PDB-5lkc: Protruding domain of GII.17 norovirus Kawasaki308 in complex with...

ID or keywords:

Entry

Database: PDB / ID: 5lkc

Title

Protruding domain of GII.17 norovirus Kawasaki308 in complex with HBGA type A (triglycan)

Components

Major capsid protein

Keywords

VIRAL PROTEIN / Norovirus / Virus capsid / HBGA / Protruding domain / P domain

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 GII

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.81 Å

Authors

Singh, B.K. / Morozov, V. / Hansman, G.S.

Citation

Journal: Virology / Year: 2017
Title: Human norovirus inhibition by a human milk oligosaccharide.
Authors: Koromyslova, A. / Tripathi, S. / Morozov, V. / Schroten, H. / Hansman, G.S.

History

Deposition	Jul 22, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 24, 2017	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5lkc_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5lkc_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5lkc_validation.xml.gz	28.4 KB	Display
Data in CIF	5lkc_validation.cif.gz	42.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lk/5lkc ftp://data.pdbj.org/pub/pdb/validation_reports/lk/5lkc	HTTPS FTP

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Related structure data

Related structure data	5lkgC 5n7mC 5f4oS 5f4j 5f4m S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ony-2 3pvd-d 3onu-d 5lkg-d 5lkk-d 3q39-d 5hza-d 6gw2-d 5zv7-d 4x0c-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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4)

Deposited unit

A: Major capsid protein

B: Major capsid protein

hetero molecules

70 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	75.870, 86.730, 97.440
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: MET / End label comp-ID: MET

Dom-ID	Beg auth comp-ID	Beg label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	SER	SER	chain A	A	A	224 - 530	2 - 308
2	GLY	GLY	chain B	B	B	223 - 530	1 - 308

#1: Protein

Major capsid protein / Major viral capsid protein

Mass: 34315.203 Da / Num. of mol.: 2 / Fragment: P DOMAIN (UNP residues 225-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Norovirus GII / Gene: VP1 / Plasmid: MBP-HTSHP / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0S1Z370, UniProt: A0A0E4B1P1*PLUS

#2: Polysaccharide

alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose

Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LFucpa1-2[DGalpNAca1-3]DGalpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Chemical

ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.35 Å³/Da / Density % sol: 47.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Magnesium Chloride, PEG8000, Tris-HCl

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.9677 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2016

Radiation

Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9677 Å / Relative weight: 1

Reflection

Resolution: 1.76→48.72 Å / Num. obs: 64128 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / B_iso Wilson estimate: 18.95 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.136 / Net I/σ(I): 15.27

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
1.76-1.8		1.128	2.92	0.761	1	94.2
1.8-1.85		0.947	3.94	0.882	1	100
1.85-1.91		0.767	5.16	0.944	1	100
1.91-1.96		0.604	6.72	0.969	1	100
1.96-2.03		0.51	8.36	0.982	1	100
2.03-2.1		0.44	9.61	0.986	1	99.5
2.1-2.18		0.349	11.29	0.988	1	99.5
2.18-2.27		0.274	13.13	0.993	1	99.2
2.27-2.37		0.231	14.23	0.993	1	98.6
2.37-2.49		0.197	15.22	0.994	1	96
2.49-2.62		0.182	18.07	0.996	1	99.6
2.62-2.78		0.149	21.12	0.997	1	100
2.78-2.97		0.121	23.91	0.997	1	100
2.97-3.21		0.099	26.72	0.998	1	100
3.21-3.51		0.085	29.48	0.998	1	100
3.51-3.93		0.074	31.74	0.998	1	100
3.93-4.54		0.069	33.46	0.999	1	100
4.54-5.56		0.069	33.76	0.998	1	100
5.56-7.86		0.069	32.78	0.998	1	100
	7.86	0.073	32.18	0.991	1	99.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	7.34 Å	48.72 Å
Translation	7.34 Å	48.72 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.6	phasing
PHENIX		refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5F4O

5f4o

Resolution: 1.81→48.72 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.01

	R_factor	Num. reflection	% reflection
R_free	0.1829	2949	5 %
R_work	0.1526	-	-
obs	0.1541	58952	99.49 %

Solvent computation

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

Displacement parameters

B_iso max: 100.21 Å² / B_iso mean: 26.3423 Å² / B_iso min: 9.8 Å²

Refinement step

Cycle: final / Resolution: 1.81→48.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4757	0	90	529	5376
B_iso mean	-	-	45.11	30.95	-
Num. residues	-	-	-	-	611

