PDB-6n81: Crystal structure of GII.4 2002 norovirus P domain in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 6n81

Title

Crystal structure of GII.4 2002 norovirus P domain in complex with cross-reactive human antibody A1227

Components

A1227 Fab heavy chain
A1227 Fab light chain
Major capsid protein

Keywords

IMMUNE SYSTEM / Norovirus / human antibody / complex / Fab

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 ...
Similarity search - Domain/homology

Biological species

Norovirus Hu/GII.4/Farmington Hills/2004/USA

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.579 Å

Authors

Changela, A. / Verardi, R. / Kwong, P.D.

Citation

Journal: 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. ...

History

Deposition	Nov 28, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2019	Group: 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 1.2	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6n81.cif.gz	576.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6n81_validation.pdf.gz	458.9 KB	Display	wwPDB validaton report
Full document	6n81_full_validation.pdf.gz	466.4 KB	Display
Data in XML	6n81_validation.xml.gz	51.2 KB	Display
Data in CIF	6n81_validation.cif.gz	72.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n8/6n81 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/6n81	HTTPS FTP

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Related structure data

Related structure data	6n8dC 3eyqS 4oovS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6csf-d 6cse-d 6t1w-1 6jht-d 6jhq-d 6jhr-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

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

Deposited unit

A: Major capsid protein

B: Major capsid protein

D: A1227 Fab light chain

C: A1227 Fab heavy chain

H: A1227 Fab heavy chain

L: A1227 Fab light chain

164 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	82.602, 150.100, 117.250
Angle α, β, γ (deg.)	90.00, 95.06, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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	A1227 Fab light chain Mass: 23309.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody	A1227 Fab heavy chain Mass: 24710.799 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 307 / 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: 4.52 Å³/Da / Density % sol: 72.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 4000, 0.1M Tris, pH 8.5, 50mM proline

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.579→50 Å / Num. obs: 84760 / % possible obs: 96 % / Redundancy: 3.2 % / CC_1/2: 0.982 / R_merge(I) obs: 0.12 / R_pim(I) all: 0.078 / R_rim(I) all: 0.144 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.453 / Num. unique obs: 4171 / CC_1/2: 0.839 / R_pim(I) all: 0.307 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4OOV, 3EYQ

4oov

3eyq

Resolution: 2.579→46.088 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.4

	R_factor	Num. reflection	% reflection
R_free	0.2109	4104	4.84 %
R_work	0.1732	-	-
obs	0.175	84727	94.72 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.579→46.088 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11232	0	0	307	11539

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11519
X-RAY DIFFRACTION	f_angle_d	0.777	15686
X-RAY DIFFRACTION	f_dihedral_angle_d	12.386	4116
X-RAY DIFFRACTION	f_chiral_restr	0.029	1757
X-RAY DIFFRACTION	f_plane_restr	0.004	2045

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 (%)
2.5795-2.6098	0.319	97	0.2448	1669	X-RAY DIFFRACTION	58
2.6098-2.6416	0.3092	142	0.231	2807	X-RAY DIFFRACTION	96
2.6416-2.6751	0.2629	171	0.2268	2805	X-RAY DIFFRACTION	96
2.6751-2.7103	0.285	147	0.2249	2777	X-RAY DIFFRACTION	97
2.7103-2.7474	0.2913	131	0.2132	2894	X-RAY DIFFRACTION	97
2.7474-2.7866	0.2216	143	0.2114	2799	X-RAY DIFFRACTION	96
2.7866-2.8282	0.2773	122	0.2169	2803	X-RAY DIFFRACTION	96
2.8282-2.8724	0.2938	150	0.2146	2772	X-RAY DIFFRACTION	94
2.8724-2.9195	0.2385	132	0.2123	2630	X-RAY DIFFRACTION	91
2.9195-2.9698	0.2403	141	0.2039	2750	X-RAY DIFFRACTION	93
2.9698-3.0238	0.2491	152	0.2005	2866	X-RAY DIFFRACTION	98
3.0238-3.082	0.2599	134	0.2063	2910	X-RAY DIFFRACTION	98
3.082-3.1449	0.2655	149	0.1993	2850	X-RAY DIFFRACTION	98
3.1449-3.2132	0.2217	143	0.1952	2892	X-RAY DIFFRACTION	99
3.2132-3.288	0.2234	161	0.1949	2911	X-RAY DIFFRACTION	99
3.288-3.3702	0.2592	162	0.1917	2851	X-RAY DIFFRACTION	98
3.3702-3.4612	0.2425	152	0.1848	2904	X-RAY DIFFRACTION	99
3.4612-3.5631	0.1968	150	0.1792	2852	X-RAY DIFFRACTION	98
3.5631-3.678	0.2176	160	0.1792	2864	X-RAY DIFFRACTION	98
3.678-3.8094	0.219	147	0.1798	2881	X-RAY DIFFRACTION	98
3.8094-3.9619	0.2006	143	0.1669	2826	X-RAY DIFFRACTION	96
3.9619-4.1421	0.1776	137	0.1557	2743	X-RAY DIFFRACTION	93
4.1421-4.3603	0.1715	129	0.1357	2584	X-RAY DIFFRACTION	88
4.3603-4.6332	0.1547	121	0.1248	2844	X-RAY DIFFRACTION	96
4.6332-4.9906	0.1381	128	0.1281	2810	X-RAY DIFFRACTION	95
4.9906-5.4921	0.1719	143	0.1373	2828	X-RAY DIFFRACTION	95
5.4921-6.2851	0.1728	163	0.152	2827	X-RAY DIFFRACTION	97
6.2851-7.912	0.177	114	0.1579	2872	X-RAY DIFFRACTION	96
7.912-46.0956	0.1642	140	0.1372	2802	X-RAY DIFFRACTION	93

