[English] 日本語
Yorodumi
- EMDB-8562: CryoEM structure of an influenza virus receptor-binding site anti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8562
TitleCryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 2
Map datainfluenza virus receptor-binding site antibody-antigen interface - Class 2
Sample
  • Complex: Influenza-virus hemagglutinin H1 complexed with K1915 single-chain variable-domain fragment
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: scFV
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsviral glycoprotein / hemagglutinin / antibody fragment / 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 / apical plasma membrane / 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
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
Biological speciesInfluenza A virus (A/Solomon Islands/3/2006(H1N1)) / Influenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLiu Y / Pan J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI-089618 United States
CitationJournal: J Mol Biol / Year: 2017
Title: CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface.
Authors: Yuhang Liu / Junhua Pan / Simon Jenni / Donald D Raymond / Tim Caradonna / Khoi T Do / Aaron G Schmidt / Stephen C Harrison / Nikolaus Grigorieff /
Abstract: Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes.Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray ...Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes.Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain variable-domain fragment complexes, by studying a complex we failed to crystallize in pursuing an extended project on the human immune response to influenza vaccines.The result shows that a combination of cryoEM and molecular modeling can yield details of the antigen-antibody interface, although small variation in the twist of the rod-likeHA trimer limited the overall resolution to about 4.5Å.Comparison of principal 3D classes suggests ways to modify the HA trimer to overcome this limitation. A closely related antibody from the same donor did yield crystals when bound with the same HA, giving us an independent validation of the cryoEM results.The two structures also augment our understanding of receptor-binding site recognition by antibodies that neutralize a wide range of influenza-virus variants.
History
DepositionJan 19, 2017-
Header (metadata) releaseFeb 15, 2017-
Map releaseMay 31, 2017-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5uk0
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8562.png

Downloads & links

-
Map

FileDownload / File: emd_8562.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationinfluenza virus receptor-binding site antibody-antigen interface - Class 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 120 pix.
= 196.8 Å		1.64 Å/pix.
x 120 pix.
= 196.8 Å		1.64 Å/pix.
x 120 pix.
= 196.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 2.08 / Movie #1: 2
Minimum - Maximum-3.94078 - 7.9769554
Average (Standard dev.)0.07065075 (±0.43216813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 196.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z196.800196.800196.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-3.9417.9770.071

-
Supplemental data

-
Sample components

-
Entire : Influenza-virus hemagglutinin H1 complexed with K1915 single-chai...

EntireName: Influenza-virus hemagglutinin H1 complexed with K1915 single-chain variable-domain fragment
Components
  • Complex: Influenza-virus hemagglutinin H1 complexed with K1915 single-chain variable-domain fragment
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: scFV
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Influenza-virus hemagglutinin H1 complexed with K1915 single-chai...

SupramoleculeName: Influenza-virus hemagglutinin H1 complexed with K1915 single-chain variable-domain fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: The complex consists of three hemagglutinin head domains bound to three single-chain variable-domain fragments.
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Molecular weightTheoretical: 320 KDa

-
Macromolecule #1: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 36.024344 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: EDTICIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDSHNG KLCLLKGIAP LQLGNCSVAG WILGNPECEL LISRESWSYI VEKPNPENG TCYPGHFADY EELREQLSSV SSFERFEIFP KESSWPNHTT TGVSASCSHN GESSFYKNLL WLTGKNGLYP N LSKSYANN ...String:
EDTICIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDSHNG KLCLLKGIAP LQLGNCSVAG WILGNPECEL LISRESWSYI VEKPNPENG TCYPGHFADY EELREQLSSV SSFERFEIFP KESSWPNHTT TGVSASCSHN GESSFYKNLL WLTGKNGLYP N LSKSYANN KEKEVLVLWG VHHPPNIGDQ RALYHTENAY VSVVSSHYSR KFTPEIAKRP KVRDREGRIN YYWTLLEPGD TI IFEANGN LIAPRYAFAL SRGFGSGIIN SNAPMDECDA KCQTPQGAIN SSLPFQNVHP VTIGECPKYV RSAKLRMVTG LRN IPS

UniProtKB: Hemagglutinin

-
Macromolecule #2: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 19.841041 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL NREKI

UniProtKB: Hemagglutinin

-
Macromolecule #3: scFV

MacromoleculeName: scFV / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.629385 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSIS GYYLTWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGISPVIT FGGGTNVEIK GGGGGSGGGG SGGGGSEVQL VESGGGLVQP GGSLRLSCAA SGFTFNIYDM H WVRQAPGK ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSIS GYYLTWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGISPVIT FGGGTNVEIK GGGGGSGGGG SGGGGSEVQL VESGGGLVQP GGSLRLSCAA SGFTFNIYDM H WVRQAPGK GLEWVSGLTT GGDTSYSGSV RGRFSISREN AKNSLYLQMN NLRAGDTAAY FCVRGVREVG ATGGDPFYYA MA VWGQGTT VTVSSASGSS GSGHHHHHH

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
Details: Beta-octylglucoside was added to a final concentration of 0.07% w/v to induce more variable particle orientations.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK I

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-38 / Number grids imaged: 1 / Number real images: 10281 / Average exposure time: 13.0 sec. / Average electron dose: 40.0 e/Å2
Details: The exposure rate was 8 electrons/physical pixel/second.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 9.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 30444 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsThe particle images were normalized to have constant variance and zero average. Movies were processed using Unblur.
Particle selectionNumber selected: 252130
Startup modelType of model: OTHER
Details: A starting map was determined using rosettes formed from Ni-NTA nanogold and His-tagged particles.
Final reconstructionNumber classes used: 3 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11)
Details: Refinement and classification were limited to 10 Angstrom resolution.
Number images used: 142314
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 7.5 degrees
Software - Name: IMAGIC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.11)
Final 3D classificationNumber classes: 4 / Avg.num./class: 35579 / Software - Name: FREALIGN (ver. 9.11)
Details: Three out of the four classes showed high-resolution features.
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsDomains were initially placed manually using Chimera. The HA trimer was from PDB ID 5UGY. Fab was initially obtained using MODELLER, with PDB ID 4K8R as template. The structure was refined using PHENIX.
RefinementSpace: REAL / Protocol: OTHER / Target criteria: Correlation coefficient
Output model

PDB-5uk0:
CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 2

+
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