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

ID or keywords:

Entry

Database: PDB / ID: 5kw9

Title

Structural 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

Keywords

ANTIVIRAL 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

Biological species

Norwalk virus

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Shanker, S. / Prasad, B.V.V.

Funding support

United States, 2items

Organization	Grant number	Country
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

Citation

Journal: 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

Deposition	Jul 15, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 19, 2016	Group: Database references
Revision 1.2	Oct 26, 2016	Group: Structure summary
Revision 1.3	Sep 27, 2017	Group: 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 1.4	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kw9.cif.gz	298.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5kw9.ent.gz	240.9 KB	Display	PDB format
PDBx/mmJSON format	5kw9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kw9_validation.pdf.gz	441.7 KB	Display	wwPDB validaton report
Full document	5kw9_full_validation.pdf.gz	446.2 KB	Display
Data in XML	5kw9_validation.xml.gz	29.7 KB	Display
Data in CIF	5kw9_validation.cif.gz	42.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kw/5kw9 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/5kw9	HTTPS FTP

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Related structure data

Related structure data	2zl5S 4rqqS S: Starting model for refinement
Similar structure data	7kmg-1 4xak-1 1fns-d 3w2d-d 6vmk-13 7cm4-d 3bry-d 6vmk-5 7kmg-2 4cad-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Capsid protein VP1

H: IgA(VH)-IgG(CH) heavy chain Fab fragment

L: IgA Light chain

hetero molecules

80.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	179
Space group name H-M	P6₅22

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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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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.47 Å³/Da / Density % sol: 64.59 %
Crystal grow	Temperature: 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

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

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
iMOSFLM		data reduction
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2123	2522	4.96 %
R_work	0.1863	-	-
obs	0.1876	50807	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5478	0	8	339	5825

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5640
X-RAY DIFFRACTION	f_angle_d	0.678	7708
X-RAY DIFFRACTION	f_dihedral_angle_d	12.625	3338
X-RAY DIFFRACTION	f_chiral_restr	0.047	859
X-RAY DIFFRACTION	f_plane_restr	0.005	1003