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	1.41	-0.5074	-2.0015	2.0148	0.6567	4.5672	0.0116	0.1082	0.0971	-0.1955	-0.0622	-0.0276	-0.2875	-0.0422	0.0561	0.2028	-0.0135	-0.036	0.1647	0.0264	0.3583	10.0518	18.3409	4.4853
2	0.9208	-0.361	-0.3869	1.487	0.4695	1.5556	0.0552	-0.105	0.2782	-0.0821	0.0407	-0.2685	-0.3132	0.1166	-0.0994	0.2224	0.0066	-0.0341	0.1826	0.0164	0.3634	13.5774	20.4753	10.6929
3	5.3586	-0.1757	0.0874	1.3089	-0.0994	0.1945	0.0301	-0.2156	-0.0418	0.0787	0.0506	-0.0279	-0.1026	0.0381	-0.0902	0.2005	0.0224	-0.0125	0.1745	-0.0011	0.2981	13.6781	-2.4482	11.0573
4	1.1003	-0.6779	-0.0451	1.3916	0.1476	0.8164	-0.0018	-0.0159	-0.095	-0.06	0.0028	0.0431	0.0048	-0.0491	-0.0045	0.1713	-0.0023	-0.0277	0.1742	0.0239	0.368	9.5663	-4.6254	5.1168
5	1.7568	-1.8853	0.7583	8.6906	-1.6368	1.3986	-0.1757	-0.1367	0.0704	0.4439	0.1954	0.4642	-0.1119	-0.1188	-0.0082	0.1675	0.026	0.0025	0.2453	-0.0168	0.3139	-21.0458	39.0711	12.5209
6	3.7342	0.9478	2.1543	2.2648	0.9411	2.7224	0.0977	0.0444	-0.2768	-0.0517	0.0278	0.2964	0.064	-0.1188	-0.1375	0.1763	0.0056	-0.0056	0.2177	0.0314	0.5158	-48.1563	54.0575	-6.8839
7	3.2746	-0.4514	1.0608	2.4553	-0.5081	2.2053	-0.0133	0.0224	-0.1276	-0.1134	0.0986	0.3937	0.157	-0.0524	-0.0786	0.2003	0.0057	-0.0398	0.1923	-0.0046	0.4617	-24.0274	21.2507	-0.1472
8	1.7877	2.0927	-0.8175	6.7641	-1.9796	2.394	-0.03	0.1145	-0.5078	-0.2712	0.0245	-0.154	0.1965	0.0502	-0.032	0.2036	-0.002	-0.0584	0.2491	-0.0272	0.4861	-39.3302	44.1172	-16.6791
9	2.9165	1.065	0.4936	7.383	-3.8145	4.5721	0.08	-0.3305	-0.0955	0.3651	0.0817	0.6027	1.0275	-0.4523	-0.1487	0.6728	-0.0875	0.1029	0.4375	0.0362	0.3453	-7.0159	-22.6927	35.2963
10	1.0902	-0.7755	-0.2115	0.8245	-1.1987	7.533	-0.198	0.1981	0.2233	-0.6764	-0.1516	-0.1819	-0.5653	0.6887	0.2967	0.8692	-0.1811	-0.0052	0.5375	0.2148	0.5608	-2.4672	-37.4502	68.0464
11	2.5265	0.8127	0.4412	2.6443	-1.3088	6.9677	0.0161	-0.486	0.0467	0.9759	-0.1727	-0.0065	0.0399	-0.329	0.138	0.5845	0.0162	0.0634	0.3849	0.0135	0.3325	2.7899	-4.7385	43.6613
12	1.0382	0.6654	1.0535	5.7469	-1.0435	2.7918	-0.087	0.274	0.4891	-0.7912	-0.1415	-0.9832	-1.1714	1.1991	0.2903	1.2371	-0.3643	0.0263	0.9783	0.2604	0.7842	10.4843	-26.7586	64.6783

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 225 through 323 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 324 through 530 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 225 through 323 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 324 through 530 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 1 through 108 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 109 through 211 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 1 through 114 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 115 through 214 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 1 through 108 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 109 through 211 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 114 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 115 through 212 )

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