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- PDB-6q23: Crystal structure of human 1G01 Fab in complex with influenza vir... -

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Basic information

Entry
Database: PDB / ID: 6q23
TitleCrystal structure of human 1G01 Fab in complex with influenza virus neuraminidase from A/California/04/2009 (H1N1)
Components
  • 1G01 Fab IgG1 heavy chain
  • 1G01 Fab kappa light chain
  • Neuraminidase
KeywordsVIRAL PROTEIN / HYDROLASE/IMMUNE SYSTEM / broadly protective human antibody / inhibition / active site / antibody-neuraminidase complex / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding ...: / : / : / exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / identical protein 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: 3.27 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 1.1Oct 30, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.2Nov 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 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 1.5Oct 11, 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
Revision 1.6Oct 30, 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
C: Neuraminidase
B: Neuraminidase
A: Neuraminidase
D: Neuraminidase
H: 1G01 Fab IgG1 heavy chain
L: 1G01 Fab kappa light chain
E: 1G01 Fab IgG1 heavy chain
F: 1G01 Fab kappa light chain
G: 1G01 Fab IgG1 heavy chain
I: 1G01 Fab kappa light chain
J: 1G01 Fab IgG1 heavy chain
K: 1G01 Fab kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,63929
Polymers370,50912
Non-polymers2,13017
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38800 Å2
ΔGint-254 kcal/mol
Surface area119590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.594, 234.985, 106.275
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
12C
22A
13C
23D
14B
24A
15B
25D
16A
26D
17H
27E
18H
28G
19H
29J
110L
210F
111L
211I
112L
212K
113E
213G
114E
214J
115F
215I
116F
216K
117G
217J
118I
218K

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
11SERSERPHEPHECA82 - 4666 - 389
21SERSERPHEPHEBB82 - 4666 - 389
12SERSERPHEPHECA82 - 4666 - 389
22SERSERPHEPHEAC82 - 4666 - 389
13SERSERPHEPHECA82 - 4666 - 389
23SERSERPHEPHEDD82 - 4666 - 389
14SERSERPHEPHEBB82 - 4666 - 389
24SERSERPHEPHEAC82 - 4666 - 389
15SERSERPHEPHEBB82 - 4666 - 389
25SERSERPHEPHEDD82 - 4666 - 389
16SERSERPHEPHEAC82 - 4666 - 389
26SERSERPHEPHEDD82 - 4666 - 389
17GLUGLULYSLYSHE1 - 2282 - 232
27GLUGLULYSLYSEG1 - 2282 - 232
18GLUGLULYSLYSHE1 - 2282 - 232
28GLUGLULYSLYSGI1 - 2282 - 232
19GLUGLULYSLYSHE1 - 2282 - 232
29GLUGLULYSLYSJK1 - 2282 - 232
110ASPASPCYSCYSLF1 - 2142 - 216
210ASPASPCYSCYSFH1 - 2142 - 216
111ASPASPCYSCYSLF1 - 2142 - 216
211ASPASPCYSCYSIJ1 - 2142 - 216
112ASPASPCYSCYSLF1 - 2142 - 216
212ASPASPCYSCYSKL1 - 2142 - 216
113GLUGLULYSLYSEG1 - 2282 - 232
213GLUGLULYSLYSGI1 - 2282 - 232
114GLUGLULYSLYSEG1 - 2282 - 232
214GLUGLULYSLYSJK1 - 2282 - 232
115ASPASPCYSCYSFH1 - 2142 - 216
215ASPASPCYSCYSIJ1 - 2142 - 216
116ASPASPCYSCYSFH1 - 2142 - 216
216ASPASPCYSCYSKL1 - 2142 - 216
117GLUGLULYSLYSGI1 - 2282 - 232
217GLUGLULYSLYSJK1 - 2282 - 232
118ASPASPCYSCYSIJ1 - 2142 - 216
218ASPASPCYSCYSKL1 - 2142 - 216

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Protein
Neuraminidase


Mass: 42968.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009 (H1N1)
Strain: A/California/04/2009 (H1N1) / Gene: NA / Cell (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: C5MQL2, UniProt: C3W5S3*PLUS, exo-alpha-sialidase
#2: Antibody
1G01 Fab IgG1 heavy chain


Mass: 25981.021 Da / Num. of mol.: 4
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
1G01 Fab kappa light chain


Mass: 23677.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): expicho / Production host: Cricetulus griseus (Chinese hamster)
#4: 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.: 8
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
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 10% (v/v) glycerol, 20% (w/v) PEG300, 5% (w/v) PEG8000

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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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.661
11-L, -K, -H20.339
ReflectionResolution: 3.27→43.3 Å / Num. obs: 70214 / % possible obs: 91.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 53 Å2 / CC1/2: 0.952 / Rpim(I) all: 0.12 / Rsym value: 0.18 / Net I/σ(I): 4.5
Reflection shellResolution: 3.27→3.38 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3688 / CC1/2: 0.876 / Rpim(I) all: 0.43 / Rsym value: 0.57 / % possible all: 73.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSS, 5ITB, 4FQL

3nss

5itb

4fql


Resolution: 3.27→43.3 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.834 / SU B: 13.665 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24078 3351 4.8 %RANDOM
Rwork0.1963 ---
obs0.19841 66845 90.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.757 Å2
Baniso -1Baniso -2Baniso -3
1--44.99 Å2-0 Å2-1.54 Å2
2--42.93 Å20 Å2
3---2.05 Å2
Refinement stepCycle: 1 / Resolution: 3.27→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25420 0 121 0 25541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01326256
X-RAY DIFFRACTIONr_bond_other_d0.0010.01723124
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.64735756
X-RAY DIFFRACTIONr_angle_other_deg1.3421.57853944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96353288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.59822.4041248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.586154068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.76215136
X-RAY DIFFRACTIONr_chiral_restr0.0550.23420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0229588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025636
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4766.14713200
X-RAY DIFFRACTIONr_mcbond_other5.4766.14713199
X-RAY DIFFRACTIONr_mcangle_it8.5999.20316472
X-RAY DIFFRACTIONr_mcangle_other8.5999.20316473
X-RAY DIFFRACTIONr_scbond_it5.1076.39913056
X-RAY DIFFRACTIONr_scbond_other5.1076.39913056
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9679.47619285
X-RAY DIFFRACTIONr_long_range_B_refined14.546106128
X-RAY DIFFRACTIONr_long_range_B_other14.546106128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C121490.11
12B121490.11
21C122190.11
22A122190.11
31C120830.12
32D120830.12
41B121350.12
42A121350.12
51B122250.11
52D122250.11
61A121220.12
62D121220.12
71H60680.14
72E60680.14
81H60530.16
82G60530.16
91H61100.15
92J61100.15
101L60340.14
102F60340.14
111L59550.15
112I59550.15
121L60000.14
122K60000.14
131E59470.16
132G59470.16
141E60060.16
142J60060.16
151F59600.16
152I59600.16
161F59840.15
162K59840.15
171G61560.15
172J61560.15
181I60390.15
182K60390.15
LS refinement shellResolution: 3.265→3.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 172 -
Rwork0.239 3174 -
obs--58.6 %

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