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- PDB-6q20: Crystal structure of human 1E01 Fab in complex with influenza vir... -

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Basic information

Entry
Database: PDB / ID: 6q20
TitleCrystal structure of human 1E01 Fab in complex with influenza virus neuraminidase from A/Japan/305/1957 (H2N2)
Components
  • 1E01 Fab IgG1 heavy chain
  • 1E01 Fab kappa light chain
  • Neuraminidase
KeywordsVIRAL PROTEIN / HYDROLASE/IMMUNE SYSTEM / broadly protective human antibody / neuraminidase / inhibition / active site / antibody-neuraminidase complex / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
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: 2.45 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675-01 United States
CitationJournal: Science / Year: 2019
Title: Broadly protective human antibodies that target the active site of influenza virus neuraminidase.
Authors: Stadlbauer, D. / Zhu, X. / McMahon, M. / Turner, J.S. / Wohlbold, T.J. / Schmitz, A.J. / Strohmeier, S. / Yu, W. / Nachbagauer, R. / Mudd, P.A. / Wilson, I.A. / Ellebedy, A.H. / Krammer, F.
History
DepositionAug 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
L: 1E01 Fab kappa light chain
H: 1E01 Fab IgG1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2068
Polymers93,2453
Non-polymers1,9615
Water1,13563
1
A: Neuraminidase
L: 1E01 Fab kappa light chain
H: 1E01 Fab IgG1 heavy chain
hetero molecules

A: Neuraminidase
L: 1E01 Fab kappa light chain
H: 1E01 Fab IgG1 heavy chain
hetero molecules

A: Neuraminidase
L: 1E01 Fab kappa light chain
H: 1E01 Fab IgG1 heavy chain
hetero molecules

A: Neuraminidase
L: 1E01 Fab kappa light chain
H: 1E01 Fab IgG1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,82232
Polymers372,97912
Non-polymers7,84320
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
Buried area47760 Å2
ΔGint-71 kcal/mol
Surface area120560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.452, 160.452, 84.173
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-512-

CA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase


Mass: 43496.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Japan/305/1957 H2N2)
Strain: A/Japan/305/1957 H2N2 / Gene: NA / Cell (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: C7RWN0, UniProt: Q1K9Q1*PLUS, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules LH

#2: Antibody 1E01 Fab kappa light chain


Mass: 23707.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody 1E01 Fab IgG1 heavy chain


Mass: 26041.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expicho / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 3 types, 3 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-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1WURCSPDB2Glycan 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]{}}}}}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
#6: 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.: 1
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, 65 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (v/v) glycerol, 24% (w/v) PEG1500

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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: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.45→47.042 Å / Num. obs: 40758 / % possible obs: 99.5 % / Redundancy: 13.8 % / Biso Wilson estimate: 50 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.03 / Rsym value: 0.12 / Net I/σ(I): 22.5
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1967 / CC1/2: 0.942 / Rpim(I) all: 0.3 / Rsym value: 0.99 / % possible all: 98.2

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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: 3TIA, 5ITB, 4FQL

3tia

5itb

4fql


Resolution: 2.45→47.042 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.66
RfactorNum. reflection% reflection
Rfree0.2724 2151 5.29 %
Rwork0.2173 --
obs0.2201 40669 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→47.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 127 63 6596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036710
X-RAY DIFFRACTIONf_angle_d0.6659147
X-RAY DIFFRACTIONf_dihedral_angle_d6.8523945
X-RAY DIFFRACTIONf_chiral_restr0.0471023
X-RAY DIFFRACTIONf_plane_restr0.0041165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4496-2.50660.47181390.3892461X-RAY DIFFRACTION97
2.5066-2.56920.38781280.35782468X-RAY DIFFRACTION98
2.5692-2.63870.40561410.33592517X-RAY DIFFRACTION98
2.6387-2.71630.37781470.30952528X-RAY DIFFRACTION99
2.7163-2.8040.34541470.29832512X-RAY DIFFRACTION99
2.804-2.90420.30911440.27322545X-RAY DIFFRACTION100
2.9042-3.02050.32391520.26942561X-RAY DIFFRACTION100
3.0205-3.15790.32351550.25512518X-RAY DIFFRACTION100
3.1579-3.32430.36481330.24722582X-RAY DIFFRACTION100
3.3243-3.53260.29991360.22252577X-RAY DIFFRACTION100
3.5326-3.80520.26381450.21772589X-RAY DIFFRACTION100
3.8052-4.18790.26691310.18732601X-RAY DIFFRACTION100
4.1879-4.79340.18791440.15452616X-RAY DIFFRACTION100
4.7934-6.03720.22821760.16992634X-RAY DIFFRACTION100
6.0372-47.05080.21491330.19242809X-RAY DIFFRACTION100
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)
10.61870.00960.08940.7746-0.10350.2725-0.0074-0.05670.00890.0166-0.0099-0.05710.02750.0328-00.44160.00770.00740.46580.00670.5731-55.6713-12.68962.0964
2-0.1708-0.122-0.24690.2404-0.01870.36130.1213-0.04920.0824-0.0749-0.0180.20130.2778-0.0966-00.6615-0.0994-0.11150.6230.110.612-54.432-60.78330.8995
3-0.1716-0.1244-0.36410.0576-0.03890.52750.05060.00970.0999-0.1949-0.1522-0.14580.21730.1531-0.00040.4679-0.0038-0.05260.53260.12560.4645-38.055-55.067825.7288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 82 through 603)
2X-RAY DIFFRACTION2(chain 'L' and resid 1 through 214)
3X-RAY DIFFRACTION3(chain 'H' and resid 1 through 228)

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