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- PDB-3v7a: Structural basis for broad detection of genogroup II noroviruses ... -

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Basic information

Entry
Database: PDB / ID: 3v7a
TitleStructural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle
Components
  • 5B18 heavy chain
  • 5B18 kappa chain
  • Capsid
KeywordsIMMUNE SYSTEM / virus / Protein-Fab complex / broadly-reactive antibody
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman calicivirus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.297 Å
AuthorsHansman, G.S. / Mclellan, J.S. / Kwong, P.D.
CitationJournal: J Virol / Year: 2012
Title: Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle.
Authors: Grant S Hansman / David W Taylor / Jason S McLellan / Thomas J Smith / Ivelin Georgiev / Jeremy R H Tame / Sam-Yong Park / Makoto Yamazaki / Fumio Gondaira / Motohiro Miki / Kazuhiko ...Authors: Grant S Hansman / David W Taylor / Jason S McLellan / Thomas J Smith / Ivelin Georgiev / Jeremy R H Tame / Sam-Yong Park / Makoto Yamazaki / Fumio Gondaira / Motohiro Miki / Kazuhiko Katayama / Kazuyoshi Murata / Peter D Kwong /
Abstract: Human noroviruses are genetically and antigenically highly divergent. Monoclonal antibodies raised in mice against one kind of norovirus virus-like particle (VLP), however, were found to have broad ...Human noroviruses are genetically and antigenically highly divergent. Monoclonal antibodies raised in mice against one kind of norovirus virus-like particle (VLP), however, were found to have broad recognition. In this study, we present the crystal structure of the antigen-binding fragment (Fab) for one of these broadly reactive monoclonal antibodies, 5B18, in complex with the capsid-protruding domain from a genogroup II genotype 10 (GII.10) norovirus at 3.3-Å resolution and, also, the cryo-electron microscopy structure of the GII.10 VLP at ∼10-Å resolution. The GII.10 VLP structure was more similar in overall architecture to the GV.1 murine norovirus virion than to the prototype GI.1 human norovirus VLP, with the GII.10 protruding domain raised ∼15 Å off the shell domain and rotated ∼40° relative to the GI.1 protruding domain. In the crystal structure, the 5B18 Fab bound to a highly conserved region of the protruding domain. Based on the VLP structure, this region is involved in interactions with other regions of the capsid and is buried in the virus particle. Despite the occluded nature of the recognized epitope in the VLP structure, enzyme-linked immunosorbent assay (ELISA) binding suggested that the 5B18 antibody was able to capture intact VLPs. Together, the results provide evidence that the norovirus particle is capable of extreme conformational flexibility, which may allow for antibody recognition of conserved surfaces that would otherwise be buried on intact particles.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 5B18 heavy chain
G: 5B18 kappa chain
E: 5B18 heavy chain
H: 5B18 kappa chain
A: Capsid
B: Capsid


Theoretical massNumber of molelcules
Total (without water)163,9776
Polymers163,9776
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-98 kcal/mol
Surface area62250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.480, 145.480, 216.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 225:345 or resseq 351:538 )
211chain B and (resseq 225:345 or resseq 351:538 )
112chain F and (resseq 1:220 )
212chain E and (resseq 1:220 )
113chain G and (resseq 1:215 )
213chain H and (resseq 1:215 )

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody 5B18 heavy chain


Mass: 23709.514 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody 5B18 kappa chain


Mass: 23772.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Capsid


Mass: 34506.660 Da / Num. of mol.: 2 / Fragment: P domain residues 224-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human calicivirus / Strain: 026Vientnam / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F4T5*PLUS

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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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 40% v/v PEG 400, 5% w/v PEG 3350, and 0.1 M acetic acid pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.297→31.537 Å / Num. all: 85009 / Num. obs: 30833

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: dev_755)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU for P domain, i.e., chains A and B and 1WEJ for Fab, i.e., chains D,E, F, G

