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- PDB-5kw9: Structural Basis for Norovirus Neutralization by a HBGA Blocking ... -

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Basic information

Entry
Database: PDB / ID: 5kw9
TitleStructural Basis for Norovirus Neutralization by a HBGA Blocking Human IgA Antibody
Components
  • Capsid protein VP1
  • IgA Light chain
  • IgA(VH)-IgG(CH) heavy chain Fab fragment
KeywordsANTIVIRAL PROTEIN / IgA / Norovirus / Neutralisation / Fab / Antibody
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
Similarity search - Function
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 speciesNorwalk virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShanker, S. / Prasad, B.V.V.
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 Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30 DK56338 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for norovirus neutralization by an HBGA blocking human IgA antibody.
Authors: Shanker, S. / Czako, R. / Sapparapu, G. / Alvarado, G. / Viskovska, M. / Sankaran, B. / Atmar, R.L. / Crowe, J.E. / Estes, M.K. / Prasad, B.V.
History
DepositionJul 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Structure summary
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.6Nov 13, 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
A: Capsid protein VP1
H: IgA(VH)-IgG(CH) heavy chain Fab fragment
L: IgA Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,25011
Polymers80,0593
Non-polymers1908
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-88 kcal/mol
Surface area30400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.000, 162.000, 146.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Capsid protein VP1 / CP / p59


Mass: 31529.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q83884

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Antibody , 2 types, 2 molecules HL

#2: Antibody IgA(VH)-IgG(CH) heavy chain Fab fragment


Mass: 24236.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody IgA Light chain


Mass: 24292.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 3 types, 347 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium Formate, 0.1M Bis Tris propane, pH 6.5 and 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.3→81 Å / Num. obs: 50863 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZL5, 4RQQ