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.3443	0.2682	145	0.2451	2605	X-RAY DIFFRACTION	100
2.3443-2.3921	0.2611	147	0.2314	2616	X-RAY DIFFRACTION	100
2.3921-2.4441	0.2468	135	0.2313	2631	X-RAY DIFFRACTION	100
2.4441-2.501	0.2563	141	0.235	2650	X-RAY DIFFRACTION	100
2.501-2.5635	0.2714	142	0.2175	2634	X-RAY DIFFRACTION	100
2.5635-2.6328	0.2627	137	0.215	2654	X-RAY DIFFRACTION	100
2.6328-2.7103	0.2289	140	0.2009	2654	X-RAY DIFFRACTION	100
2.7103-2.7978	0.2625	139	0.2047	2649	X-RAY DIFFRACTION	100
2.7978-2.8978	0.2424	140	0.2143	2654	X-RAY DIFFRACTION	100
2.8978-3.0138	0.275	135	0.2153	2661	X-RAY DIFFRACTION	100
3.0138-3.151	0.2338	143	0.2071	2666	X-RAY DIFFRACTION	100
3.151-3.3171	0.2297	126	0.2044	2686	X-RAY DIFFRACTION	100
3.3171-3.525	0.2528	141	0.1942	2693	X-RAY DIFFRACTION	100
3.525-3.7971	0.2068	142	0.1822	2679	X-RAY DIFFRACTION	100
3.7971-4.1792	0.1554	145	0.1556	2714	X-RAY DIFFRACTION	100
4.1792-4.7839	0.1411	159	0.1379	2709	X-RAY DIFFRACTION	100
4.7839-6.027	0.1622	134	0.1506	2780	X-RAY DIFFRACTION	100
6.027-81.0502	0.2206	131	0.1826	2950	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	2.8069	0.4573	-0.3629	2.7593	0.9448	3.0859	0.0014	0.0898	0.0998	-0.2435	-0.0548	-0.0358	-0.2596	-0.002	0.0723	0.1716	-0.0006	-0.0199	0.2035	-0.0062	0.1855	39.0951	153.219	143.9805
2	2.7049	0.3717	-1.1716	1.5902	-0.4503	1.5874	-0.0051	-0.4625	0.0848	0.4106	-0.0055	-0.0523	-0.2324	0.0486	0.0091	0.2207	0.018	-0.0231	0.2646	-0.0475	0.1915	30.5489	147.4818	159.509
3	1.1946	0.2501	-0.32	1.3424	-0.1188	1.2989	0.0083	-0.1143	0.0844	0.1632	-0.0272	0.2774	-0.0905	-0.2669	0.0315	0.1682	0.0466	0.0101	0.323	-0.0471	0.3059	19.0867	150.986	154.5139
4	4.1494	1.2921	-0.1956	1.5639	0.1255	6.2629	0.2522	-0.2	0.3528	0.4018	-0.1783	0.1142	-0.5305	0.1834	-0.1641	0.347	0.0142	-0.0031	0.187	-0.0347	0.3289	36.7279	161.1748	150.4608
5	2.3959	-0.0868	0.5937	1.4791	-0.4832	1.1952	-0.0586	0.1273	0.0351	-0.1645	-0.0088	-0.2961	-0.1062	0.1706	0.0822	0.242	-0.0269	0.0216	0.2719	-0.0512	0.2752	45.5113	153.0939	142.1544
6	0.7369	-0.7089	0.0384	1.431	-0.2018	0.0521	0.0527	0.9662	0.5209	-1.1073	-0.0177	0.4684	-0.531	-0.2557	0.0668	0.5406	0.0357	-0.0322	0.4981	0.1245	0.3709	41.2711	159.2548	130.5719
7	6.0046	1.2237	0.1953	6.0276	-0.2485	2.0995	0.096	-0.0111	0.5548	-0.064	0.056	-0.6479	-0.5782	0.6374	-0.0447	0.2391	-0.1336	0.1147	0.3725	-0.0042	0.3762	54.1858	160.1878	139.6169
8	7.1023	1.2656	0.2192	3.5569	-1.4988	1.5403	0.0174	0.5462	0.7125	-0.2507	-0.133	0.2053	-0.1932	-0.3283	0.089	0.3923	0.2051	-0.0339	0.5563	0.0458	0.3674	-13.8337	169.6498	137.781
9	7.322	-0.0276	0.3914	2.9287	-0.2996	3.3813	-0.0503	0.3695	0.4813	-0.1959	0.0482	-0.2194	-0.0216	-0.2891	0.0136	0.3848	0.1408	-0.0107	0.4372	0.0068	0.3752	-1.2975	170.8487	143.2625
10	6.8899	1.7278	0.2496	6.3257	-1.6544	5.4114	-0.0877	0.9345	0.0335	-0.7215	0.0032	-0.4158	0.3499	0.134	-0.0778	0.3974	0.1344	0.0047	0.5005	-0.0177	0.3681	-1.8785	167.7381	136.862
11	7.4235	1.0156	1.7922	3.611	-0.2599	3.0147	-0.0809	0.186	-0.0005	0.1476	0.1924	0.0275	0.2857	-0.3939	-0.0482	0.3919	0.1031	-0.013	0.467	-0.0198	0.236	-8.6058	164.8384	143.2467
12	2.6163	-0.7188	1.0345	0.3763	0.3011	2.1598	-0.221	-0.352	0.8504	-0.2171	-0.0449	-0.0753	-0.3116	-0.2233	0.2209	0.3778	0.1159	0.003	0.3958	-0.0062	0.6037	0.5754	172.5946	148.3054
13	1.9022	-0.1403	-0.5187	0.7761	0.4568	3.277	-0.0441	0.0109	-0.0568	-0.0982	0.2043	0.2494	-0.2355	-0.2199	-0.2239	0.5182	0.0358	-0.0132	0.6128	0.0911	0.3997	-34.4598	168.4769	150.7235
