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- PDB-6oc3: Crystal structure of FluA-20 Fab in complex with the head domain ... -

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Basic information

Entry
Database: PDB / ID: 6oc3
TitleCrystal structure of FluA-20 Fab in complex with the head domain of H1 (A/Solomon Islands/3/2006)
Components
  • Heavy chain of FluA-20 Fab
  • Hemagglutinin
  • Light chain of FluA-20 Fab
KeywordsIMMUNE SYSTEM / anti-flu antibody / HA head domain
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWilson, I.A. / Lang, S.
CitationJournal: Cell / Year: 2019
Title: A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface.
Authors: Bangaru, S. / Lang, S. / Schotsaert, M. / Vanderven, H.A. / Zhu, X. / Kose, N. / Bombardi, R. / Finn, J.A. / Kent, S.J. / Gilchuk, P. / Gilchuk, I. / Turner, H.L. / Garcia-Sastre, A. / Li, S. ...Authors: Bangaru, S. / Lang, S. / Schotsaert, M. / Vanderven, H.A. / Zhu, X. / Kose, N. / Bombardi, R. / Finn, J.A. / Kent, S.J. / Gilchuk, P. / Gilchuk, I. / Turner, H.L. / Garcia-Sastre, A. / Li, S. / Ward, A.B. / Wilson, I.A. / Crowe Jr., J.E.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of FluA-20 Fab
B: Light chain of FluA-20 Fab
C: Heavy chain of FluA-20 Fab
D: Light chain of FluA-20 Fab
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9477
Polymers148,7266
Non-polymers2211
Water00
1
A: Heavy chain of FluA-20 Fab
B: Light chain of FluA-20 Fab
F: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)74,3633
Polymers74,3633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heavy chain of FluA-20 Fab
D: Light chain of FluA-20 Fab
E: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5844
Polymers74,3633
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.468, 109.775, 146.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Heavy chain of FluA-20 Fab


Mass: 25154.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain of FluA-20 Fab


Mass: 23508.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Hemagglutinin


Mass: 25700.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1
#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.: 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
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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 277.12 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate-citrate, pH 4.2 40%(v/v) PEG300

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Data collection

DiffractionMean temperature: 78 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 36821 / % possible obs: 95.7 % / Redundancy: 6.8 % / CC1/2: 1 / Rpim(I) all: 0.05 / Rsym value: 0.13 / Net I/σ(I): 20.6
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1436 / CC1/2: 0.91 / Rpim(I) all: 0.31 / Rsym value: 0.78 / % possible all: 74.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJZ and 6OBZ

4yjz

6obz


Resolution: 2.85→48.168 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 1788 4.86 %
Rwork0.2366 --
obs0.2375 36821 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→48.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10024 0 14 0 10038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110375
X-RAY DIFFRACTIONf_angle_d1.60114152
X-RAY DIFFRACTIONf_dihedral_angle_d18.0793774
X-RAY DIFFRACTIONf_chiral_restr0.2071573
X-RAY DIFFRACTIONf_plane_restr0.0111815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8497-2.92680.3554940.35412125X-RAY DIFFRACTION76
2.9268-3.01290.33941240.30482255X-RAY DIFFRACTION81
3.0129-3.11010.31751210.28622474X-RAY DIFFRACTION89
3.1101-3.22120.31911430.28322691X-RAY DIFFRACTION96
3.2212-3.35020.28871420.26962760X-RAY DIFFRACTION100
3.3502-3.50260.31171710.25892744X-RAY DIFFRACTION100
3.5026-3.68720.24111430.2532794X-RAY DIFFRACTION100
3.6872-3.91810.26541390.2572819X-RAY DIFFRACTION100
3.9181-4.22050.28681310.24622820X-RAY DIFFRACTION100
4.2205-4.64490.20591270.19982840X-RAY DIFFRACTION100
4.6449-5.31630.1991430.19872849X-RAY DIFFRACTION100
5.3163-6.69510.24171450.22162873X-RAY DIFFRACTION100
6.6951-48.17490.24731650.21912989X-RAY DIFFRACTION100

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