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- EMDB-70441: HCoV-229E S2P bound by two DH1533 Fabs -

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Basic information

Entry
Database: EMDB / ID: EMD-70441
TitleHCoV-229E S2P bound by two DH1533 Fabs
Map dataFull map, sharpened with DeepEMhancer
Sample
  • Complex: HCoV-229E spike protein bound by two copies of the antigen binding fragment from human mAb DH1533
    • Protein or peptide: Surface glycoprotein
    • Protein or peptide: DH1533 heavy chain
    • Protein or peptide: DH1533 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscoronavirus spike / antibody / HCoV-229E / alphacoronavirus / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 membrane / membrane
Similarity search - Function
Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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. ...Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 speciesHuman coronavirus 229E / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsWrapp D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)3P01AI158571-01A1S1 United States
CitationJournal: To Be Published
Title: A potently neutralizing human antibody induces movement of the HCoV-229E receptor binding domain
Authors: Liccione MF / Scobey T / Froggatt HM / Pajon C / Yount BL / Yin Q / Spence TN / Walter EB / Saunders KO / Edwards RJ / Baric RS / Haynes BF / Cain DW / Sheahan TP / Wrapp D
History
DepositionApr 30, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70441.png

Downloads & links

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Map

FileDownload / File: emd_70441.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map, sharpened with DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 432 pix.
= 466.56 Å		1.08 Å/pix.
x 432 pix.
= 466.56 Å		1.08 Å/pix.
x 432 pix.
= 466.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-0.004677849 - 2.4466193
Average (Standard dev.)0.0022323958 (±0.035624664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 466.56003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full map, unsharpened

Fileemd_70441_additional_1.map
AnnotationFull map, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_70441_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: Half map B

Fileemd_70441_half_map_2.map
AnnotationHalf 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 : HCoV-229E spike protein bound by two copies of the antigen bindin...

EntireName: HCoV-229E spike protein bound by two copies of the antigen binding fragment from human mAb DH1533
Components
  • Complex: HCoV-229E spike protein bound by two copies of the antigen binding fragment from human mAb DH1533
    • Protein or peptide: Surface glycoprotein
    • Protein or peptide: DH1533 heavy chain
    • Protein or peptide: DH1533 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCoV-229E spike protein bound by two copies of the antigen bindin...

SupramoleculeName: HCoV-229E spike protein bound by two copies of the antigen binding fragment from human mAb DH1533
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human coronavirus 229E / Strain: BN1/GER/2015
Molecular weightTheoretical: 722 KDa

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Macromolecule #1: Surface glycoprotein

MacromoleculeName: Surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus 229E / Strain: BN1/GER/2015
Molecular weightTheoretical: 123.593859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVLLVAYAL LHIAGCQTTN GTNTSHSVCN GCVGHSENVF AVESGGYIPS NFAFNNWFLL TNTSSVVDGV VRSFQPLLLN CLWSVSGSQ FTTGFVYFNG TGRGACKGFY SNASSDVIRY NINFEENLRR GTILFKTSYG AVVFYCTNNT LVSGDAHIPS G TVLGNFYC ...String:
MFVLLVAYAL LHIAGCQTTN GTNTSHSVCN GCVGHSENVF AVESGGYIPS NFAFNNWFLL TNTSSVVDGV VRSFQPLLLN CLWSVSGSQ FTTGFVYFNG TGRGACKGFY SNASSDVIRY NINFEENLRR GTILFKTSYG AVVFYCTNNT LVSGDAHIPS G TVLGNFYC FVNTTIGNET TSAFVGALPK TVREFVISRT GHFYINGYRY FSLGDVEAVN FNVTNAATTV CTVALASYAD VL VNVSQTA IANIIYCNSV INRLRCDQLS FDVPDGFYST SPIQPVELPV SIVSLPVYHK HTFIVLYVNF EHRRGPGKCY NCR PAVINI TLANFNETKG PLCVDTSHFT TQFVDNVKLA RWSASINTGN CPFSFGKVNN FVKFGSVCFS LKDIPGGCAM PIMA NLVNS KSHNIGSLYV SWSDGDVITG VPKPVEGVSS FMNVTLNKCT KYNIYDVSGV GVIRISNDTF LNGITYTSTS GNLLG FKDV TNGTIYSITP CNPPDQLVVY QQAVVGAMLS ENFTSYGFSN VVEMPKFFYA SNGTYNCTDA VLTYSSFGVC ADGSII AVQ PRNVSYDSVS AIVTANLSIP FNWTTSVQVE YLQITSTPIV VDCSTYVCNG NVRCVELLKQ YTSACKTIED ALRNSAM LE SADVSEMLTF DKKAFTLANV SSFGDYNLSS VIPSLPRSGS RVAGRSAIED ILFSKLVTSG LGTVDADYKK CTKGLSIA D LACAQYYNGI MVLPGVADAE RMAMYTGSLI GGIALGGLTS AASIPFSLAI QSRLNYVALQ TDVLQENQRI LAASFNKAM TNIVDAFTGV NDAITQTSQA LQTVATALNK IQDVVNQQGN SLNHLTSQLR QNFQAISSSI QAIYDRLDPP QADQQVDRLI TGRLAALNV FVSHTLTKYT EVRASRQLAQ QKVNECVKSQ SKRYGFCGNG THIFSLVNAA PEGLVFLHTV LLPTQYKDVE A WSGLCVDG INGYVLRQPN LALYKEGNYY RITSRIMFEP RIPTIADFVQ IENCNVTFVN ISRSELQTIV PEYIDVNKTL QE LSYKLPN YTVPDLVGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGG GSGGSA WSHPQFEK

UniProtKB: S

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Macromolecule #2: DH1533 heavy chain

MacromoleculeName: DH1533 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.302258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVSA IIGSGSNTYY ADSVKGRFTI SRDNAKNTLY LQMNSLRAE DTAVYYCAKD TTPRPLYSSG WYGSFDYWGQ GTPVSVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVSA IIGSGSNTYY ADSVKGRFTI SRDNAKNTLY LQMNSLRAE DTAVYYCAKD TTPRPLYSSG WYGSFDYWGQ GTPVSVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKGLEVLF Q

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Macromolecule #3: DH1533 light chain

MacromoleculeName: DH1533 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.42491 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCQASQDIT TYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTLTISSLQP EDIATYYCQ QYDNLFLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCQASQDIT TYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTLTISSLQP EDIATYYCQ QYDNLFLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 45 / 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

Concentration0.35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
2.0 mMC4H11NO3Tris
200.0 mMNaClsodium chloride
0.02 %NaN3sodium azide
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 45 sec.
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: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 19477 / Average electron dose: 49.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6573334
CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.2) / Details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Details: Non-uniform refinement / Number images used: 122657
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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