3onu

1wej


Resolution: 3.297→31.537 Å / SU ML: 0.97 / σ(F): 1 / Phase error: 34.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 1532 4.97 %Random
Rwork0.2268 ---
obs0.2295 30833 86.38 %-
all-85009 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.231 Å2 / ksol: 0.259 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8221 Å20 Å2-0 Å2
2--5.8221 Å2-0 Å2
3----11.6441 Å2
Refinement stepCycle: LAST / Resolution: 3.297→31.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11459 0 0 0 11459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411769
X-RAY DIFFRACTIONf_angle_d0.79516061
X-RAY DIFFRACTIONf_dihedral_angle_d12.8424205
X-RAY DIFFRACTIONf_chiral_restr0.0541799
X-RAY DIFFRACTIONf_plane_restr0.0032085
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2397X-RAY DIFFRACTIONPOSITIONAL
12B2397X-RAY DIFFRACTIONPOSITIONAL0.021
21F1643X-RAY DIFFRACTIONPOSITIONAL
22E1643X-RAY DIFFRACTIONPOSITIONAL0.02
31G1671X-RAY DIFFRACTIONPOSITIONAL
32H1671X-RAY DIFFRACTIONPOSITIONAL0.018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2973-3.40360.43151180.34872643X-RAY DIFFRACTION87
3.4036-3.52510.38981330.32482695X-RAY DIFFRACTION89
3.5251-3.6660.35031380.28762700X-RAY DIFFRACTION89
3.666-3.83260.33021310.25912693X-RAY DIFFRACTION88
3.8326-4.03430.32271510.24142693X-RAY DIFFRACTION89
4.0343-4.28650.25911520.20292633X-RAY DIFFRACTION87
4.2865-4.61650.19881350.19072614X-RAY DIFFRACTION86
4.6165-5.07930.27081370.18162643X-RAY DIFFRACTION85
5.0793-5.81040.28321530.20352689X-RAY DIFFRACTION87
5.8104-7.30540.23841520.19752695X-RAY DIFFRACTION86
7.3054-31.53810.25811320.20572603X-RAY DIFFRACTION79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16020.1389-0.09310.30190.03040.09990.0837-0.09980.02250.27260.12920.50170.19390.02470.0530.57880.0332-0.1820.28060.11730.595679.5027-47.533459.0273
20.04880.0359-0.00030.09580.0760.09080.1166-0.0936-0.2841-0.23730.00920.155-0.13360.01870.11060.40280.0876-0.09820.42340.38750.44387.6546-70.811485.402
33.4-0.27832.3073.2645-1.66342.9748-0.0225-0.222-0.31260.03530.29060.62950.0576-0.7082-0.28020.4907-0.0326-0.05010.43450.05680.524769.4371-12.966730.2995
42.0361-0.2140.40421.6854-0.78442.21790.07220.2028-0.40070.14340.08490.57030.0302-0.1075-0.12340.3094-0.0622-0.05510.22920.00450.527272.2559-12.445635.9097
50.0222-0.0312-0.01060.05780.01950.0101-0.10180.3189-0.20010.05910.04490.1160.03020.0760.00910.4970.0733-0.0050.9051-0.27830.4875107.8853-19.8138-15.9685
60.26350.0890.14020.03140.04650.11250.22720.0232-0.22150.04530.0428-0.21810.0185-0.38660.01870.4740.14520.00260.4929-0.02370.4988141.956-29.6926-27.8582
70.18460.0937-0.05090.1283-0.12480.10240.07810.30150.240.2013-0.01030.21410.00430.19430.0050.73570.03610.05480.7237-0.15180.4598120.1486-6.3617-4.3
80.03710.05150.03580.11180.03570.053-0.0988-0.27430.1103-0.1170.0837-0.0191-0.06430.0767-0.01320.64490.10730.19720.5617-0.09650.177143.1279-14.6166-30.9143
90.0980.08870.02470.09680.01020.01040.1393-0.0682-0.01580.05810.0378-0.061-0.32720.1280.03350.5004-0.03820.02930.1853-0.0590.226585.99283.550425.3253
100.57350.10160.08170.2035-0.07830.29770.1870.5740.1580.09090.071-0.1083-0.26520.25990.2860.30180.00010.0228-0.1997-0.02610.265684.95930.884720.3636
110.21750.04480.15980.01330.02810.1202-0.02340.10070.04790.2465-0.032-0.03990.01670.27350.02940.60250.0894-0.19470.34240.07560.50792.8201-35.399971.0682
120.03380.03570.03710.13860.14970.27150.1636-0.0246-0.2808-0.03950.1528-0.1344-0.297-0.12960.18760.36450.13260.03080.05760.20230.6969102.7721-69.54882.6632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain F and resid 1:122
2X-RAY DIFFRACTION2chain F and resid 123:220
3X-RAY DIFFRACTION3chain B and resid 225:323
4X-RAY DIFFRACTION4chain B and resid 324:538
5X-RAY DIFFRACTION5chain H and resid 1:105
6X-RAY DIFFRACTION6chain H and resid 106:215
7X-RAY DIFFRACTION7chain E and resid 1:122
8X-RAY DIFFRACTION8chain E and resid 123:220
9X-RAY DIFFRACTION9chain A and resid 225:323
10X-RAY DIFFRACTION10chain A and resid 324:538
11X-RAY DIFFRACTION11chain G and resid 1:105
12X-RAY DIFFRACTION12chain G and resid 106:215

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