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- PDB-6pze: Crystal structure of human NA-45 Fab in complex with neuraminidas... -

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Basic information

Entry
Database: PDB / ID: 6pze
TitleCrystal structure of human NA-45 Fab in complex with neuraminidase Y169aH mutant from A/Shanghai/2/2013 (H7N9)
Components
  • NA-45 FAB HEAVY CHAIN
  • NA-45 FAB LIGHT CHAIN
  • Neuraminidase
KeywordsIMMUNE SYSTEM / antibody / inhibition mechanism
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 / 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 / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neuraminidase / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 2items
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)HHSN272201400024C 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
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
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_struct_special_symmetry / pdbx_validate_close_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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4746
Polymers92,2883
Non-polymers2,1863
Water10,629590
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN

L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN

L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN

L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)377,89424
Polymers369,15012
Non-polymers8,74412
Water21612
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
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_456-x-1,-y,z+11
crystal symmetry operation3_456-y-1/2,x+1/2,z+11
crystal symmetry operation4_446y-1/2,-x-1/2,z+11
Buried area40520 Å2
ΔGint14 kcal/mol
Surface area123810 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint11 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.268, 161.268, 87.382
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
11A-782-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase /


Mass: 44014.000 Da / Num. of mol.: 1 / Mutation: Y169H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Shanghai/02/2013(H7N9))
Strain: A/Shanghai/02/2013(H7N9) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: V9NZ28, UniProt: R4NFR6*PLUS, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules LH

#2: Antibody NA-45 FAB LIGHT CHAIN


Mass: 22909.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody NA-45 FAB HEAVY CHAIN


Mass: 25364.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 2 molecules

#4: 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-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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

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Non-polymers , 2 types, 591 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes, pH 7.0 and 10% (w/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→45.8 Å / Num. obs: 51133 / % possible obs: 98.3 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rpim(I) all: 0.05 / Rsym value: 0.12 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.35 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3164 / CC1/2: 0.962 / Rpim(I) all: 0.26 / Rsym value: 0.62 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L14, 5T93, 5BV7