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5059
X-RAY DIFFRACTION	f_angle_d	1.007	6921
X-RAY DIFFRACTION	f_chiral_restr	0.04	758
X-RAY DIFFRACTION	f_plane_restr	0.005	924
X-RAY DIFFRACTION	f_dihedral_angle_d	12.244	1836

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	3500	X-RAY DIFFRACTION	5.7	TORSIONAL
1	2	B	3500	X-RAY DIFFRACTION	5.7	TORSIONAL

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 (%)
1.81-1.8397	0.3315	140	0.302	2652	X-RAY DIFFRACTION	100
1.8397-1.8714	0.2872	138	0.2363	2632	X-RAY DIFFRACTION	100
1.8714-1.9054	0.2122	138	0.2102	2611	X-RAY DIFFRACTION	100
1.9054-1.9421	0.1987	141	0.1767	2678	X-RAY DIFFRACTION	100
1.9421-1.9817	0.2172	139	0.1612	2646	X-RAY DIFFRACTION	100
1.9817-2.0248	0.2054	139	0.1558	2643	X-RAY DIFFRACTION	100
2.0248-2.0719	0.1974	139	0.1553	2647	X-RAY DIFFRACTION	100
2.0719-2.1237	0.1807	139	0.1503	2628	X-RAY DIFFRACTION	99
2.1237-2.1812	0.2002	139	0.1485	2642	X-RAY DIFFRACTION	100
2.1812-2.2453	0.1815	139	0.1413	2651	X-RAY DIFFRACTION	99
2.2453-2.3178	0.1643	139	0.1409	2630	X-RAY DIFFRACTION	99
2.3178-2.4007	0.1508	137	0.1409	2611	X-RAY DIFFRACTION	98
2.4007-2.4968	0.177	134	0.1434	2543	X-RAY DIFFRACTION	96
2.4968-2.6104	0.1855	141	0.1509	2673	X-RAY DIFFRACTION	100
2.6104-2.748	0.1993	141	0.153	2683	X-RAY DIFFRACTION	100
2.748-2.9202	0.1891	141	0.1509	2678	X-RAY DIFFRACTION	100
2.9202-3.1456	0.178	142	0.1494	2703	X-RAY DIFFRACTION	100
3.1456-3.4621	0.1824	142	0.1461	2697	X-RAY DIFFRACTION	100
3.4621-3.9628	0.18	144	0.1375	2740	X-RAY DIFFRACTION	100
3.9628-4.992	0.1362	145	0.1233	2747	X-RAY DIFFRACTION	100
4.992-48.72	0.1806	152	0.1696	2868	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	2.1858	-0.2684	0.2088	1.5659	0.4931	2.2242	0.0421	-0.0948	0.1292	0.0135	-0.082	-0.0629	-0.0596	-0.0486	0.0297	0.1119	-0.0342	0.0342	0.0994	-0.0304	0.1466	-38.5975	12.5769	3.5655
2	2.2355	0.5353	1.2332	1.5673	1.172	3.5016	0.0486	-0.0042	-0.0024	0.0069	-0.1196	0.2078	0.0608	-0.1939	0.0394	0.1057	-0.0035	0.0166	0.1241	-0.0231	0.1781	-52.7826	1.2502	-9.8837
3	1.467	-0.0468	-0.5365	3.7448	0.8795	1.5674	-0.0036	0.0506	-0.0305	-0.2143	-0.1075	0.0627	-0.0153	-0.0983	0.1107	0.0577	0.0122	-0.0195	0.1094	-0.0097	0.0556	-47.4929	-2.5114	-16.1357
4	1.2927	-0.1022	-0.0361	2.1994	0.8362	1.2018	0.0571	0.102	0.1681	-0.2019	-0.1128	0.0782	-0.1317	-0.1434	0.0454	0.113	0.0225	0.0004	0.1309	0.0009	0.1175	-49.7466	7.8957	-16.3996
5	0.5969	0.1428	-0.2842	1.0522	0.006	2.3751	0.0298	-0.0878	0.202	0.0829	-0.1024	0.1023	-0.054	-0.0356	0.0536	0.0912	-0.0227	0.0161	0.1374	-0.033	0.1931	-38.4607	14.9886	0.5695
6	5.2717	0.5642	-1.8846	2.739	0.5306	3.0685	0.0457	-0.4801	0.159	0.1824	0.0912	-0.4466	0.0847	0.1599	-0.1008	0.1889	-0.022	-0.0255	0.2094	-0.085	0.2096	-34.2351	14.8565	16.6791
7	2.6263	-0.7993	0.4866	2.127	-0.128	2.588	0.0019	0.1098	0.0712	-0.0581	0.0298	-0.4863	-0.2119	0.2049	-0.0161	0.1528	-0.0619	0.0269	0.1643	-0.0877	0.2938	-33.7989	21.4914	8.1668
8	3.0845	-1.0401	-1.1512	5.8653	2.1209	3.3906	-0.1032	-0.3193	0.4631	0.1684	0.1583	-0.2251	-0.0667	-0.018	-0.0179	0.1406	-0.0325	-0.036	0.2593	-0.0927	0.2249	-36.4756	20.9724	17.2474
