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

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Basic information

Entry
Database: PDB / ID: 6ocb
TitleCrystal structure of FluA-20 Fab in complex with the head domain of H3 (A/Hong Kong/1/1968)
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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon / 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: 2.1 Å
AuthorsWilson, I.A. / Lang, S.
Funding support United States, 7items
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)R56 AI127371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI097092 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400024C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HSN272201400008C United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)No. UL1 TR002243 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)No. HHSN27220170041I United States
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 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / 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.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 9, 2020Group: Data collection / Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / diffrn
Item: _chem_comp.pdbx_synonyms / _citation.journal_abbrev ..._chem_comp.pdbx_synonyms / _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 / _diffrn.ambient_temp
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 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
H: Heavy chain of FluA-20 Fab
L: Light chain of FluA-20 Fab
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2754
Polymers79,0533
Non-polymers2211
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.554, 84.554, 271.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody Heavy chain of FluA-20 Fab


Mass: 25154.039 Da / Num. of mol.: 1
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Hemagglutinin


Mass: 30391.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Variant: A/Hong Kong/1/1968 H3N2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 8.5 0.2 M lithium sulfate 40% (v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 59126 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 1 / Rpim(I) all: 0.04 / Rsym value: 0.11 / Net I/σ(I): 18.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2895 / CC1/2: 0.7 / Rpim(I) all: 0.33 / Rsym value: 0.83 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FP8, 6OBZ

4fp8

6obz


Resolution: 2.1→37.814 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.68
RfactorNum. reflection% reflection
Rfree0.2388 2963 5.01 %
Rwork0.2021 --
obs0.2039 59094 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5381 0 14 345 5740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145610
X-RAY DIFFRACTIONf_angle_d1.6227660
X-RAY DIFFRACTIONf_dihedral_angle_d13.8543361
X-RAY DIFFRACTIONf_chiral_restr0.099861
X-RAY DIFFRACTIONf_plane_restr0.013985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12450.26641395.220.2461252595
2.1245-2.16110.26071350.24632614100
2.1611-2.20040.30831420.24492623100
2.2004-2.24270.2721470.23332633100
2.2427-2.28850.28021280.23422663100
2.2885-2.33820.2521440.22412643100
2.3382-2.39260.23331340.21752648100
2.3926-2.45250.23731370.20662647100
2.4525-2.51880.28381260.20642656100
2.5188-2.59290.26171230.21332680100
2.5929-2.67650.24571880.2182604100
2.6765-2.77220.2581350.2242671100
2.7722-2.88310.30071440.21832677100
2.8831-3.01430.29831390.22462692100
3.0143-3.17310.27391560.21222658100
3.1731-3.37180.22111350.20782727100
3.3718-3.6320.22751450.19662680100
3.632-3.99710.22051340.18322735100
3.9971-4.57460.18281320.1638272799
4.5746-5.76030.20071400.169275298
5.7603-37.8140.23831600.2123287697
Refinement TLS params.Method: refined / Origin x: -27.2244 Å / Origin y: 11.8877 Å / Origin z: 17.6889 Å
111213212223313233
T0.2685 Å20.0108 Å20.0209 Å2-0.1497 Å20.0083 Å2--0.2718 Å2
L0.3855 °20.1311 °20.3588 °2-0.7877 °20.3841 °2--1.7104 °2
S-0.0595 Å °0.0906 Å °0.0362 Å °-0.1122 Å °-0.0314 Å °0.0347 Å °-0.2521 Å °0.0703 Å °0.0884 Å °
Refinement TLS groupSelection details: all

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