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- PDB-6q1z: Crystal structure of human 1G04 Fab in complex with influenza vir... -

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Basic information

Entry
Database: PDB / ID: 6q1z
TitleCrystal structure of human 1G04 Fab in complex with influenza virus neuraminidase from A/Hunan/02650/2016 (H7N9)
Components
  • 1G04 Fab IgG1 heavy chain
  • 1G04 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-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion 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
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.446 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 / chem_comp ...atom_site / 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 / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
L: 1G04 Fab kappa light chain
H: 1G04 Fab IgG1 heavy chain
C: 1G04 Fab kappa light chain
D: 1G04 Fab IgG1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,77514
Polymers187,3126
Non-polymers5,4638
Water0
1
A: Neuraminidase
L: 1G04 Fab kappa light chain
H: 1G04 Fab IgG1 heavy chain
hetero molecules

A: Neuraminidase
L: 1G04 Fab kappa light chain
H: 1G04 Fab IgG1 heavy chain
hetero molecules

A: Neuraminidase
L: 1G04 Fab kappa light chain
H: 1G04 Fab IgG1 heavy chain
hetero molecules

A: Neuraminidase
L: 1G04 Fab kappa light chain
H: 1G04 Fab IgG1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,55128
Polymers374,62512
Non-polymers10,92616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area53700 Å2
ΔGint42 kcal/mol
Surface area123710 Å2
MethodPISA
2
B: Neuraminidase
C: 1G04 Fab kappa light chain
D: 1G04 Fab IgG1 heavy chain
hetero molecules

B: Neuraminidase
C: 1G04 Fab kappa light chain
D: 1G04 Fab IgG1 heavy chain
hetero molecules

B: Neuraminidase
C: 1G04 Fab kappa light chain
D: 1G04 Fab IgG1 heavy chain
hetero molecules

B: Neuraminidase
C: 1G04 Fab kappa light chain
D: 1G04 Fab IgG1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,55128
Polymers374,62512
Non-polymers10,92616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area54610 Å2
ΔGint40 kcal/mol
Surface area123720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.242, 180.242, 148.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Antibody , 2 types, 4 molecules LCHD

#2: Antibody 1G04 Fab kappa light chain


Mass: 23564.133 Da / Num. of mol.: 2
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 1G04 Fab IgG1 heavy chain


Mass: 26109.111 Da / Num. of mol.: 2
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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Protein / Non-polymers , 2 types, 4 molecules AB

#1: Protein Neuraminidase /


Mass: 43982.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Cell (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5A4LHS4*PLUS, exo-alpha-sialidase
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Sugars , 3 types, 6 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-(1-2)-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: 1883.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 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]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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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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: 3.28 Å3/Da / Density % sol: 62.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 5%(w/v) PEG3000, 30% (w/v) PEG400, 10%(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03309 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03309 Å / Relative weight: 1
ReflectionResolution: 3.446→47.4 Å / Num. obs: 30994 / % possible obs: 99.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 126 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05 / Rsym value: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 3.45→3.51 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1539 / CC1/2: 0.844 / Rpim(I) all: 0.48 / Rsym value: 0.87 / % possible all: 0.87

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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, 5ITB, 4FQL

5l14

5itb

4fql


Resolution: 3.446→47.365 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.02
RfactorNum. reflection% reflection
Rfree0.2472 1493 4.82 %
Rwork0.1971 --
obs0.1995 30967 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.446→47.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12874 0 362 0 13236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113632
X-RAY DIFFRACTIONf_angle_d1.26518628
X-RAY DIFFRACTIONf_dihedral_angle_d4.5959472
X-RAY DIFFRACTIONf_chiral_restr0.0652110
X-RAY DIFFRACTIONf_plane_restr0.0092348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4463-3.55750.35441290.28662634X-RAY DIFFRACTION99
3.5575-3.68460.34111240.25992737X-RAY DIFFRACTION100
3.6846-3.83210.29991470.23522656X-RAY DIFFRACTION100
3.8321-4.00640.29151400.22922702X-RAY DIFFRACTION100
4.0064-4.21750.27471490.19582702X-RAY DIFFRACTION100
4.2175-4.48150.26321190.18882725X-RAY DIFFRACTION100
4.4815-4.82720.24731370.18452677X-RAY DIFFRACTION99
4.8272-5.31250.221370.17732670X-RAY DIFFRACTION98
5.3125-6.07980.24451150.19232687X-RAY DIFFRACTION99
6.0798-7.65470.25441710.19482633X-RAY DIFFRACTION98
7.6547-47.36990.18711250.18012651X-RAY DIFFRACTION95

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