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- EMDB-31744: MERS S ectodomain trimer in complex with neutralizing antibody 11... -

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Basic information

Entry
Database: EMDB / ID: EMD-31744
TitleMERS S ectodomain trimer in complex with neutralizing antibody 111 (state 2)
Map data
Sample
  • Complex: MERS spike glycoprotein
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: 111 L
    • Protein or peptide: 111 H
KeywordsMERS / spike / antibody / PROTEIN BINDING
Function / homology
Function and homology information


receptor-mediated endocytosis of virus by host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / 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 / symbiont entry into host cell / host cell plasma membrane ...receptor-mediated endocytosis of virus by host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / 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 / symbiont entry into host cell / 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, 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 (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, 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. / 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 S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-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 speciesMiddle East respiratory syndrome-related coronavirus / Human betacoronavirus 2c EMC/2012 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.56 Å
AuthorsWang X / Zhao J / Wang Z / Zeng J / Zhang S / Wang Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: MERS S ectodomain trimer in complex with neutralizing antibody 111 (state 2)
Authors: Wang X / Zhao J / Wang Z / Zeng J / Zhang S / Wang Y
History
DepositionAug 20, 2021-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31744.png

Downloads & links

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Map

FileDownload / File: emd_31744.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 351.328 Å		1.1 Å/pix.
x 320 pix.
= 351.328 Å		1.1 Å/pix.
x 320 pix.
= 351.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.011943761 - 0.04776972
Average (Standard dev.)0.0002538794 (±0.0017726688)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 351.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : MERS spike glycoprotein

EntireName: MERS spike glycoprotein
Components
  • Complex: MERS spike glycoprotein
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: 111 L
    • Protein or peptide: 111 H

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Supramolecule #1: MERS spike glycoprotein

SupramoleculeName: MERS spike glycoprotein / 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: Human betacoronavirus 2c EMC/2012
Molecular weightTheoretical: 130.718586 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC G TLLRAFYC ...String:
YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC G TLLRAFYC ILEPRSGNHC PAGNSYTSFA TYHTPATDCS DGNYNRNASL NSFKEYFNLR NCTFMYTYNI TEDEILEWFG IT QTAQGVH LFSSRYVDLY GGNMFQFATL PVYDTIKYYS IIPHSIRSIQ SDRKAWAAFY VYKLQPLTFL LDFSVDGYIR RAI DCGFND LSQLHCSYES FDVESGVYSV SSFEAKPSGS VVEQAEGVEC DFSPLLSGTP PQVYNFKRLV FTNCNYNLTK LLSL FSVND FTCSQISPAA IASNCYSSLI LDYFSYPLSM KSDLSVSSAG PISQFNYKQS FSNPTCLILA TVPHNLTTIT KPLKY SYIN KCSRLLSDDR TEVPQLVNAN QYSPCVSIVP STVWEDGDYY RKQLSPLEGG GWLVASGSTV AMTEQLQMGF GITVQY GTD TNSVCPKLEF ANDTKIASQL GNCVEYSLYG VSGRGVFQNC TAVGVRQQRF VYDAYQNLVG YYSDDGNYYC LRACVSV PV SVIYDKETKT HATLFGSVAC EHISSTMSQY SRSTRSMLKR RDSTYGPLQT PVGCVLGLVN SSLFVEDCKL PLGQSLCA L PDTPSTLTPR SVRSVPGEMR LASIAFNHPI QVDQLNSSYF KLSIPTNFSF GVTQEYIQTT IQKVTVDCKQ YVCNGFQKC EQLLREYGQF CSKINQALHG ANLRQDDSVR NLFASVKSSQ SSPIIPGFGG DFNLTLLEPV SISTGSRSAR SAIEDLLFDK VTIADPGYM QGYDDCMQQG PASARDLICA QYVAGYKVLP PLMDVNMEAA YTSSLLGSIA GVGWTAGLSS FAAIPFAQSI F YRLNGVGI TQQVLSENQK LIANKFNQAL GAMQTGFTTT NEAFQKVQDA VNNNAQALSK LASELSNTFG AISASIGDII QR LDVLEQD AQIDRLINGR LTTLNAFVAQ QLVRSESAAL SAQLAKDKVN ECVKAQSKRS GFCGQGTHIV SFVVNAPNGL YFM HVGYYP SNHIEVVSAY GLCDAANPTN CIAPVNGYFI KTNNTRIVDE WSYTGSSFYA PEPITSLNTK YVA

UniProtKB: Spike glycoprotein

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Macromolecule #2: 111 L

MacromoleculeName: 111 L / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.786467 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQTPAS LSASVGDRVT ITCRASQNIS SYLNWYQQKP GKAPKVLIYD TSRLQSGVPS RFSGSASGTD FTLTISSLQP EDFATYYCQ QSCTTLRCWT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
DIQMTQTPAS LSASVGDRVT ITCRASQNIS SYLNWYQQKP GKAPKVLIYD TSRLQSGVPS RFSGSASGTD FTLTISSLQP EDFATYYCQ QSCTTLRCWT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: 111 H

MacromoleculeName: 111 H / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.524377 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG VVQPGRSLRL SCAASAFTFS NYGMHWVRQA PGKGLEWVAV IWSAGSLKYY ADSVKGRFII SRDNSKNTLY LQMDSLRPE DTAVYYCARE NTTYYYETSG SWGASYYFDF WGQGTLVTVS SSTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
EVQLVESGGG VVQPGRSLRL SCAASAFTFS NYGMHWVRQA PGKGLEWVAV IWSAGSLKYY ADSVKGRFII SRDNSKNTLY LQMDSLRPE DTAVYYCARE NTTYYYETSG SWGASYYFDF WGQGTLVTVS SSTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRV

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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

Concentration3.0 mg/mL
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: 4.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1463548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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