[English] 日本語
Yorodumi
- EMDB-36437: Cryo-EM structure of dengue virus serotype 3 strain 863DK in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36437
TitleCryo-EM structure of dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 4 deg C
Map datapostprocessed map
Sample
  • Complex: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 4 deg C
    • Complex: Dengue virus serotype 3 strain 863DK
      • Protein or peptide: Envelope protein
      • Protein or peptide: Membrane protein
    • Complex: Human antibody DENV-115 Fab (heavy and light chain)
      • Protein or peptide: Human antibody DENV-115 heavy chain
      • Protein or peptide: Human antibody DENV-115 light chain
Keywordsdengue virus / human antibody / dengue-antibody structure / virus
Biological speciesDengue virus type 3 / Homo sapiens (human) / Aedes albopictus (Asian tiger mosquito)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFibriansah G / Ng TS / Tan AWK / Shi J / Lok SM
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
CitationJournal: To Be Published
Title: Ultrapotent human antibodies lock E protein dimers of diverse DENV3 morphological variants
Authors: Fibriansah G / Ng TS / Lim XN / Shebanova A / Ng LC / Tan SL / Tan AWK / Shi J / Crowe JE / Lok SM
History
DepositionJun 6, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36437.png

Downloads & links

-
Map

FileDownload / File: emd_36437.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 512 pix.
= 875.52 Å		1.71 Å/pix.
x 512 pix.
= 875.52 Å		1.71 Å/pix.
x 512 pix.
= 875.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-8.891859999999999 - 14.820964
Average (Standard dev.)-0.000000002200449 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 875.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_36437_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_36437_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_36437_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dengue virus serotype 3 strain 863DK in complex with human antibo...

EntireName: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 4 deg C
Components
  • Complex: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 4 deg C
    • Complex: Dengue virus serotype 3 strain 863DK
      • Protein or peptide: Envelope protein
      • Protein or peptide: Membrane protein
    • Complex: Human antibody DENV-115 Fab (heavy and light chain)
      • Protein or peptide: Human antibody DENV-115 heavy chain
      • Protein or peptide: Human antibody DENV-115 light chain

-
Supramolecule #1: Dengue virus serotype 3 strain 863DK in complex with human antibo...

SupramoleculeName: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 4 deg C
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Dengue virus serotype 3 strain 863DK

SupramoleculeName: Dengue virus serotype 3 strain 863DK / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Dengue virus type 3

-
Supramolecule #3: Human antibody DENV-115 Fab (heavy and light chain)

SupramoleculeName: Human antibody DENV-115 Fab (heavy and light chain) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Envelope protein

MacromoleculeName: Envelope protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Aedes albopictus (Asian tiger mosquito)
SequenceString: mrcvgvgnrd fveglsgat w vdvvlehg gc vttmakn kpt ldielq ktea tqlat lrklc iegk itnitt dsr cptqgea vl peeqdqny v ckhtyvdrg wgngcglfgk gslvtcakf q clepiegk vv qyenlky tvi itvhtg dqhq vgnet ...String:
mrcvgvgnrd fveglsgat w vdvvlehg gc vttmakn kpt ldielq ktea tqlat lrklc iegk itnitt dsr cptqgea vl peeqdqny v ckhtyvdrg wgngcglfgk gslvtcakf q clepiegk vv qyenlky tvi itvhtg dqhq vgnet qgvta eitp qastte ail peygtlg le csprtgld f nemilltmk nkawmvhrqw ffdlplpwa s gattetpt wn rkellvt fkn ahakkq evvv lgsqe gamht altg ateiqn sgg tsifagh lk crlkmdkl e lkgmsyamc tntfvlkkev setqhgtil i kveykged ap ckipfst edg qgkahn grli tanpv vtkke epvn ieaepp fge snivigi gd nalkinwy k kgssigkmf eatargarrm ailgdtawd f gsvggvln sl gkmvhqi fgs aytalf sgvs wvmki gigvl ltwi glnskn tsm sfsciai gi itlylgav v qa

-
Macromolecule #2: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Aedes albopictus (Asian tiger mosquito)
SequenceString:
svala phvg mgldtr tqt wmsaega wr qvekvetw a lrhpgftil alflahyigt sltqkvvif i llmlvtps mt

-
Macromolecule #3: Human antibody DENV-115 heavy chain

MacromoleculeName: Human antibody DENV-115 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGAPVKV SCEASGYTFT DYFIHWVRQA PGQGLEWMGW INPISGGTNY HPRFHGGVTM TRDTSMKVAY MELKRLTSDD TAVYFCARGR DFRGGYSQLD YWGQGTLVTV SS

-
Macromolecule #4: Human antibody DENV-115 light chain

MacromoleculeName: Human antibody DENV-115 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSA SGTPGQRVTI SCSGGSSNIA INTVNWYQQV PGTAPKLLMY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYCA TWDDSLKDVL FGGGTKLTVL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Details: NTE buffer (12 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA)
VitrificationCryogen name: ETHANE
DetailsThe purified virus was mixed with DENV-115 Fab at a molar ratio of 1.5 Fab for every E-protein and then the mixture was incubated at 4 deg C for 30 min.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 18.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5933

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 29511
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

+
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