14	0.6704	0.4506	-0.326	2.3102	-0.594	7.4385	0.0187	0.1635	0.3932	-0.0744	0.4363	0.3348	-0.8487	-0.8133	-0.4536	0.5173	0.0699	-0.0025	0.7343	0.149	0.4944	-40.1605	174.406	153.1891
15	3.5319	-0.2133	-2.5442	1.2927	0.006	1.8956	-0.1209	-0.884	-0.1193	0.1609	0.1552	0.277	-0.3487	-1.1319	0.3179	0.3851	0.1926	-0.0042	1.095	-0.0662	0.4126	-6.1725	162.5741	168.2771
16	7.7241	1.1157	-0.2872	1.2838	-2.2493	4.3146	-0.0466	-0.3801	0.674	-0.1136	0.1561	-0.0486	-0.1909	-0.1843	0.3051	0.2631	0.0813	-0.0056	0.4075	-0.0965	0.4214	13.5512	165.038	160.9636
17	1.4063	-0.0381	-0.4277	1.0083	-0.2259	0.6417	-0.4555	-1.3732	0.8568	0.1549	0.3785	0.0248	-0.6782	-0.8889	-0.0323	0.4212	0.3916	-0.0258	0.9374	-0.2926	0.5291	-3.8677	171.9029	164.8322
18	2.6849	0.0221	-1.9395	0.1507	-0.0102	1.1989	-0.0703	-0.8372	0.2649	0.0919	0.2082	0.0417	-0.0128	-0.0238	-0.1595	0.3791	0.1721	0.0277	0.7659	-0.0129	0.3899	-9.5917	164.2151	163.4624
19	4.595	2.3321	-0.2619	5.6301	2.0404	5.7514	-0.3664	0.2912	0.0284	-0.0893	0.3833	0.3923	0.6954	0.3257	0.0167	0.4935	0.1262	0.0665	0.621	0.0679	0.38	-38.5935	159.1024	160.1023
20	1.3367	-0.1968	0.042	2.605	3.5975	5.1819	-0.3403	0.1228	-0.5856	0.4362	0.2895	0.2425	1.1382	0.3195	0.0398	0.819	0.1589	0.1397	0.7655	0.0481	0.5856	-36.2374	150.3959	157.8368
21	4.7165	1.5882	0.5944	4.1661	2.0873	4.6933	-0.3708	0.2456	-0.139	-0.1501	0.3773	0.0849	0.5239	0.2324	-0.0127	0.4978	0.078	0.0559	0.6353	0.0466	0.3232	-37.6156	157.9407	159.8759
22	3.8545	-1.1881	-0.8136	3.2478	0.4866	1.6305	-0.2183	0.3783	-0.2603	0.2817	-0.0393	0.2238	1.3687	0.1941	-0.1537	0.6012	0.018	0.1994	0.6159	0.0534	0.4256	-42.0755	155.1832	168.2973

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 229 through 269 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 270 through 326 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 327 through 397 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 398 through 425 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 426 through 484 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 485 through 499 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 500 through 518 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 3 through 17 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 18 through 60 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 61 through 83 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 84 through 100 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 101 through 122 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 123 through 186 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 187 through 224 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 1 through 25 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 26 through 38 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 39 through 96 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 97 through 119 )
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 120 through 156 )
20	X-RAY DIFFRACTION	20	chain 'L' and (resid 157 through 169 )
21	X-RAY DIFFRACTION	21	chain 'L' and (resid 170 through 203 )
22	X-RAY DIFFRACTION	22	chain 'L' and (resid 204 through 219 )

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Non-polymers , 3 types, 347 molecules

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Protein , 1 types, 1 molecules A

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Antibody , 2 types, 2 molecules HL

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Non-polymers , 3 types, 347 molecules

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