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- EMDB-75698: 1332D4 Spike KP3.1.1 Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-75698
Title1332D4 Spike KP3.1.1 Complex
Map dataMap
Sample
  • Complex: 1332D4 Fab / SARS-CoV-2 KP3.1.1 Variant Complex
    • Protein or peptide: 1332D4 Heavy Chain
    • Protein or peptide: 1332D4 Light Chain
    • Protein or peptide: SARS-CoV-2 KP3.1.1 variant
  • 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: 3.26 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: Piepenbrink MS / Ma Y / Panjwani S / Blake AR / Bell AM / Kizziah JL / Mahmoud SH / Ippolito GC / Erdmann NB / Goepfert PA / Martinez-Sobrido L / Kobie JJ / Walter MR
History
DepositionFeb 24, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75698.png

Downloads & links

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Map

FileDownload / File: emd_75698.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 384 pix.
= 367.104 Å		0.96 Å/pix.
x 384 pix.
= 367.104 Å		0.96 Å/pix.
x 384 pix.
= 367.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.956 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.24673417 - 0.53044194
Average (Standard dev.)-0.0004620265 (±0.012910819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 367.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: A half map

Fileemd_75698_half_map_1.map
AnnotationA half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: B half map

Fileemd_75698_half_map_2.map
AnnotationB half 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 Fab / SARS-CoV-2 KP3.1.1 Variant Complex

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

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Supramolecule #1: 1332D4 Fab / SARS-CoV-2 KP3.1.1 Variant Complex

SupramoleculeName: 1332D4 Fab / SARS-CoV-2 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: 1332D4 Heavy Chain

MacromoleculeName: 1332D4 Heavy Chain / type: protein_or_peptide / ID: 1 / 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 #2: 1332D4 Light Chain

MacromoleculeName: 1332D4 Light Chain / type: protein_or_peptide / ID: 2 / 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 #3: SARS-CoV-2 KP3.1.1 variant

MacromoleculeName: SARS-CoV-2 KP3.1.1 variant / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 135.418172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AYTNFTRGVY YPDKVFRSSV LHLTQDLFLP FFSNVTWFHA ISGTNGTKRF DNPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLL IVNNATNVFI KVCEFQFCND PFLDVYHKNN KSWMESESGV YSSANNCTFE YVSQPFLMDL EGKQGNFKNL R EFVFKNID ...String:
AYTNFTRGVY YPDKVFRSSV LHLTQDLFLP FFSNVTWFHA ISGTNGTKRF DNPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLL IVNNATNVFI KVCEFQFCND PFLDVYHKNN KSWMESESGV YSSANNCTFE YVSQPFLMDL EGKQGNFKNL R EFVFKNID GYFKIYSKHT PIIGRDFPQG FSALEPLVDL PIGINITRFQ TLLALNRSYL TPGDSSSGWT AGAADYYVGY LQ PRTFLLK YNENGTITDA VDCALDPLSE TKCTLKSFTV EKGIYQTSNF RVQPTESIVR FPNVTNLCPF HEVFNATRFA SVY AWNRTR ISNCVADYSV LYNFAPFFAF KCYGVSPTKL NDLCFTNVYA DSFVIKGNEV SQIAPGQTGN IADYNYKLPD DFTG CVIAW NSNKLDSKHS GNYDYWYRSL RKSKLKPFER DISTEIYQAG NKPCKGKGPN CYFPLESYGF RPTYGVGHQP YRVVV LSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL TGTGVLTKSN KKFLPFQQFG RDIVDTTDAV RDPQTLEILD ITPCSF GGV SVITPGTNTS NQVAVLYQGV NCTEVSVAIH ADQLTPTWRV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICA SY QTQTKSRGSA GSVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISVTT EILPVSMTKT SVDCTMYICG DSTECSNL L LQYGSFCTQL KRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAG FIKQYGDCLG DIAARDLICA QKFNGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQK LIANQFNSAI GKIQDSLFST PSALGKLQDV VNHNAQALNT LVKQLSSKFG AISSVLNDIL SRLDPPEAEV Q IDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QE KNFTTAP AICHDGKAHF PREGVFVSNG THWFLTQRNF YEPQIITTDN TFVSGNCDVV IGIVNNTVYD PLQLELDSFK EEL DKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ YIASSGYIPE APRDGQAYVR KDGE WVLLS TFLEGTKHHH HHH

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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: 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) / 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: 2.0 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 124495
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-11ho:
1332D4 Spike KP3.1.1 Complex

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