLEWMGII YPDDSDTRYS PSFQGQVTI SADKSISTAY LQWSTLKASD TAMYYCVRPD GVNDWFGVDP WGQGTLVTVS SASTKGPSVF PLAPCSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EP

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Macromolecule #3: 1332D4 Light Chain

MacromoleculeName: 1332D4 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.559523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE TTLTQSPATL SVSPGERATL SCRASQSVTT NLAWYQQKPG RAPRLLIYGA STRATGIPAR FSGSGSGTE FTLTISSLQS EDFALYYCQQ YNHWPPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW ...String:
MGWSCIILFL VATATGVHSE TTLTQSPATL SVSPGERATL SCRASQSVTT NLAWYQQKPG RAPRLLIYGA STRATGIPAR FSGSGSGTE FTLTISSLQS EDFALYYCQQ YNHWPPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / 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: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
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) / 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: 1.0 µm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9bll

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 120091
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)

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