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- PDB-5wko: Crystal structure of antibody 27F3 recognizing the HA from A/Cali... -

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Basic information

Entry
Database: PDB / ID: 5wko
TitleCrystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1) influenza virus
Components
  • (Hemagglutinin) x 2
  • Antibody 27F3 heavy chain
  • Antibody 27F3 light chain
KeywordsANTIVIRAL PROTEIN / 27F3 H1 HA A/California/04/2009
Function / homology
Function and homology information


immunoglobulin complex / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...immunoglobulin complex / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / host cell surface receptor binding / apical plasma membrane / 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 / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / : / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Ribbon / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Hemagglutinin / Ig-like domain-containing protein / IGK@ protein / Myosin-reactive immunoglobulin light chain variable region
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.492 Å
AuthorsWilson, I.A. / Lang, S. / Zhu, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
CitationJournal: Cell Rep / Year: 2017
Title: Antibody 27F3 Broadly Targets Influenza A Group 1 and 2 Hemagglutinins through a Further Variation in VH1-69 Antibody Orientation on the HA Stem.
Authors: Lang, S. / Xie, J. / Zhu, X. / Wu, N.C. / Lerner, R.A. / Wilson, I.A.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 1.4May 15, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody 27F3 heavy chain
B: Antibody 27F3 light chain
C: Antibody 27F3 heavy chain
D: Antibody 27F3 light chain
E: Antibody 27F3 heavy chain
F: Antibody 27F3 light chain
G: Antibody 27F3 heavy chain
H: Antibody 27F3 light chain
I: Antibody 27F3 heavy chain
J: Antibody 27F3 light chain
K: Antibody 27F3 heavy chain
L: Antibody 27F3 light chain
M: Hemagglutinin
N: Hemagglutinin
O: Hemagglutinin
P: Hemagglutinin
Q: Hemagglutinin
R: Hemagglutinin
S: Hemagglutinin
T: Hemagglutinin
U: Hemagglutinin
V: Hemagglutinin
W: Hemagglutinin
X: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)623,36524
Polymers623,36524
Non-polymers00
Water00
1
A: Antibody 27F3 heavy chain
B: Antibody 27F3 light chain
E: Antibody 27F3 heavy chain
F: Antibody 27F3 light chain
I: Antibody 27F3 heavy chain
J: Antibody 27F3 light chain
M: Hemagglutinin
N: Hemagglutinin
O: Hemagglutinin
P: Hemagglutinin
Q: Hemagglutinin
R: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)311,68212
Polymers311,68212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Antibody 27F3 heavy chain
D: Antibody 27F3 light chain
G: Antibody 27F3 heavy chain
H: Antibody 27F3 light chain
K: Antibody 27F3 heavy chain
L: Antibody 27F3 light chain
S: Hemagglutinin
T: Hemagglutinin
U: Hemagglutinin
V: Hemagglutinin
W: Hemagglutinin
X: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)311,68212
Polymers311,68212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.580, 191.486, 391.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Antibody
Antibody 27F3 heavy chain


Mass: 23817.703 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220 / Production host: Homo sapiens (human) / References: UniProt: Q6N089
#2: Antibody
Antibody 27F3 light chain


Mass: 23140.697 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGK@ / Production host: Homo sapiens (human) / References: UniProt: Q9UL78, UniProt: Q6P5S8
#3: Protein
Hemagglutinin


Mass: 36729.402 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: HA / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C3W5S1
#4: Protein
Hemagglutinin


Mass: 20206.320 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A023ZYH9, UniProt: C5MVT7*PLUS
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: 5.72 Å3/Da / Density % sol: 78.51 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 177944 / % possible obs: 97 % / Redundancy: 5.7 % / CC1/2: 0.97 / Rpim(I) all: 0.08 / Rsym value: 0.13 / Net I/av σ(I): 8.7 / Net I/σ(I): 8.7
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 8765 / CC1/2: 0.73 / Rpim(I) all: 0.45 / Rsym value: 0.76 / % possible all: 94.4

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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: 4M4Y 4FQH 4FQL

4m4y

4fqh

4fql


Resolution: 3.492→49.451 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 8902 5.01 %
Rwork0.2462 --
obs0.2473 177692 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.492→49.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43322 0 0 0 43322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01844410
X-RAY DIFFRACTIONf_angle_d1.58860342
X-RAY DIFFRACTIONf_dihedral_angle_d15.94716258
X-RAY DIFFRACTIONf_chiral_restr0.1756624
X-RAY DIFFRACTIONf_plane_restr0.017764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.53210.34832650.32824867X-RAY DIFFRACTION86
3.5321-3.57370.31832880.29675622X-RAY DIFFRACTION99
3.5737-3.61720.33723000.30375655X-RAY DIFFRACTION99
3.6172-3.6630.3013120.29925649X-RAY DIFFRACTION99
3.663-3.71120.30433150.28145611X-RAY DIFFRACTION99
3.7112-3.7620.30482820.27855686X-RAY DIFFRACTION99
3.762-3.81570.29412930.27365671X-RAY DIFFRACTION99
3.8157-3.87270.27342910.28175616X-RAY DIFFRACTION99
3.8727-3.93320.27522680.28445683X-RAY DIFFRACTION99
3.9332-3.99760.29852980.27395698X-RAY DIFFRACTION99
3.9976-4.06650.27383090.26795625X-RAY DIFFRACTION99
4.0665-4.14040.28622950.26915659X-RAY DIFFRACTION99
4.1404-4.220.26662920.25035657X-RAY DIFFRACTION99
4.22-4.30610.27452690.24555666X-RAY DIFFRACTION99
4.3061-4.39970.26562900.2395622X-RAY DIFFRACTION99
4.3997-4.5020.26353040.23335643X-RAY DIFFRACTION99
4.502-4.61450.25463140.23495627X-RAY DIFFRACTION99
4.6145-4.73910.24222980.22755681X-RAY DIFFRACTION99
4.7391-4.87850.26072970.24215627X-RAY DIFFRACTION99
4.8785-5.03580.26083120.23355671X-RAY DIFFRACTION99
5.0358-5.21560.24673180.23335620X-RAY DIFFRACTION99
5.2156-5.42420.24333100.23045642X-RAY DIFFRACTION98
5.4242-5.67070.25232950.24815639X-RAY DIFFRACTION98
5.6707-5.96920.293000.25675668X-RAY DIFFRACTION98
5.9692-6.34250.28533160.25085646X-RAY DIFFRACTION98
6.3425-6.8310.25523000.25545679X-RAY DIFFRACTION98
6.831-7.51630.28943090.24525679X-RAY DIFFRACTION98
7.5163-8.5990.30652970.22345675X-RAY DIFFRACTION98
8.599-10.81520.19212840.18215693X-RAY DIFFRACTION96
10.8152-49.45560.25022810.22575613X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 98.7608 Å / Origin y: 0.2239 Å / Origin z: 46.8985 Å
111213212223313233
T0.6596 Å2-0.0813 Å20.0111 Å2-0.6776 Å20.0233 Å2--0.7102 Å2
L0.0405 °2-0.1227 °20.0037 °2-0.1309 °20.0057 °2--0.007 °2
S0.0249 Å °0.0296 Å °-0.0017 Å °-0.0751 Å °-0.0066 Å °-0.0052 Å °-0.0036 Å °-0.0082 Å °-0.0226 Å °
Refinement TLS groupSelection details: all

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