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- EMDB-35422: MERS-CoV spike trimer in complex with nanobody VHH-T148 -

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Basic information

Entry
Database: EMDB / ID: EMD-35422
TitleMERS-CoV spike trimer in complex with nanobody VHH-T148
Map data
Sample
  • Complex: MERS-CoV spike trimer in complex with nanobody VHH-T148
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: VHH-T148
KeywordsMERS-CoV / nanobody / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome-related coronavirus / Camelus dromedarius (Arabian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsWang X / Tian L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structures and neutralizing mechanisms of camel nanobodies targeting the receptor-binding domain of MERS-CoV spike glycoprotein
Authors: Tian L / Wang R / Zhang L / Wang X
History
DepositionFeb 19, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35422.png

Downloads & links

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Map

FileDownload / File: emd_35422.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 303.1 Å		1.08 Å/pix.
x 280 pix.
= 303.1 Å		1.08 Å/pix.
x 280 pix.
= 303.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0116
Minimum - Maximum-0.066547096 - 0.14322881
Average (Standard dev.)0.00030777144 (±0.0034254487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 303.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35422_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_35422_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 : MERS-CoV spike trimer in complex with nanobody VHH-T148

EntireName: MERS-CoV spike trimer in complex with nanobody VHH-T148
Components
  • Complex: MERS-CoV spike trimer in complex with nanobody VHH-T148
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: VHH-T148

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Supramolecule #1: MERS-CoV spike trimer in complex with nanobody VHH-T148

SupramoleculeName: MERS-CoV spike trimer in complex with nanobody VHH-T148
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus

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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: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 148.400031 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MIHSVFLLMF LLTPTESYVD VGPDSVKSAC IEVDIQQTFF DKTWPRPIDV SKADGIIYPQ GRTYSNITIT YQGLFPYQGD HGDMYVYSA GHATGTTPQK LFVANYSQDV KQFANGFVVR IGAAANSTGT VIISPSTSAT IRKIYPAFML GSSVGNFSDG K MGRFFNHT ...String:
MIHSVFLLMF LLTPTESYVD VGPDSVKSAC IEVDIQQTFF DKTWPRPIDV SKADGIIYPQ GRTYSNITIT YQGLFPYQGD HGDMYVYSA GHATGTTPQK LFVANYSQDV KQFANGFVVR IGAAANSTGT VIISPSTSAT IRKIYPAFML GSSVGNFSDG K MGRFFNHT LVLLPDGCGT LLRAFYCILE PRSGNHCPAG NSYTSFATYH TPATDCSDGN YNRNASLNSF KEYFNLRNCT FM YTYNITE DEILEWFGIT QTAQGVHLFS SRYVDLYGGN MFQFATLPVY DTIKYYSIIP HSIRSIQSDR KAWAAFYVYK LQP LTFLLD FSVDGYIRRA IDCGFNDLSQ LHCSYESFDV ESGVYSVSSF EAKPSGSVVE QAEGVECDFS PLLSGTPPQV YNFK RLVFT NCNYNLTKLL SLFSVNDFTC SQISPAAIAS NCYSSLILDY FSYPLSMKSD LSVSSAGPIS QFNYKQSFSN PTCLI LATV PHNLTTITKP LKYSYINKCS RLLSDDRTEV PQLVNANQYS PCVSIVPSTV WEDGDYYRKQ LSPLEGGGWL VASGST VAM TEQLQMGFGI TVQYGTDTNS VCPKLEFAND TKIASQLGNC VEYSLYGVSG RGVFQNCTAV GVRQQRFVYD AYQNLVG YY SDDGNYYCLR ACVSVPVSVI YDKETKTHAT LFGSVACEHI SSTMSQYSRS TRSMLKRRDS TYGPLQTPVG CVLGLVNS S LFVEDCKLPL GQSLCALPDT PSTLTPSSVG SVPGEMRLAS IAFNHPIQVD QLNSSYFKLS IPTNFSFGVT QEYIQTTIQ KVTVDCKQYV CNGFQKCEQL LREYGQFCSK INQALHGANL RQDDSVRNLF ASVKSSQSSP IIPGFGGDFN LTLLEPVSIS TGSRSARSA IEDLLFDKVT IADPGYMQGY DDCMQQGPAS ARDLICAQYV AGYKVLPPLM DVNMEAAYTS SLLGSIAGVG W TAGLSSFA AIPFAQSIFY RLNGVGITQQ VLSENQKLIA NKFNQALGAM QTGFTTTNEA FQKVQDAVNN NAQALSKLAS EL SNTFGAI SASIGDIIQR LDPPEQDAQI DRLINGRLTT LNAFVAQQLV RSESAALSAQ LAKDKVNECV KAQSKRSGFC GQG THIVSF VVNAPNGLYF MHVGYYPSNH IEVVSAYGLC DAANPTNCIA PVNGYFIKTN NTRIVDEWSY TGSSFYAPEP ITSL NTKYV APQVTYQNIS TNLPPPLLGN STGIDFQDEL DEFFKNVSTS IPNFGSLTQI NTTLLDLTYE MLSLQQVVKA LNESY IDLK ELGNYTSREN LYFQGGGSAG SGYIPEAPRD GQAYVRKDGE WVLLSTFLGH HHHHHWSHPQ FEK

UniProtKB: Spike glycoprotein

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Macromolecule #2: VHH-T148

MacromoleculeName: VHH-T148 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Camelus dromedarius (Arabian camel)
Molecular weightTheoretical: 14.802287 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGGG SVQAGGSLKL SCSVSGYTYS TYCIAWFRQV PGKEREGLAF IKNPEGNTDY ADSVQGRFFI SQDTVDNTVY LSMNSLKPE DTATYYCAGA VSNWVCGMSI KSQGYGMDYW GKGTQVTVSS HHHHHH

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5x5f

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216306
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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