2zl5

4rqq


Resolution: 2.3→81 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 2522 4.96 %
Rwork0.1863 --
obs0.1876 50807 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 8 339 5825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035640
X-RAY DIFFRACTIONf_angle_d0.6787708
X-RAY DIFFRACTIONf_dihedral_angle_d12.6253338
X-RAY DIFFRACTIONf_chiral_restr0.047859
X-RAY DIFFRACTIONf_plane_restr0.0051003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34430.26821450.24512605X-RAY DIFFRACTION100
2.3443-2.39210.26111470.23142616X-RAY DIFFRACTION100
2.3921-2.44410.24681350.23132631X-RAY DIFFRACTION100
2.4441-2.5010.25631410.2352650X-RAY DIFFRACTION100
2.501-2.56350.27141420.21752634X-RAY DIFFRACTION100
2.5635-2.63280.26271370.2152654X-RAY DIFFRACTION100
2.6328-2.71030.22891400.20092654X-RAY DIFFRACTION100
2.7103-2.79780.26251390.20472649X-RAY DIFFRACTION100
2.7978-2.89780.24241400.21432654X-RAY DIFFRACTION100
2.8978-3.01380.2751350.21532661X-RAY DIFFRACTION100
3.0138-3.1510.23381430.20712666X-RAY DIFFRACTION100
3.151-3.31710.22971260.20442686X-RAY DIFFRACTION100
3.3171-3.5250.25281410.19422693X-RAY DIFFRACTION100
3.525-3.79710.20681420.18222679X-RAY DIFFRACTION100
3.7971-4.17920.15541450.15562714X-RAY DIFFRACTION100
4.1792-4.78390.14111590.13792709X-RAY DIFFRACTION100
4.7839-6.0270.16221340.15062780X-RAY DIFFRACTION100
6.027-81.05020.22061310.18262950X-RAY DIFFRACTION100
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)
12.80690.4573-0.36292.75930.94483.08590.00140.08980.0998-0.2435-0.0548-0.0358-0.2596-0.0020.07230.1716-0.0006-0.01990.2035-0.00620.185539.0951153.219143.9805
22.70490.3717-1.17161.5902-0.45031.5874-0.0051-0.46250.08480.4106-0.0055-0.0523-0.23240.04860.00910.22070.018-0.02310.2646-0.04750.191530.5489147.4818159.509
31.19460.2501-0.321.3424-0.11881.29890.0083-0.11430.08440.1632-0.02720.2774-0.0905-0.26690.03150.16820.04660.01010.323-0.04710.305919.0867150.986154.5139
44.14941.2921-0.19561.56390.12556.26290.2522-0.20.35280.4018-0.17830.1142-0.53050.1834-0.16410.3470.0142-0.00310.187-0.03470.328936.7279161.1748150.4608
52.3959-0.08680.59371.4791-0.48321.1952-0.05860.12730.0351-0.1645-0.0088-0.2961-0.10620.17060.08220.242-0.02690.02160.2719-0.05120.275245.5113153.0939142.1544
60.7369-0.70890.03841.431-0.20180.05210.05270.96620.5209-1.1073-0.01770.4684-0.531-0.25570.06680.54060.0357-0.03220.49810.12450.370941.2711159.2548130.5719
76.00461.22370.19536.0276-0.24852.09950.096-0.01110.5548-0.0640.056-0.6479-0.57820.6374-0.04470.2391-0.13360.11470.3725-0.00420.376254.1858160.1878139.6169
87.10231.26560.21923.5569-1.49881.54030.01740.54620.7125-0.2507-0.1330.2053-0.1932-0.32830.0890.39230.2051-0.03390.55630.04580.3674-13.8337169.6498137.781
97.322-0.02760.39142.9287-0.29963.3813-0.05030.36950.4813-0.19590.0482-0.2194-0.0216-0.28910.01360.38480.1408-0.01070.43720.00680.3752-1.2975170.8487143.2625
106.88991.72780.24966.3257-1.65445.4114-0.08770.93450.0335-0.72150.0032-0.41580.34990.134-0.07780.39740.13440.00470.5005-0.01770.3681-1.8785167.7381136.862
117.42351.01561.79223.611-0.25993.0147-0.08090.186-0.00050.14760.19240.02750.2857-0.3939-0.04820.39190.1031-0.0130.467-0.01980.236-8.6058164.8384143.2467
122.6163-0.71881.03450.37630.30112.1598-0.221-0.3520.8504-0.2171-0.0449-0.0753-0.3116-0.22330.22090.37780.11590.0030.3958-0.00620.60370.5754172.5946148.3054
131.9022-0.1403-0.51870.77610.45683.277-0.04410.0109-0.0568-0.09820.20430.2494-0.2355-0.2199-0.22390.51820.0358-0.01320.61280.09110.3997-34.4598168.4769150.7235
140.67040.4506-0.3262.3102-0.5947.43850.01870.16350.3932-0.07440.43630.3348-0.8487-0.8133-0.45360.51730.0699-0.00250.73430.1490.4944-40.1605174.406153.1891
153.5319-0.2133-2.54421.29270.0061.8956-0.1209-0.884-0.11930.16090.15520.277-0.3487-1.13190.31790.38510.1926-0.00421.095-0.06620.4126-6.1725162.5741168.2771
167.72411.1157-0.28721.2838-2.24934.3146-0.0466-0.38010.674-0.11360.1561-0.0486-0.1909-0.18430.30510.26310.0813-0.00560.4075-0.09650.421413.5512165.038160.9636
171.4063-0.0381-0.42771.0083-0.22590.6417-0.4555-1.37320.85680.15490.37850.0248-0.6782-0.8889-0.03230.42120.3916-0.02580.9374-0.29260.5291-3.8677171.9029164.8322
182.68490.0221-1.93950.1507-0.01021.1989-0.0703-0.83720.26490.09190.20820.0417-0.0128-0.0238-0.15950.37910.17210.02770.7659-0.01290.3899-9.5917164.2151163.4624
194.5952.3321-0.26195.63012.04045.7514-0.36640.29120.0284-0.08930.38330.39230.69540.32570.01670.49350.12620.06650.6210.06790.38-38.5935159.1024160.1023
201.3367-0.19680.0422.6053.59755.1819-0.34030.1228-0.58560.43620.28950.24251.13820.31950.03980.8190.15890.13970.76550.04810.5856-36.2374150.3959157.8368
214.71651.58820.59444.16612.08734.6933-0.37080.2456-0.139-0.15010.37730.08490.52390.2324-0.01270.49780.0780.05590.63530.04660.3232-37.6156157.9407159.8759
223.8545-1.1881-0.81363.24780.48661.6305-0.21830.3783-0.26030.2817-0.03930.22381.36870.1941-0.15370.60120.0180.19940.61590.05340.4256-42.0755155.1832168.2973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 229 through 269 )
2X-RAY DIFFRACTION2chain 'A' and (resid 270 through 326 )
3X-RAY DIFFRACTION3chain 'A' and (resid 327 through 397 )
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 425 )
5X-RAY DIFFRACTION5chain 'A' and (resid 426 through 484 )
6X-RAY DIFFRACTION6chain 'A' and (resid 485 through 499 )
7X-RAY DIFFRACTION7chain 'A' and (resid 500 through 518 )
8X-RAY DIFFRACTION8chain 'H' and (resid 3 through 17 )
9X-RAY DIFFRACTION9chain 'H' and (resid 18 through 60 )
10X-RAY DIFFRACTION10chain 'H' and (resid 61 through 83 )
11X-RAY DIFFRACTION11chain 'H' and (resid 84 through 100 )
12X-RAY DIFFRACTION12chain 'H' and (resid 101 through 122 )
13X-RAY DIFFRACTION13chain 'H' and (resid 123 through 186 )
14X-RAY DIFFRACTION14chain 'H' and (resid 187 through 224 )
15X-RAY DIFFRACTION15chain 'L' and (resid 1 through 25 )
16X-RAY DIFFRACTION16chain 'L' and (resid 26 through 38 )
17X-RAY DIFFRACTION17chain 'L' and (resid 39 through 96 )
18X-RAY DIFFRACTION18chain 'L' and (resid 97 through 119 )
19X-RAY DIFFRACTION19chain 'L' and (resid 120 through 156 )
20X-RAY DIFFRACTION20chain 'L' and (resid 157 through 169 )
21X-RAY DIFFRACTION21chain 'L' and (resid 170 through 203 )
22X-RAY DIFFRACTION22chain 'L' and (resid 204 through 219 )

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