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- PDB-7jie: Structure of GII.4 P-domain in Complex with NORO-320 FAB -

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Basic information

Entry
Database: PDB / ID: 7jie
TitleStructure of GII.4 P-domain in Complex with NORO-320 FAB
Components
  • IgA Fab Heavy Chain
  • IgA Fab Light Chain
  • VP1
KeywordsVIRAL PROTEIN / Antibody / Complex / Viral capsid protein / Neutralization
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / VP1
Function and homology information
Biological speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.254 Å
AuthorsSalmen, W. / Hu, L. / Prasad, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI057788 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM120011 United States
CitationJournal: Nat Commun / Year: 2021
Title: Broadly cross-reactive human antibodies that inhibit genogroup I and II noroviruses.
Authors: Alvarado, G. / Salmen, W. / Ettayebi, K. / Hu, L. / Sankaran, B. / Estes, M.K. / Venkataram Prasad, B.V. / Crowe Jr., J.E.
History
DepositionJul 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Oct 18, 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
A: VP1
B: VP1
C: IgA Fab Heavy Chain
D: IgA Fab Light Chain
E: IgA Fab Heavy Chain
F: IgA Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)166,2786
Polymers166,2786
Non-polymers00
Water18,9341051
1
A: VP1
E: IgA Fab Heavy Chain
F: IgA Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)83,1393
Polymers83,1393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VP1
C: IgA Fab Heavy Chain
D: IgA Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)83,1393
Polymers83,1393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.254, 186.273, 73.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein VP1


Mass: 34030.934 Da / Num. of mol.: 2 / Fragment: P-domain, residues 225-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Production host: Escherichia coli (E. coli) / References: UniProt: K4LM89
#2: Antibody IgA Fab Heavy Chain


Mass: 25202.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody IgA Fab Light Chain


Mass: 23905.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1051 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M BIS-TRIS prop 8.5 pH, 0.2 M KSCN, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 78053 / % possible obs: 99.82 % / Redundancy: 6.5 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.129 / Net I/σ(I): 15.6875
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 3854 / Rpim(I) all: 0.34 / Rrim(I) all: 0.846

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Processing

Software
NameVersionClassification
PHENIX(dev_3386)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SJP and 5KW9

3sjp

5kw9


Resolution: 2.254→37.112 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 3926 5.04 %
Rwork0.1808 --
obs0.183 77891 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.254→37.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11472 0 0 1054 12526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311763
X-RAY DIFFRACTIONf_angle_d0.60916036
X-RAY DIFFRACTIONf_dihedral_angle_d2.9346992
X-RAY DIFFRACTIONf_chiral_restr0.0451789
X-RAY DIFFRACTIONf_plane_restr0.0042091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.254-2.28110.38061410.3042500X-RAY DIFFRACTION97
2.2811-2.30990.29931370.21772628X-RAY DIFFRACTION100
2.3099-2.34030.31461400.2142591X-RAY DIFFRACTION100
2.3403-2.37240.2551470.21472632X-RAY DIFFRACTION100
2.3724-2.40630.3051390.20882562X-RAY DIFFRACTION100
2.4063-2.44220.31261440.21122635X-RAY DIFFRACTION100
2.4422-2.48030.25621320.20892631X-RAY DIFFRACTION100
2.4803-2.5210.2261340.2042617X-RAY DIFFRACTION100
2.521-2.56450.25881320.1962607X-RAY DIFFRACTION100
2.5645-2.61110.23741450.19962615X-RAY DIFFRACTION100
2.6111-2.66130.26111420.22772623X-RAY DIFFRACTION100
2.6613-2.71560.27841480.22992609X-RAY DIFFRACTION99
2.7156-2.77460.2571390.21372614X-RAY DIFFRACTION100
2.7746-2.83910.25911150.21312659X-RAY DIFFRACTION100
2.8391-2.91010.2551260.21022652X-RAY DIFFRACTION100
2.9101-2.98880.27571500.20822615X-RAY DIFFRACTION100
2.9888-3.07670.26951460.20282611X-RAY DIFFRACTION100
3.0767-3.17590.21181390.18682657X-RAY DIFFRACTION100
3.1759-3.28940.20141580.17672607X-RAY DIFFRACTION100
3.2894-3.4210.23331580.17842631X-RAY DIFFRACTION100
3.421-3.57660.22431440.18072657X-RAY DIFFRACTION100
3.5766-3.7650.23361190.16592665X-RAY DIFFRACTION100
3.765-4.00060.18781420.16262666X-RAY DIFFRACTION100
4.0006-4.3090.16571450.14282677X-RAY DIFFRACTION100
4.309-4.74190.17181330.12632694X-RAY DIFFRACTION100
4.7419-5.42620.19241440.14582709X-RAY DIFFRACTION100
5.4262-6.82950.19771380.16852724X-RAY DIFFRACTION100
6.8295-37.1120.19171490.17912877X-RAY DIFFRACTION100

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