[English] 日本語
Yorodumi
- EMDB-27541: Postfusion Nipah virus fusion protein in complex with Fab 1H1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27541
TitlePostfusion Nipah virus fusion protein in complex with Fab 1H1
Map dataPostfusion Nipah virus fusion protein in complex with Fab 1H1
Sample
  • Complex: Postfusion Nipah virus fusion protein in complex with Fab 1H1
    • Protein or peptide: Fusion glycoprotein F0,Fusion glycoprotein F1
    • Protein or peptide: antibody 1H1 heavy chain
    • Protein or peptide: antibody 1H1 light chain
KeywordsNipah / Nipah virus / NiV / fusion / F / antibody / neutralizing / conserved epitope / neutralizing antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesNipah henipavirus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsByrne PO / Blade EG / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: To Be Published
Title: Postfusion Nipah virus fusion protein in complex with Fab 1H1
Authors: Byrne PO / Blade EG / McLellan JS
History
DepositionJul 8, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27541.png

Downloads & links

-
Map

FileDownload / File: emd_27541.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostfusion Nipah virus fusion protein in complex with Fab 1H1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 448 pix.
= 362.88 Å		0.81 Å/pix.
x 448 pix.
= 362.88 Å		0.81 Å/pix.
x 448 pix.
= 362.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.02771756 - 1.842539
Average (Standard dev.)0.0005613041 (±0.015173635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 362.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_27541_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Additional Map 1

Fileemd_27541_additional_1.map
AnnotationAdditional Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Additional Map 2

Fileemd_27541_additional_2.map
AnnotationAdditional Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 1

Fileemd_27541_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_27541_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Postfusion Nipah virus fusion protein in complex with Fab 1H1

EntireName: Postfusion Nipah virus fusion protein in complex with Fab 1H1
Components
  • Complex: Postfusion Nipah virus fusion protein in complex with Fab 1H1
    • Protein or peptide: Fusion glycoprotein F0,Fusion glycoprotein F1
    • Protein or peptide: antibody 1H1 heavy chain
    • Protein or peptide: antibody 1H1 light chain

-
Supramolecule #1: Postfusion Nipah virus fusion protein in complex with Fab 1H1

SupramoleculeName: Postfusion Nipah virus fusion protein in complex with Fab 1H1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nipah henipavirus

-
Macromolecule #1: Fusion glycoprotein F0,Fusion glycoprotein F1

MacromoleculeName: Fusion glycoprotein F0,Fusion glycoprotein F1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nipah henipavirus
Molecular weightTheoretical: 58.45198 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYSMQLASCV TLTLVLLVNS QGILHYEKLS KIGLVKGVTR KYKIKSNPLT KDIVIKMIPN VSNMSQCTGS VMENYKTRLN GILTPIKGA LEIYKNGGSG VAIGIATAAQ ITAGVALYEA MKNADNINKL KSSIESTNEA VVKLQETAEK TVYVLTALQD Y INTNLVPT ...String:
MYSMQLASCV TLTLVLLVNS QGILHYEKLS KIGLVKGVTR KYKIKSNPLT KDIVIKMIPN VSNMSQCTGS VMENYKTRLN GILTPIKGA LEIYKNGGSG VAIGIATAAQ ITAGVALYEA MKNADNINKL KSSIESTNEA VVKLQETAEK TVYVLTALQD Y INTNLVPT IDKISCKQTE LSLDLALSKY LSDLLFVFGP NLQDPVSNSM TIQAISQAFG GNYETLLRTL GYATEDFDDL LE SDSITGQ IIYVDLSSYY IIVRVYFPIL TEIQQAYIQE LLPVSFNNDN SEWISIVPNF ILVRNTLISN IEIGFCLITK RSV ICNQDY ATPMTNNMRE CLTGSTEKCP RELVVSSHVP RFALSNGVLF ANCISVTCQC QTTGRAISQS GEQTLLMIDN TTCP TAVLG NVIISLGKYL GSVNYNSEGI AIGPPVFTDK VDISSQISSM NQSLQQSKDY IKEAQRLLDT VNPSLKLMKQ IEDKI EEIL SKIYHIENEI ARIKKLIGEA PGGLVPRGSH HHHHHSAWSH PQFEK

UniProtKB: Fusion glycoprotein F0, Fusion glycoprotein F0

-
Macromolecule #2: antibody 1H1 heavy chain

MacromoleculeName: antibody 1H1 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.256589 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVQLQQSGAE LMRPGASMKI SCKATGYTFS SYWIDWVKQR PGHGLEWIGE ILPGSGDTNY NENFKGKAAF TADTSSNTAY MQLTSLTSE DSAVFYCARG GRYHGQGFFD YWGQGTTLTV SS

-
Macromolecule #3: antibody 1H1 light chain

MacromoleculeName: antibody 1H1 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.752168 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIQMTQSPAS LSASVGETVT ITCRPSENVH IYLAWYQQKQ GKSPQLLVYN AKTLADGVPS RFSGSASGTQ FSLKINSLQP EDFGSYYCQ HFWSIPYTFG GGTKLEIK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 312805
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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