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- PDB-6n8d: Crystal structure of GII.4 2002 norovirus P domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6n8d
TitleCrystal structure of GII.4 2002 norovirus P domain in complex with neutralizing human antibody A1431
Components
  • A1431 Fab heavy chain
  • A1431 Fab light chain
  • Major capsid protein
KeywordsIMMUNE SYSTEM / Norovirus / human antibody / Fab / complex / neutralizing
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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 ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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 / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GII.4/Farmington Hills/2004/USA
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChangela, A. / Verardi, R. / Kwong, P.D.
CitationJournal: Immunity / Year: 2019
Title: Sera Antibody Repertoire Analyses Reveal Mechanisms of Broad and Pandemic Strain Neutralizing Responses after Human Norovirus Vaccination.
Authors: Lindesmith, L.C. / McDaniel, J.R. / Changela, A. / Verardi, R. / Kerr, S.A. / Costantini, V. / Brewer-Jensen, P.D. / Mallory, M.L. / Voss, W.N. / Boutz, D.R. / Blazeck, J.J. / Ippolito, G.C. ...Authors: Lindesmith, L.C. / McDaniel, J.R. / Changela, A. / Verardi, R. / Kerr, S.A. / Costantini, V. / Brewer-Jensen, P.D. / Mallory, M.L. / Voss, W.N. / Boutz, D.R. / Blazeck, J.J. / Ippolito, G.C. / Vinje, J. / Kwong, P.D. / Georgiou, G. / Baric, R.S.
History
DepositionNov 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 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 1.3Oct 16, 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
C: Major capsid protein
E: A1431 Fab light chain
F: A1431 Fab heavy chain
A: Major capsid protein
B: A1431 Fab light chain
D: A1431 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)164,7766
Polymers164,7766
Non-polymers00
Water00
1
C: Major capsid protein
E: A1431 Fab light chain
F: A1431 Fab heavy chain

C: Major capsid protein
E: A1431 Fab light chain
F: A1431 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)164,7766
Polymers164,7766
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
A: Major capsid protein
B: A1431 Fab light chain
D: A1431 Fab heavy chain

A: Major capsid protein
B: A1431 Fab light chain
D: A1431 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)164,7766
Polymers164,7766
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)147.369, 157.356, 110.362
Angle α, β, γ (deg.)90.00, 112.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Major capsid protein


Mass: 33940.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Farmington Hills/2004/USA
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4I4P2
#2: Antibody A1431 Fab light chain


Mass: 23520.264 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: Antibody A1431 Fab heavy chain


Mass: 24926.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 8000, 0.1M CHES, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 39673 / % possible obs: 94.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 15.7
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2068 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOV, 3EYQ

4oov

3eyq


Resolution: 3.1→41.622 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.44
RfactorNum. reflection% reflection
Rfree0.2267 1908 4.81 %
Rwork0.1763 --
obs0.1787 39662 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→41.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11214 0 0 0 11214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611516
X-RAY DIFFRACTIONf_angle_d0.92915710
X-RAY DIFFRACTIONf_dihedral_angle_d4.1486776
X-RAY DIFFRACTIONf_chiral_restr0.0531736
X-RAY DIFFRACTIONf_plane_restr0.0072058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1004-3.17790.34391340.27082643X-RAY DIFFRACTION93
3.1779-3.26370.30821390.24642713X-RAY DIFFRACTION95
3.2637-3.35970.31311090.22512465X-RAY DIFFRACTION87
3.3597-3.46810.25631670.19742737X-RAY DIFFRACTION97
3.4681-3.5920.26631380.18472789X-RAY DIFFRACTION98
3.592-3.73580.22331220.1782797X-RAY DIFFRACTION98
3.7358-3.90570.21231380.16682780X-RAY DIFFRACTION98
3.9057-4.11140.21491200.15882827X-RAY DIFFRACTION98
4.1114-4.36870.18451420.14532758X-RAY DIFFRACTION97
4.3687-4.70560.18411480.13352661X-RAY DIFFRACTION93
4.7056-5.17840.19641130.14882441X-RAY DIFFRACTION86
5.1784-5.92590.20831560.16682778X-RAY DIFFRACTION97
5.9259-7.4590.23021520.18782765X-RAY DIFFRACTION97
7.459-41.62530.22751300.1882600X-RAY DIFFRACTION89
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)
11.66940.5772-0.07232.5042-1.32484.1618-0.1265-0.0143-0.05520.06910.09650.20250.0799-0.5430.04240.21860.03710.00890.3132-0.07480.2255-30.2944-18.84442.6242
21.65050.2771-0.58821.65970.74522.1819-0.33391.0236-0.3229-0.80330.4371-0.5222-0.03850.4335-0.14620.7662-0.29530.15760.9853-0.28450.6124-17.0347-34.4684-6.428
31.9249-0.29660.02512.14081.34812.4803-0.05140.7426-0.4766-0.47760.1849-0.13520.03660.1891-0.11140.5003-0.2141-0.03450.5598-0.18660.5329-34.7776-38.085-1.7608
42.2358-1.07760.41043.4771-0.60392.0412-0.0585-0.0693-0.11610.08290.00990.0508-0.0383-0.05170.04990.2250.00260.00370.1722-0.00350.1596-10.657315.74175.2777
50.84170.3427-0.07970.59870.17090.6991-0.36821.0266-0.8105-0.74760.29931.04480.5312-1.26580.07391.0313-0.5102-0.37051.7798-0.20471.6331-52.9327-1.3339-22.1898
60.71980.0657-0.38441.04560.09341.3487-0.11810.205-0.8301-0.29050.02740.85980.9344-1.46870.10340.8558-0.4621-0.09691.3710.05621.4779-53.4349-4.7368-3.5587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'C' and resid 225 through 530)
2X-RAY DIFFRACTION2(chain 'E' and resid 1 through 211)
3X-RAY DIFFRACTION3(chain 'F' and resid 1 through 212)
4X-RAY DIFFRACTION4(chain 'A' and resid 225 through 530)
5X-RAY DIFFRACTION5(chain 'B' and resid 1 through 211)
6X-RAY DIFFRACTION6(chain 'D' and resid 1 through 212)

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