1NMC Complex (Single-Chain Antibody Antigen) date Dec 21, 1997
title Complex Between Nc10 Anti-Influenza Virus Neuraminidase Single Chain Antibody With A 15 Residue Linker And Influenza Virus Neuraminidase
authors R.L.Malby, A.J.Mccoy, A.A.Kortt, P.J.Hudson, P.M.Colman
compound source
Molecule: Neuraminidase
Chain: N, A
Fragment: Residues 82 - 468
Ec: 3.2.1.18
Engineered: Yes
Organism_scientific: Influenza A Virus
Organism_taxid: 11320
Strain: N9
Variant: Aternaustraliag70c75
Expression_system: Gallus Gallus
Expression_system_common: Chicken
Expression_system_taxid: 9031
Expression_system_cell: Egg

Molecule: Single Chain Antibody
Chain: H, B
Fragment: Vh And Vl Domains Of Anti-Neuraminidase Antibody Nc10 Covalently Joined By A Fifteen Residue Polypeptide Linker;
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Single Chain Antibody
Chain: L, C
Fragment: Vh And Vl Domains Of Anti-Neuraminidase Antibody Nc10 Covalently Joined By A Fifteen Residue Polypeptide Linker;
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 4 21 2
R_factor 0.220 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.400 144.400 227.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2 Å
ligand BMA, CA, MAN, NAG enzyme Exo-alpha-sialidase;. Neuraminidase;. Sialidase;. Alpha-neuraminidase;. Acetylneuraminidase. Hydrolase E.C.3.2.1.18 BRENDA
related structures by homologous chain: 1KB5, 1MNU, 1NCC, 1NNB, 1P84, 1PG7
domain The transmembrane domain also plays a role in lipid raft association (by similarity). Intact n-terminus is essential for virion morphogenesis. Possess two apical sorting signals, one in the ectodomain, which is likely to be a glycan, and the other in the transmembrane domain.
similarity Belongs to the glycosyl hydrolase 34 family.[Neur]
subunit Homotetramer (by similarity).
catalytic activ. Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
post-translat. modifications N-glycosylated (by similarity).
subcellular loc. Preferentially accumulates at the apical plasma membrane in infected polarized epithelial cells, which is the virus assembly site. Uses lipid rafts for cell surface transport and apical sorting. Type ii membrane protein. In the virion, forms a mushroom-shaped spike on the surface of the membrane (by similarity).
enzyme regulation These drugs interfere with the release of progeny virus from infected cells and are effective against all influenza strains. Inhibited by the neuraminidase inhibitors zanamivir (relenza) and oseltamivir (tamiflu). Resistance to neuraminidase inhibitors is quite rare.
Gene NA
function Catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates. May facilitate viral invasion of the upper airways by cleaving the sialic acid moities on the mucin of the airway epithelial cells. Described as a receptor-destroying enzyme because it cleaves a terminal sialic acid from the cellular receptors. Otherwise, infection would be limited to one round of replication. Cleaves off the terminal sialic acids on the glycosylated ha during virus budding to facilitate virus release. Likely to plays a role in the budding process through its association with lipid rafts during intracellular transport. Additionally helps virus spread through the circulation by further removing sialic acids from the cell surface. These cleavages prevent self-aggregation and ensure the efficient spread of the progeny virus from cell to cell. Plays a role in the determination of host range restriction on replication and virulence. Sialidase activity in late endosome/lysosome traffic seems to enhance virus replication. May additionally display a raft-association independent effect on budding.
Gene
Ontology
ChainFunctionProcessComponent
A, N
  • exo-alpha-sialidase activity...
  • calcium ion binding
  • hydrolase activity
  • hydrolase activity, acting o...
  • metal ion binding
  • carbohydrate metabolic proce...
  • metabolic process
  • plasma membrane
  • membrane
  • integral to membrane
  • virion
  • host cell plasma membrane
  • virion membrane
  • Primary referenceThree-dimensional structures of single-chain Fv-neuraminidase complexes., Malby RL, McCoy AJ, Kortt AA, Hudson PJ, Colman PM, J Mol Biol 1998 Jun 19;279(4):901-10. PMID:9642070
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (214 Kb) [Save to disk]
  • Biological Unit Coordinates (1nmc.pdb1.gz) 207 Kb
  • Biological Unit Coordinates (1nmc.pdb2.gz) 207 Kb
  • CSU: Contacts of Structural Units for 1NMC
  • Likely Quarternary Molecular Structure file(s) for 1NMC
  • Structure Factors (657 Kb)
  • Retrieve 1NMC in mmCIF format [Save to disk]
  • View 1NMC in 3D
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  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1NMC, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nmca_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1nmcb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1nmcc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1nmch_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1nmcl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1nmcn_, region N [Jmol] [rasmolscript] [script source]
  • Fold representative 1nmc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nmc_C] [1nmc_L] [1nmc_H] [1nmc_N] [1nmc_B] [1nmc_A]
  • Other resources with information on 1NMC
  • InterPro: IPR001860
  • MMDB (Entrez's Structure Database)
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