[English] 日本語
Yorodumi
- EMDB-45930: Structure of 16.ND.92 Fab in complex with A/Solomon Islands/3/200... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45930
TitleStructure of 16.ND.92 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus Hemagglutinin
Map data
Sample
  • Complex: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
    • Protein or peptide: Variable Heavy Chain of 16.ND.92 Fab
    • Protein or peptide: Variable Light Chain of 16.ND.92 Fab
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
KeywordsAntibody / Influenza / Hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsOuyang WO / Pholcharee T / Wu NC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)DP2 AT011966 United States
CitationJournal: To Be Published
Title: Structure of 16.ND.92 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus Hemagglutinin
Authors: Ouyang WO / Pholcharee T / Wu NC
History
DepositionJul 25, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45930.png

Downloads & links

-
Map

FileDownload / File: emd_45930.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 720 pix.
= 380.88 Å		0.53 Å/pix.
x 720 pix.
= 380.88 Å		0.53 Å/pix.
x 720 pix.
= 380.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.529 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.089
Minimum - Maximum-0.0018061608 - 1.8738102
Average (Standard dev.)0.00070432463 (±0.01964024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 380.87997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_45930_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_45930_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hema...

EntireName: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
Components
  • Complex: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
    • Protein or peptide: Variable Heavy Chain of 16.ND.92 Fab
    • Protein or peptide: Variable Light Chain of 16.ND.92 Fab
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2

-
Supramolecule #1: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hema...

SupramoleculeName: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Both Hemagglutinin and Fab were recombinantly expressed and purified. The Fab was then mixed with Hemagglutinin at 3.5:1 ratio. The complex were then isolated using size exclusion chromatography.
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Variable Heavy Chain of 16.ND.92 Fab

MacromoleculeName: Variable Heavy Chain of 16.ND.92 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.659272 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVESGGGL VQPGGSLRLS CEASGFTLSS YWMHWVRQDP GKGLVWVAVI NSDGSSTDYA DFVKGRFTIS RDNAKNTVYL QMNSLRAED TAVYYCARAP QGTVFGVVII GADGFDIWGQ GTMVTVSS

-
Macromolecule #2: Variable Light Chain of 16.ND.92 Fab

MacromoleculeName: Variable Light Chain of 16.ND.92 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.800195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQMTHIPVSL SASVGDRVTI TCRASQSISS WLAWYQQKPG KAPKLLIYKA STLESGVPSR FSGSGSGTDF TLTINSLQPD DFATYYCQH YNTYSRAWTF GQGTKVEV

-
Macromolecule #3: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Molecular weightTheoretical: 35.851199 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAPL QLGNCSVAGW ILGNPECELL ISRESWSYIV EKPNPENGT CYPGHFADYE ELREQLSSVS SFERFEIFPK ESSWPNHTTT GVSASCSHNG ESSFYKNLLW LTGKNGLYPN L SKSYANNK ...String:
DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAPL QLGNCSVAGW ILGNPECELL ISRESWSYIV EKPNPENGT CYPGHFADYE ELREQLSSVS SFERFEIFPK ESSWPNHTTT GVSASCSHNG ESSFYKNLLW LTGKNGLYPN L SKSYANNK EKEVLVLWGV HHPPNIGDQR ALYHKENAYV SVVSSHYSRK FTPEIAKRPK VRDQEGRINY YWTLLEPGDT II FEANGNL IAPRYAFALS RGFGSGIINS NAPMDECDAK CQTPQGAINS SLPFQNVHPV TIGECPKYVR SAKLRMVTGL RNI P

UniProtKB: Hemagglutinin

-
Macromolecule #4: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Molecular weightTheoretical: 19.412537 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
LFGAIAGFIE GGWTGMVDGW YGYHHQNEQG SGYAADQKST QNAINGITNK VNSVIEKMNT QFTAVGKEFN KLERRMENLN KKVDDGFID IWTYNAELLV LLENERTLDF HDSNVKNLYE KVKSQLKNNA KEIGNGCFEF YHKCNDECME SVKNGTYDYP K YSEESKLN R

UniProtKB: Hemagglutinin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5 / Details: 20mM Tris-HCl, 150mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Blot force: 0, Blot time: 3 s, Humidity 90%, and 4 C..

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.35 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 152449
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
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