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- PDB-3nn9: REFINED ATOMIC STRUCTURES OF N9 SUBTYPE INFLUENZA VIRUS NEURAMINI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nn9 | |||||||||
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Title | REFINED ATOMIC STRUCTURES OF N9 SUBTYPE INFLUENZA VIRUS NEURAMINIDASE AND ESCAPE MUTANTS | |||||||||
![]() | NEURAMINIDASE N9 | |||||||||
![]() | HYDROLASE(O-GLYCOSYL) | |||||||||
Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Tulip, W.R. / Varghese, J.N. / Baker, A.T. / Vandonkelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M. | |||||||||
![]() | ![]() Title: Refined atomic structures of N9 subtype influenza virus neuraminidase and escape mutants. Authors: Tulip, W.R. / Varghese, J.N. / Baker, A.T. / van Donkelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M. #1: ![]() Title: Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution Authors: Varghese, J.N. / Colman, P.M. #2: ![]() Title: Three Dimensional Structure of Neuraminidase of Subtype N9 from an Avian Influenza Virus Authors: Baker, A.T. / Varghese, J.N. / Laver, W.G. / Air, G.M. / Colman, P.M. #3: ![]() Title: Gene and Protein Sequence of an Influenza Virus Neuraminidase with Hemagglutinin Activity Authors: Air, G.M. / Ritchie, L.R. / Laver, W.G. / Colman, P.M. #4: ![]() Title: Influenza Virus Neuraminidase with Hemmagglutinin Activity Authors: Laver, W.G. / Colman, P.M. / Webster, R.G. / Hinshaw, V.S. / Air, G.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.5 KB | Display | ![]() |
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PDB format | ![]() | 72.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Atom site foot note | 1: RESIDUES 326 AND 431 ARE CIS PROLINES. |
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Components
#1: Protein | Mass: 43724.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Sugar | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.6 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. obs: 17915 / % possible obs: 68.6 % / Num. measured all: 104979 / Rmerge(I) obs: 0.121 |
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Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→6 Å / Rfactor Rwork: 0.178 Details: SIDE CHAINS AND/OR WHOLE RESIDUES WERE OMITTED FROM THE CRYSTALLOGRAPHIC REFINEMENT BY ASSIGNING THEM OCCUPANCIES OF 0.02. BECAUSE AN ERROR IN THE REGISTRATION OF THE NEURAMINIDASE C- ...Details: SIDE CHAINS AND/OR WHOLE RESIDUES WERE OMITTED FROM THE CRYSTALLOGRAPHIC REFINEMENT BY ASSIGNING THEM OCCUPANCIES OF 0.02. BECAUSE AN ERROR IN THE REGISTRATION OF THE NEURAMINIDASE C-TERMINAL SEGMENT WAS DISCOVERED LATE IN THE REFINEMENT PROCESS, THE COORDINATES OF RESIDUES 458 - 468 IN THIS MUTANT WERE TAKEN DIRECTLY FROM THE REFINED COORDINATES OF S370L. THE OCCUPANCY AND B VALUE OF THE CALCIUM ION ARE TENTATIVE AND REQUIRE HIGH RESOLUTION DATA REFINEMENT. THE CALCIUM WAS REFINED AS A NON-BONDED ION. THE FIVE LIGANDS ARE O ASP 293, O GLY 297, OD2 ASP 324, O ASN 347, AND HOH 8. THEY ARE IN OCTAHEDRAL GEOMETRY (NO RESTRAINTS WERE IMPOSED) AND THE SIXTH LIGAND (PRESUMABLY ANOTHER WATER MOLECULE) IS NOT SEEN IN THE ELECTRON DENSITY MAPS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 4 |