5l14

5t93

5bv7


Resolution: 2.3→45.786 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.85
RfactorNum. reflection% reflection
Rfree0.1973 2564 5.02 %
Rwork0.1559 --
obs0.158 51085 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 145 590 6995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076596
X-RAY DIFFRACTIONf_angle_d0.9449037
X-RAY DIFFRACTIONf_dihedral_angle_d5.6643894
X-RAY DIFFRACTIONf_chiral_restr0.0551031
X-RAY DIFFRACTIONf_plane_restr0.0061132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2944-2.33850.25111380.18842631X-RAY DIFFRACTION98
2.3385-2.38620.26421310.18222677X-RAY DIFFRACTION98
2.3862-2.43810.25061550.18182672X-RAY DIFFRACTION99
2.4381-2.49480.22891380.17872626X-RAY DIFFRACTION97
2.4948-2.55720.23621230.17352566X-RAY DIFFRACTION95
2.5572-2.62640.21961430.16822697X-RAY DIFFRACTION99
2.6264-2.70360.20861330.16822688X-RAY DIFFRACTION99
2.7036-2.79090.18771420.15352686X-RAY DIFFRACTION99
2.7909-2.89060.22421370.1572712X-RAY DIFFRACTION99
2.8906-3.00630.20681590.15842698X-RAY DIFFRACTION99
3.0063-3.14310.20441300.16122707X-RAY DIFFRACTION99
3.1431-3.30880.20391230.16012591X-RAY DIFFRACTION94
3.3088-3.5160.17811640.15882716X-RAY DIFFRACTION99
3.516-3.78740.22781300.16972744X-RAY DIFFRACTION99
3.7874-4.16830.16261560.14112759X-RAY DIFFRACTION100
4.1683-4.77090.16311420.11712707X-RAY DIFFRACTION97
4.7709-6.00870.16541680.12992745X-RAY DIFFRACTION98
6.0087-45.79490.19791520.16842899X-RAY DIFFRACTION97
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)
10.55390.3897-0.22150.4612-0.08160.49760.0378-0.02730.04470.01320.0270.0488-0.00870.0018-0.07470.1630.0208-0.01220.12930.00460.1547-66.197-10.073137.5891
20.3422-0.079-0.25380.82430.06691.26580.0007-0.0038-0.04120.04740.0089-0.02680.0631-0.0677-0.04940.15070.0276-0.02710.1948-0.0260.1464-51.3051-5.21743.4068
30.7936-0.21720.07620.90970.39861.1739-0.0237-0.1273-0.09570.07180.0371-0.09790.05290.1086-0.03660.15240.0395-0.06380.20050.01760.1967-47.0605-17.903846.2027
40.81390.3504-0.05810.6513-0.08370.30340.0307-0.0197-0.10650.01270.0136-0.07590.07120.0869-0.04150.14050.0287-0.02640.149-0.01630.1334-58.2613-21.929234.057
50.85890.03140.3891.2182-0.94763.5533-0.07290.2843-0.2598-0.28950.2370.21190.2068-0.4054-0.1240.3379-0.0089-0.00520.4761-0.05910.2189-47.5155-20.1779-3.6987
62.12740.30430.42621.4840.43163.51830.01530.41940.1792-0.15120.06260.04810.0734-0.0334-0.06110.1743-0.00860.00610.27530.01780.2121-48.754-12.93314.8695
70.4822-0.1397-0.6260.30610.18220.8072-0.25790.04440.20350.008-0.003-0.02780.21550.14190.26220.335-0.0193-0.0980.52210.00570.2536-38.1283-11.7565-17.9329
83.3570.97090.74632.92080.32852.3837-0.21950.47440.0347-0.64170.11-0.2805-0.56670.37010.08550.3927-0.12380.02450.5491-0.0280.3572-20.5651-8.4499-25.3875
90.85980.3579-1.32722.25810.21812.31970.12860.06510.4354-0.03750.0576-0.1877-0.10840.4377-0.18550.2309-0.04380.06920.3099-0.01630.3275-25.11420.65518.4749
101.81731.25710.3541.5909-0.7272.26350.1020.20460.2319-0.02260.09070.0185-0.17520.0057-0.19020.18030.02040.0420.2712-0.06750.2907-36.1313-1.434512.7898
113.44240.1655-0.31143.26180.34923.20930.1637-0.4616-0.10240.16540.0191-0.2386-0.13950.2764-0.15340.2023-0.02440.0060.2583-0.0270.2066-33.9043-5.683722.2792
122.1551-1.1353-0.52510.94370.07571.41650.1007-0.09120.25460.11220.0166-0.2833-0.10520.1449-0.14360.2023-0.04780.0250.2979-0.0490.2663-28.11380.065415.8282
132.210.3522-1.89620.3517-0.27381.65210.21120.22940.26580.11470.18470.0231-0.0691-0.1476-0.30580.19170.03470.01330.2303-0.01040.2338-42.8034-6.264217.3429
143.26120.5717-3.65461.0837-0.60684.1146-0.09580.0520.4339-0.08180.23810.0293-0.0091-0.1255-0.16330.18350.00280.00910.2325-0.01210.2527-39.3763-2.79987.9702
152.51991.10840.10351.63160.36433.7552-0.30850.23420.5892-0.4358-0.04070.3482-0.7663-0.07050.33180.43780.0021-0.07940.33540.00570.4377-21.10411.486-12.7435
160.1645-0.0091-0.002-0.0004-0.0018-0.0010.10011.03560.9809-0.899-0.08760.4131-0.6745-0.0973-0.12911.26680.1426-0.32350.65090.3431.0297-27.188111.1918-25.5233
172.2013-0.78390.89631.1566-0.51841.7082-0.46430.12041.1428-0.6886-0.0360.4558-1.17-0.04940.40350.9056-0.0387-0.20110.37490.05060.8755-19.182910.3189-12.2936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 82:190 )A82 - 190
2X-RAY DIFFRACTION2( CHAIN A AND RESID 191:246 )A191 - 246
3X-RAY DIFFRACTION3( CHAIN A AND RESID 247:318 )A247 - 318
4X-RAY DIFFRACTION4( CHAIN A AND RESID 319:468 )A319 - 468
5X-RAY DIFFRACTION5( CHAIN L AND RESID 2:18 )L2 - 18
6X-RAY DIFFRACTION6( CHAIN L AND RESID 19:98 )L19 - 98
7X-RAY DIFFRACTION7( CHAIN L AND RESID 99:118 )L99 - 118
8X-RAY DIFFRACTION8( CHAIN L AND RESID 119:208 )L119 - 208
9X-RAY DIFFRACTION9( CHAIN H AND RESID 2:17 )H2 - 17
10X-RAY DIFFRACTION10( CHAIN H AND RESID 18:51 )H18 - 51
11X-RAY DIFFRACTION11( CHAIN H AND RESID 52:66 )H52 - 66
12X-RAY DIFFRACTION12( CHAIN H AND RESID 67:87 )H67 - 87
13X-RAY DIFFRACTION13( CHAIN H AND RESID 88:100 )H88 - 100
14X-RAY DIFFRACTION14( CHAIN H AND RESID 101:109 )H101 - 109
15X-RAY DIFFRACTION15( CHAIN H AND RESID 110:177 )H110 - 177
16X-RAY DIFFRACTION16( CHAIN H AND RESID 178:194 )H178 - 194
17X-RAY DIFFRACTION17( CHAIN H AND RESID 195:213 )H195 - 213

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  • 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

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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

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