[English] 日本語
Yorodumi
- EMDB-20540: CryoEM map of NA-73 Fab in complex with N9 Shanghai2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20540
TitleCryoEM map of NA-73 Fab in complex with N9 Shanghai2
Map dataCryoEM map of NA-73 Fab in complex with N9 Shanghai
Sample
  • Complex: NA-73 Fab in complex with N9 Shanghai2
    • Complex: N9 Shanghai2
      • Protein or peptide: Neuraminidase
    • Complex: NA-73 Fab
      • Protein or peptide: NA-73 fragment antibody heavy chain
      • Protein or peptide: NA-73 fragment antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeuraminidase / NA / Sh2 / N9Shanghai / N9Sh2 / antibody / Fab / NA-73 / Influenza / VIRAL PROTEIN-IMMUNE SYSTEM complex / H7N9
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/environment/Shanghai/S1439/2013(H7N9)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsWard AB / Turner HL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN 272201400024C United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies.
Authors: Xueyong Zhu / Hannah L Turner / Shanshan Lang / Ryan McBride / Sandhya Bangaru / Iuliia M Gilchuk / Wenli Yu / James C Paulson / James E Crowe / Andrew B Ward / Ian A Wilson /
Abstract: Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host ...Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host protection. However, our understanding of the nature and range of target epitopes is limited because of a lack of human antibody structures with influenza neuraminidase. Here, we describe crystal and cryogenic electron microscopy (cryo-EM) structures of NAs from human-infecting avian H7N9 viruses in complex with five human anti-N9 antibodies, systematically defining several antigenic sites and antibody epitope footprints. These antibodies either fully or partially block the NA active site or bind to epitopes distant from the active site while still showing neuraminidase inhibition. The inhibition of antibodies to NAs was further analyzed by glycan array and solution-based NA activity assays. Together, these structural studies provide insights into protection by anti-NA antibodies and templates for the development of NA-based influenza virus vaccines and therapeutics.
History
DepositionAug 1, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseDec 4, 2019-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.488
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.488
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6pzy
  • Surface level: 0.488
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20540.png

Downloads & links

-
Map

FileDownload / File: emd_20540.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of NA-73 Fab in complex with N9 Shanghai
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.488 / Movie #1: 0.488
Minimum - Maximum-0.62393063 - 1.5987233
Average (Standard dev.)-0.000000052889686 (±0.07490613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z263.680263.680263.680
α/β/γ90.00090.00090.000
start NX/NY/NZ111-94150
NX/NY/NZ111123111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.6241.599-0.000

-
Supplemental data

-
Mask #1

Fileemd_20540_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Halfmap A of CryoEM map of NA-73 Fab in complex with N9 Shanghai

Fileemd_20540_half_map_1.map
AnnotationHalfmap A of CryoEM map of NA-73 Fab in complex with N9 Shanghai
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Halfmap B of CryoEM map of NA-73 Fab in complex with N9 Shanghai

Fileemd_20540_half_map_2.map
AnnotationHalfmap B of CryoEM map of NA-73 Fab in complex with N9 Shanghai
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NA-73 Fab in complex with N9 Shanghai2

EntireName: NA-73 Fab in complex with N9 Shanghai2
Components
  • Complex: NA-73 Fab in complex with N9 Shanghai2
    • Complex: N9 Shanghai2
      • Protein or peptide: Neuraminidase
    • Complex: NA-73 Fab
      • Protein or peptide: NA-73 fragment antibody heavy chain
      • Protein or peptide: NA-73 fragment antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: NA-73 Fab in complex with N9 Shanghai2

SupramoleculeName: NA-73 Fab in complex with N9 Shanghai2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

-
Supramolecule #2: N9 Shanghai2

SupramoleculeName: N9 Shanghai2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9))

-
Supramolecule #3: NA-73 Fab

SupramoleculeName: NA-73 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9))
Strain: A/environment/Shanghai/S1439/2013(H7N9)
Molecular weightTheoretical: 48.214508 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LKPGCNCSHS QPETTNTSQT IINNYYNETN ITNIQMEERT SRNFNNLTKG LCTINSWHIY GKDNAVRIGE SSDVLVTREP YVSCDPDEC RFYALSQGTT IRGKHSNGTI HDRSQYRALI SWPLSSPPTV YNSRVECIGW SSTSCHDGKS RMSICISGPN N NASAVVWY ...String:
LKPGCNCSHS QPETTNTSQT IINNYYNETN ITNIQMEERT SRNFNNLTKG LCTINSWHIY GKDNAVRIGE SSDVLVTREP YVSCDPDEC RFYALSQGTT IRGKHSNGTI HDRSQYRALI SWPLSSPPTV YNSRVECIGW SSTSCHDGKS RMSICISGPN N NASAVVWY NRRPVAEINT WARNILRTQE SECVCHNGVC PVVFTDGSAT GPADTRIYYF KEGKILKWES LTGTAKHIEE CS CYGERTG ITCTCRDNWQ GSNRPVIQID PVAMTHTSQY ICSPVLTDNP RPNDPNIGKC NDPYPGNNNN GVKGFSYLDG ANT WLGRTI STASRSGYEM LKVPNALTDD RSKPIQGQTI VLNADWSGYS GSFMDYWAEG DCYRACFYVE LIRGRPKEDK VWWT SNSIV SMCSSTEFLG QWNWPDGAKI EYFL

UniProtKB: Neuraminidase

-
Macromolecule #2: NA-73 fragment antibody heavy chain

MacromoleculeName: NA-73 fragment antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.822797 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: QVQLEESGPG LVKPSETLSL TCTVSGYTIS SGYYWGWIRQ PPGKGLEWIG CNNHRGSSYY NPSLKSRVII SVDTTKNKFS LKLSSVTAA DTAVYYCARD PSFWSSTSRT SPYYYGMDVW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
QVQLEESGPG LVKPSETLSL TCTVSGYTIS SGYYWGWIRQ PPGKGLEWIG CNNHRGSSYY NPSLKSRVII SVDTTKNKFS LKLSSVTAA DTAVYYCARD PSFWSSTSRT SPYYYGMDVW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKSC

-
Macromolecule #3: NA-73 fragment antibody light chain

MacromoleculeName: NA-73 fragment antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.792084 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: QSVLTQPPSA SGTPGQRVTI SCSGSSSNIG INTVNWYQQL PGTAPKLLIY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC AAWDDNLNGW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVLTQPPSA SGTPGQRVTI SCSGSSSNIG INTVNWYQQL PGTAPKLLIY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC AAWDDNLNGW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / 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

Concentration0.14 mg/mL
BufferpH: 7.4
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 157751
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5l14


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6pzy:
CryoEM derived model of NA-73 Fab in complex with N9 Shanghai2

+
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