9	1.5533	-0.5718	-0.144	1.5826	-0.6934	2.1275	0.1378	-0.2572	0.0842	0.1883	-0.0513	0.0377	-0.1025	-0.0438	-0.0507	0.17	-0.058	0.0039	0.1461	0.0011	0.1179	-38.4712	-8.3228	5.3247
10	3.5878	2.7643	0.335	3.0103	-0.0935	0.7825	-0.0651	0.1851	-0.2498	-0.0082	-0.0341	-0.3184	0.3768	0.0942	0.0795	0.2667	0.0135	0.0415	0.1669	0.0458	0.1726	-30.5021	-19.587	0.577
11	2.2368	0.2838	-1.0672	1.7353	-0.8078	2.8472	0.0663	0.0842	0.0769	-0.0707	-0.1525	-0.3261	0.0918	0.2351	0.0595	0.117	0.0259	0.0293	0.1494	0.0569	0.2373	-20.5132	-0.8906	-9.9862
12	0.9671	0.1466	0.322	1.5505	-0.1664	1.1666	0.027	0.0634	0.0977	-0.0323	-0.1295	-0.0453	0.0284	0.1472	0.1063	0.086	0.0123	0.0545	0.1507	0.0478	0.1355	-25.8438	2.85	-15.3501
13	1.2372	-0.2575	0.0989	1.6786	-0.4458	1.0224	0.0515	0.11	-0.0742	-0.1683	-0.173	-0.2155	0.1952	0.2064	0.1168	0.1598	0.039	0.0631	0.1601	0.0379	0.1523	-23.4823	-7.1442	-16.1871
14	1.0968	0.2454	0.3312	1.3801	0.0631	1.7548	0.0926	-0.0945	-0.1523	0.1667	-0.1353	-0.1244	0.2948	0.0512	0.0126	0.1843	-0.0253	0.0283	0.1224	0.0283	0.1385	-35.2661	-14.8927	-0.1573
15	2.8709	-0.2172	1.1669	2.9421	-0.5796	2.5943	0.2211	-0.4135	-0.2735	0.3855	-0.0396	0.2711	0.0218	-0.1517	-0.175	0.2705	-0.1017	0.0277	0.2646	0.0613	0.1386	-40.0725	-15.7015	16.1387
16	2.7631	-0.4178	-0.3892	2.8009	-0.7882	2.2732	0.0679	0.0081	-0.2197	0.0625	-0.0636	0.1348	0.3752	-0.1934	0.0124	0.2696	-0.1046	0.002	0.1647	0.0249	0.1968	-39.9585	-21.8246	7.3431
17	2.5572	-0.9635	1.5539	5.0521	-2.5848	3.4542	0.1081	-0.301	-0.3712	0.2003	-0.1565	0.0974	0.4165	-0.0075	0.0482	0.3905	-0.1253	0.0355	0.298	0.0908	0.1927	-37.7689	-21.1469	16.4113

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 224 through 268 )	A	224 - 268
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 269 through 319 )	A	269 - 319
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 320 through 347 )	A	320 - 347
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 348 through 422 )	A	348 - 422
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 423 through 464 )	A	423 - 464
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 465 through 484 )	A	465 - 484
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 485 through 513 )	A	485 - 513
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 514 through 530 )	A	514 - 530
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 223 through 247 )	B	223 - 247
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 248 through 268 )	B	248 - 268
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 269 through 319 )	B	269 - 319
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 320 through 347 )	B	320 - 347
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 348 through 422 )	B	348 - 422
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 423 through 464 )	B	423 - 464
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 465 through 484 )	B	465 - 484
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 485 through 513 )	B	485 - 513
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 514 through 530 )	B	514 - 530

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