[English] 日本語
Yorodumi
- EMDB-39371: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (2-up state) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39371
TitleSARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (2-up state)
Map data0.004
Sample
  • Complex: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv
    • Complex: SARS-CoV-2 spike glycoprotein
      • Protein or peptide: SARS-CoV-2 spike glycoprotein
    • Complex: NT-108 scFv
      • Protein or peptide: NT-108 scFv
KeywordsAntibody / Complex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsAnraku Y / Kita S / Onodera T / Tadokoro T / Ito S / Adachi Y / Kotaki R / Suzuki T / Hashiguchi T / Takahashi Y / Maenaka K
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am0101093 Japan
Japan Agency for Medical Research and Development (AMED)JP20ae0101047 Japan
Japan Agency for Medical Research and Development (AMED)JP21fk0108463 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121037 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05873 Japan
Japan Agency for Medical Research and Development (AMED)JP223fa627005 Japan
Japan Agency for Medical Research and Development (AMED)JP223fa627009 Japan
Japan Agency for Medical Research and Development (AMED)JP23jf0126002 Japan
CitationJournal: To Be Published
Title: Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
Authors: Anraku Y / Maenaka K
History
DepositionMar 5, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39371.png

Downloads & links

-
Map

FileDownload / File: emd_39371.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation0.004
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 384 pix.
= 289.459 Å		0.75 Å/pix.
x 384 pix.
= 289.459 Å		0.75 Å/pix.
x 384 pix.
= 289.459 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7538 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.011741532 - 0.036826417
Average (Standard dev.)0.00006987358 (±0.0014140297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 289.4592 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_39371_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 0.0187

Fileemd_39371_half_map_1.map
Annotation0.0187
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 0.0187

Fileemd_39371_half_map_2.map
Annotation0.0187
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv

EntireName: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv
Components
  • Complex: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv
    • Complex: SARS-CoV-2 spike glycoprotein
      • Protein or peptide: SARS-CoV-2 spike glycoprotein
    • Complex: NT-108 scFv
      • Protein or peptide: NT-108 scFv

-
Supramolecule #1: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv

SupramoleculeName: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 20 KDa

-
Supramolecule #2: SARS-CoV-2 spike glycoprotein

SupramoleculeName: SARS-CoV-2 spike glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Supramolecule #3: NT-108 scFv

SupramoleculeName: NT-108 scFv / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: SARS-CoV-2 spike glycoprotein

MacromoleculeName: SARS-CoV-2 spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSQCVNLTTR TQLPPAYTNS FTRGVYYPDK VFRSSVLHST QDLFLPFFSN VTWFHAIHVS GTNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG ...String:
SSQCVNLTTR TQLPPAYTNS FTRGVYYPDK VFRSSVLHST QDLFLPFFSN VTWFHAIHVS GTNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSYLTP GDSSSGWTAG AAAYYVGYLQ PRTFLLKYNE NGTITDAVDC ALDPLSETKC TLKSFTVEKG IYQTSNFRVQ PTESIVRFPN ITNLCPFGEV FNATRFASVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP LQSYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGPKKST NLVKNKCVNF NFNGLTGTGV LTESNKKFLP FQQFGRDIAD TTDAVRDPQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQDVNCTEVP VAIHADQLTP TWRVYSTGSN VFQTRAGCLI GAEHVNNSYE CDIPIGAGIC ASYQTQTNSP GSAGSVASQS IIAYTMSLGA ENSVAYSNNS IAIPTNFTIS VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGFN FSQILPDPSK PSKRSPIEDL LFNKVTLADA GFIKQYGDCL GDIAARDLIC AQKFNGLTVL PPLLTDEMIA QYTSALLAGT ITSGWTFGAG PALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQDV VNQNAQALNT LVKQLSSNFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FPQSAPHGVV FLHVTYVPAQ EKNFTTAPAI CHDGKAHFPR EGVFVSNGTH WFVTQRNFYE PQIITTDNTF VSGNCDVVIG IVNNTVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGKYEQYI

-
Macromolecule #2: NT-108 scFv

MacromoleculeName: NT-108 scFv / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSVS STFLAWYQQK PGQAPRLLIY GASYMATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSLTFG GGTKLEIKGG GGSGGGGSGG GGSQVQLQQS GPGLVKPSQT LSLTCSISGD SVSSNSAAWN W IRQSPSRG ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS STFLAWYQQK PGQAPRLLIY GASYMATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSLTFG GGTKLEIKGG GGSGGGGSGG GGSQVQLQQS GPGLVKPSQT LSLTCSISGD SVSSNSAAWN W IRQSPSRG LEWLGRTYYR SKWYNDYAGT VKSRIAINPD TSKNQFSLHL NSVTPEDTAV YFCARVISVA GYAFDIWGQG TM VTVSSHH HHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.14 mol/LNaClsodium chloride
0.0027 mol/LKClkalium chloride
0.01 mol/LH3PO4phosphoric acid

Details: PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blotting time 5 s and blotting force 5..

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4792 pixel / Number real images: 2832 / Average exposure time: 1.5 sec. / Average electron dose: 53.52 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 652138
Startup modelType of model: OTHER
Details: the map of SARS-CoV-2 Spike glycoprotein close state reconstructed using EMPIAR-10514 dataset
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 73060
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more