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- PDB-4qnp: Crystal structure of the 2009 pandemic H1N1 influenza virus neura... -

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Basic information

Entry
Database: PDB / ID: 4qnp
TitleCrystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a neutralizing antibody
Components
  • (neutralizing antibody, ...) x 2
  • Neuraminidase
KeywordsHYDROLASE/IMMUNE SYSTEM / influenza / neuraminidase / antibody / neutralizing antibody / HYDROLASE-IMMUNE SYSTEM complex
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 / B cell differentiation / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane ...exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / B cell differentiation / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neuraminidase / Immunoglobulin kappa constant / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWan, H.Q. / Yang, H. / Shore, D.A. / Garten, R.J. / Couzens, L. / Gao, J. / Jiang, L.L. / Carney, P.J. / Villanueva, J. / Stevens, J. / Eichelberger, M.C.
CitationJournal: Nat Commun / Year: 2015
Title: Structural characterization of a protective epitope spanning A(H1N1)pdm09 influenza virus neuraminidase monomers.
Authors: Wan, H. / Yang, H. / Shore, D.A. / Garten, R.J. / Couzens, L. / Gao, J. / Jiang, L. / Carney, P.J. / Villanueva, J. / Stevens, J. / Eichelberger, M.C.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_validate_symm_contact / struct_asym / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
F: neutralizing antibody, light chain
E: neutralizing antibody, heavy chain
L: neutralizing antibody, light chain
H: neutralizing antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,92416
Polymers180,0316
Non-polymers1,89410
Water3,261181
1
A: Neuraminidase
B: Neuraminidase
F: neutralizing antibody, light chain
E: neutralizing antibody, heavy chain
L: neutralizing antibody, light chain
H: neutralizing antibody, heavy chain
hetero molecules

A: Neuraminidase
B: Neuraminidase
F: neutralizing antibody, light chain
E: neutralizing antibody, heavy chain
L: neutralizing antibody, light chain
H: neutralizing antibody, heavy chain
hetero molecules

A: Neuraminidase
B: Neuraminidase
F: neutralizing antibody, light chain
E: neutralizing antibody, heavy chain
L: neutralizing antibody, light chain
H: neutralizing antibody, heavy chain
hetero molecules

A: Neuraminidase
B: Neuraminidase
F: neutralizing antibody, light chain
E: neutralizing antibody, heavy chain
L: neutralizing antibody, light chain
H: neutralizing antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)727,69864
Polymers720,12224
Non-polymers7,57640
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_654-x+1,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area84690 Å2
ΔGint-510 kcal/mol
Surface area234280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.290, 202.951, 143.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12F
22L
13E
23H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILEAA82 - 4671 - 386
21SERSERILEILEBB82 - 4671 - 386
12GLNGLNARGARGFC1 - 2101 - 210
22GLNGLNARGARGLE1 - 2101 - 210
13GLNGLNARGARGED1 - 2241 - 224
23GLNGLNARGARGHF1 - 2241 - 224

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase


Mass: 42483.363 Da / Num. of mol.: 2 / Fragment: UNP residues 82-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: S5N0T0, UniProt: D5KL82*PLUS, exo-alpha-sialidase

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Antibody , 2 types, 4 molecules FLEH

#2: Antibody neutralizing antibody, light chain


Mass: 23269.615 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: hybridoma / References: UniProt: P01837*PLUS
#3: Antibody neutralizing antibody, heavy chain


Mass: 24262.281 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: hybridoma

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Sugars , 2 types, 6 molecules

#4: 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.: 2
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 , 2 types, 185 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09 M malonic acid, 0.013 M ammonium citrate tribasic, 0.006 M succinic acid, 0.015 M DL-malic acid, 0.02 M sodium acetate, 0.025 M sodium formate, 0.008 M ammonium tartrate dibasic, 0.1 M ...Details: 0.09 M malonic acid, 0.013 M ammonium citrate tribasic, 0.006 M succinic acid, 0.015 M DL-malic acid, 0.02 M sodium acetate, 0.025 M sodium formate, 0.008 M ammonium tartrate dibasic, 0.1 M HEPES/NaOH, 10% w/v PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2012
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→47.853 Å / Num. all: 52272 / Num. obs: 48574 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.87 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B7M

4b7m


Resolution: 2.8→47.85 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 26.084 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22379 2458 5.1 %RANDOM
Rwork0.18103 ---
all0.19 48633 --
obs0.18318 46115 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12635 0 116 181 12932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213113
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211768
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.94417870
X-RAY DIFFRACTIONr_angle_other_deg0.957327189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3451637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6124.011541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.025152030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3541562
X-RAY DIFFRACTIONr_chiral_restr0.0860.21947
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114915
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023039
X-RAY DIFFRACTIONr_mcbond_it2.4693.7526566
X-RAY DIFFRACTIONr_mcbond_other2.4693.7516565
X-RAY DIFFRACTIONr_mcangle_it3.9585.6248197
X-RAY DIFFRACTIONr_mcangle_other3.9585.6248198
X-RAY DIFFRACTIONr_scbond_it2.7983.9736546
X-RAY DIFFRACTIONr_scbond_other2.7983.9746547
X-RAY DIFFRACTIONr_scangle_other4.4295.8689674
X-RAY DIFFRACTIONr_long_range_B_refined6.40730.01214332
X-RAY DIFFRACTIONr_long_range_B_other6.40429.99714314
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A227910.07
12B227910.07
21F110050.1
22L110050.1
31E119890.1
32H119890.1
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 179 -
Rwork0.236 3291 -
obs--91.44 %
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)
10.5964-0.04160.0430.36870.10530.5401-0.003-0.0605-0.12820.00230.00870.00440.0563-0.0514-0.00580.1017-0.01330.0090.0132-0.00050.119345.065-29.3939-78.8716
20.58520.0809-0.15920.37270.17310.4591-0.0211-0.0708-0.09760.0198-0.0023-0.01760.05840.04960.02350.10690.00150.00440.01480.02850.096865.2434-29.317-44.9645
31.9349-0.0478-0.6280.2187-0.14560.32550.01980.1815-0.1510.0277-0.0280.0429-0.0392-0.04240.00820.0702-0.03670.00250.0844-0.06290.0942.3292-19.0855-48.1479
42.13270.158-0.03520.1016-0.09140.10360.0621-0.1881-0.2666-0.0179-0.0566-0.0247-0.00960.0516-0.00550.08-0.014-0.00940.0491-0.00040.094615.654-19.1468-34.9936
50.5388-0.2611.01310.2814-0.17312.5680.0022-0.05790.05150.049-0.0284-0.04680.1426-0.22680.02620.0766-0.04680.01040.06070.02310.0596.0279-18.8006-2.4556
60.252-0.14950.23230.1109-0.00541.7006-0.02280.0682-0.0415-0.0044-0.03370.03770.15480.13160.05650.1142-0.0080.00840.03450.01970.0704109.2558-19.1412-15.6365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A82 - 467
2X-RAY DIFFRACTION1A501 - 506
3X-RAY DIFFRACTION2B82 - 467
4X-RAY DIFFRACTION2B501 - 506
5X-RAY DIFFRACTION3F1 - 212
6X-RAY DIFFRACTION4E1 - 224
7X-RAY DIFFRACTION5L1 - 211
8X-RAY DIFFRACTION6H1 - 224

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