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- EMDB-49372: PRO-37587 bound to SARS-CoV-2 Spike protein -

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Basic information

Entry
Database: EMDB / ID: EMD-49372
TitlePRO-37587 bound to SARS-CoV-2 Spike protein
Map dataComposite Cryo-EM map of SARS-CoV-2 BA.1 Spike protein bound to class 4 RBD binder PRO-37587.
Sample
  • Complex: Complex structure of SARS-CoV-2 BA.1 Spike trimer bound to anti-RBD antibodies PRO-37587
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: PRO-37587 FAB light chain
    • Protein or peptide: PRO-37587 FAB heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS / Spike / Antibody / Inhibitor / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / membrane / identical protein binding / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / 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, 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: 3.0 Å
AuthorsZimmerman MI / Jecrois A
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: SARS-CoV-2 BA.1 Spike protein bound to anti-RBD antibody PRO-37587
Authors: Zimmerman MI / Jecrois A
History
DepositionFeb 21, 2025-
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_49372.png

Downloads & links

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Map

FileDownload / File: emd_49372.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite Cryo-EM map of SARS-CoV-2 BA.1 Spike protein bound to class 4 RBD binder PRO-37587.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 588 pix.
= 420.48 Å		0.72 Å/pix.
x 588 pix.
= 420.48 Å		0.72 Å/pix.
x 588 pix.
= 420.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7151 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.818578 - 3.4543693
Average (Standard dev.)-0.00007936725 (±0.047553685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 420.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus Cryo-EM map of SARS-CoV-2 BA.1 Spike protein...

Fileemd_49372_additional_1.map
AnnotationConsensus Cryo-EM map of SARS-CoV-2 BA.1 Spike protein bound to class 4 RBD binder PRO-37587.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement Cryo-EM map of SARS-CoV-2 BA.1 Spike...

Fileemd_49372_additional_2.map
AnnotationLocal refinement Cryo-EM map of SARS-CoV-2 BA.1 Spike protein bound to class 4 RBD binder PRO-37587.
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 structure of SARS-CoV-2 BA.1 Spike trimer bound to anti-R...

EntireName: Complex structure of SARS-CoV-2 BA.1 Spike trimer bound to anti-RBD antibodies PRO-37587
Components
  • Complex: Complex structure of SARS-CoV-2 BA.1 Spike trimer bound to anti-RBD antibodies PRO-37587
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: PRO-37587 FAB light chain
    • Protein or peptide: PRO-37587 FAB heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex structure of SARS-CoV-2 BA.1 Spike trimer bound to anti-R...

SupramoleculeName: Complex structure of SARS-CoV-2 BA.1 Spike trimer bound to anti-RBD antibodies PRO-37587
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 / Strain: BA.1
Molecular weightTheoretical: 126.724203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DHKNNKSWME SEFRVYSSAN N CTFEYVSQ ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DHKNNKSWME SEFRVYSSAN N CTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPIIVR EPEDLPQGFS ALEPLVDLPI GINITRFQTL LA LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NLAPFFTFKC YGVSPTKLND LCFTNVYADS FVIR GDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVSGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGV AGFN CYFPLRSYSF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLK GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHRAAA SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFKGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NHNAQALNTL V KQLSSKFG AISSVLNDIF SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPE

UniProtKB: Spike glycoprotein

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Macromolecule #2: PRO-37587 FAB light chain

MacromoleculeName: PRO-37587 FAB light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.843283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TVLTQPPSVS GAPGQRVTIS CTGSSSNIGA GYRVHWYQQL PGTAPKLLIA GRSNRPSGVP DRFSGSKSGT SASLAITGLQ AEDEADYYC QSYDSSLFDP HWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT ...String:
TVLTQPPSVS GAPGQRVTIS CTGSSSNIGA GYRVHWYQQL PGTAPKLLIA GRSNRPSGVP DRFSGSKSGT SASLAITGLQ AEDEADYYC QSYDSSLFDP HWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT TPSKQSNNKY AASSYLSLTP EQWKSHRSYS CQVTHEGSTV EKTVAPTE

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Macromolecule #3: PRO-37587 FAB heavy chain

MacromoleculeName: PRO-37587 FAB heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.607324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLVQSGAEV KKPGSSVKVS CKASGDTSDT YTISWVRQAP GQGLEWMGRI ILLSGYANYA QKIQGRVTIT ADKSTSTAYM ELTSLRSDD TAVYYCARGF NGDYYGWGDD DAFDFWGQGT LVTVYSASTK GPSVFPLAPS GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
VQLVQSGAEV KKPGSSVKVS CKASGDTSDT YTISWVRQAP GQGLEWMGRI ILLSGYANYA QKIQGRVTIT ADKSTSTAYM ELTSLRSDD TAVYYCARGF NGDYYGWGDD DAFDFWGQGT LVTVYSASTK GPSVFPLAPS GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKS

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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: 39 / 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 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMtris(hydroxymethyl)aminomethane hydrochloride
300.0 mMsodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112195
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9nft:
PRO-37587 bound to SARS-CoV-2 Spike protein

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