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Entry
Database: PDB / ID: 4fvk
TitleStructural and functional characterization of neuraminidase-like molecule N10 derived from bat influenza A virus
ComponentsNeuraminidase
KeywordsHYDROLASE / 6-bladed beta-propeller / Calcium binding / Glycosylation / Membrane
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsLi, Q. / Sun, X.M. / Li, Z.X. / Liu, Y. / Vavricka, C.J. / Qi, J.X. / Gao, G.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and functional characterization of neuraminidase-like molecule N10 derived from bat influenza A virus
Authors: Li, Q. / Sun, X.M. / Li, Z.X. / Liu, Y. / Vavricka, C.J. / Qi, J.X. / Gao, G.F.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,40514
Polymers83,8442
Non-polymers1,56112
Water5,044280
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,10132
Polymers167,6894
Non-polymers4,41228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area15150 Å2
ΔGint-42 kcal/mol
Surface area50750 Å2
MethodPISA
2
B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,51924
Polymers167,6894
Non-polymers1,83020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Buried area12560 Å2
ΔGint-79 kcal/mol
Surface area49150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.496, 122.496, 110.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-672-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase /


Mass: 41922.180 Da / Num. of mol.: 2 / Fragment: UNP residues 76-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/153/2009(H17N10)
Gene: NA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM75, exo-alpha-sialidase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 288 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30%(w/v) PEG2000 MME, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2012
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.198→50 Å / Num. all: 43363 / Num. obs: 43333 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.5 % / Biso Wilson estimate: 36.99 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 27.907
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 6 / Rsym value: 0.554 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSS

3nss


Resolution: 2.198→41.026 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8027 / SU ML: 0.22 / σ(F): 2 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 2176 5.03 %Random
Rwork0.2074 ---
all0.2093 ---
obs0.2093 43301 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.6 Å2 / Biso mean: 44.0391 Å2 / Biso min: 13.62 Å2
Refinement stepCycle: LAST / Resolution: 2.198→41.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 78 280 6108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095977
X-RAY DIFFRACTIONf_angle_d1.3338086
X-RAY DIFFRACTIONf_chiral_restr0.088879
X-RAY DIFFRACTIONf_plane_restr0.0051041
X-RAY DIFFRACTIONf_dihedral_angle_d17.4942193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1984-2.24620.3121260.266225112637100
2.2462-2.29850.27451420.248525332675100
2.2985-2.3560.27591420.230625262668100
2.356-2.41970.27681420.230425172659100
2.4197-2.49090.29941300.238925212651100
2.4909-2.57120.30951510.243825372688100
2.5712-2.66310.33941330.245125572690100
2.6631-2.76970.25941230.239425372660100
2.7697-2.89580.28941300.224525742704100
2.8958-3.04840.21721360.215225492685100
3.0484-3.23930.2531350.198825572692100
3.2393-3.48930.22811400.188525742714100
3.4893-3.84020.20751280.178426092737100
3.8402-4.39530.19511330.174125962729100
4.3953-5.53550.20041480.17426362784100
5.5355-41.03270.30491370.23992791292899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.34520.039-0.12061.4031-0.53340.76290.0123-0.07230.08240.042-0.0547-0.0368-0.04490.0524-0.02110.13190.0190.00130.1192-0.01010.1459-5.7227-43.199517.3337
21.2131-0.04060.29761.4066-0.51010.7983-0.0351-0.05460.13990.04770.08250.1667-0.1294-0.1563-0.04340.15220.04210.00570.15060.01620.1913-19.7425-32.510515.2557
30.6696-0.1663-0.30280.48310.13080.9577-0.25160.1939-0.3876-0.2848-0.1786-0.15670.13920.0463-0.12920.5755-0.10010.13450.60.01620.5273-41.114510.921438.8751
41.30950.0344-0.61761.1305-0.00691.1447-0.07190.0675-0.1987-0.1057-0.0971-0.0329-0.00550.204-0.08590.44270.02260.05090.4348-0.01480.404-45.0677-3.436546.4317
51.714-0.6403-0.42242.3191-0.06821.1383-0.00450.1732-0.7517-0.2184-0.0168-0.37870.3268-0.0257-0.06740.5266-0.02880.07750.5702-0.04310.6184-36.919-14.561638.1711
60.85030.2808-0.47891.37740.11290.5894-0.04770.2048-0.1947-0.37480.1625-0.9364-0.13350.4939-0.1410.57260.01060.18650.7189-0.05650.7988-22.68280.285838.2031
70.7983-0.1056-0.43681.48530.18730.68280.02410.05060.3146-0.13260.0507-0.6476-0.55980.2634-0.14570.5741-0.05360.08010.61340.00890.6329-33.275514.712244.5221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 83:216 )A83 - 216
2X-RAY DIFFRACTION2( CHAIN A AND RESID 217:460 )A217 - 460
3X-RAY DIFFRACTION3( CHAIN B AND RESID 83:114 )B83 - 114
4X-RAY DIFFRACTION4( CHAIN B AND RESID 115:188 )B115 - 188
5X-RAY DIFFRACTION5( CHAIN B AND RESID 189:216 )B189 - 216
6X-RAY DIFFRACTION6( CHAIN B AND RESID 217:364 )B217 - 364
7X-RAY DIFFRACTION7( CHAIN B AND RESID 365:460 )B365 - 460

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