PDB-4x7c: Crystal structure of Saga-2006 GII.4 P domain in complex with Nano-85

ID or keywords:

Entry

Database: PDB / ID: 4x7c

Title

Crystal structure of Saga-2006 GII.4 P domain in complex with Nano-85

Components

Nano-85 Nanobody
VP1

Keywords

VIRAL PROTEIN / Nanobody / VHH domain / Norovirus / Protruding domain

Function / homology

Function and homology information

virion component / host cell cytoplasm
Similarity search - Function

Biological species

Norovirus Hu/GII-4/Saga1/2006/JP

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Koromyslova, A.D. / Hansman, G.S.

Citation

Journal: J.Virol. / Year: 2015
Title: Nanobody binding to a conserved epitope promotes norovirus particle disassembly.
Authors: Koromyslova, A.D. / Hansman, G.S.

History

Deposition	Dec 9, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 31, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 14, 2015	Group: Database references
Revision 1.2	Feb 18, 2015	Group: Database references
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4x7c.cif.gz	344.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4x7c_validation.pdf.gz	436.5 KB	Display	wwPDB validaton report
Full document	4x7c_full_validation.pdf.gz	438.5 KB	Display
Data in XML	4x7c_validation.xml.gz	33.5 KB	Display
Data in CIF	4x7c_validation.cif.gz	48.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7c ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7c	HTTPS FTP

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Related structure data

Related structure data	4x7dC 4x7eC 4x7fC 4ooxS 4x73 PDB Unreleased entryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x7d-d 5o05-d 3l4j-d 3do7-1 3wfq-4 5zen-d 6h71-d 6b9f-d 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	#136 - Apr 2011 Nanobodies similarity (1) #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)

Deposited unit

A: VP1

B: VP1

C: Nano-85 Nanobody

D: Nano-85 Nanobody

94.8 kDa, 4 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)	50.150, 125.230, 133.040
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A and segid
2	1	chain B and segid
1	2	chain C and segid D000
2	2	chain D and segid D000

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID
1	1	1	chain A and segid	A
2	1	1	chain B and segid	B
1	1	2	chain C and segid D000	C
2	1	2	chain D and segid D000	D

NCS ensembles :

ID
1
2

Details

The biological unit is a dimer. There is 1 biological unit in the asymmetric unit (chains A & B)

#1: Protein	VP1 Mass: 33882.902 Da / Num. of mol.: 2 / Fragment: UNP residues 225-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus Hu/GII-4/Saga1/2006/JP / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5BTR4
#2: Antibody	Nano-85 Nanobody Mass: 13497.894 Da / Num. of mol.: 2 / Fragment: VHH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN6C / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.2 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: ammonium fluoride, PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2014

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.98→46.93 Å / Num. obs: 58332 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / B_iso Wilson estimate: 29.46 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.12 / R_rim(I) all: 0.127 / Χ²: 0.997 / Net I/σ(I): 13 / Num. measured all: 554153

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.98-2.03		8.8	0.794	0.813	2.49	30021	4298	3593	0.863	83.6
2.03-2.09			0.891	0.668	3.64	41548	4235	4212	0.704	99.5
2.09-2.15			0.912	0.596	4.2	40422	4085	4072	0.628	99.7
2.15-2.22			0.912	0.506	5.14	38242	3948	3940	0.534	99.8
2.22-2.29			0.925	0.429	6.11	36766	3877	3871	0.454	99.8
2.29-2.37			0.937	0.374	7	34493	3750	3747	0.397	99.9
2.37-2.46			0.948	0.33	7.77	32350	3584	3569	0.351	99.6
2.46-2.56			0.968	0.287	9.64	34948	3475	3469	0.303	99.8
2.56-2.67			0.983	0.24	11.32	33904	3347	3347	0.253	100
2.67-2.8			0.989	0.191	13.26	32116	3200	3196	0.201	99.9
2.8-2.96			0.99	0.154	15.08	30244	3077	3077	0.163	100
2.96-3.13			0.994	0.118	17.53	25648	2884	2866	0.125	99.4
3.13-3.35			0.996	0.098	21.48	26935	2723	2723	0.103	100
3.35-3.62			0.997	0.084	24.64	25001	2538	2535	0.088	99.9
3.62-3.96			0.997	0.074	26.68	22272	2358	2358	0.078	100
3.96-4.43			0.997	0.066	27.98	19048	2152	2152	0.07	100
4.43-5.12			0.998	0.06	28.94	16727	1908	1897	0.063	99.4
5.12-6.27			0.998	0.06	29.61	15692	1652	1652	0.064	100
6.27-8.87			0.998	0.053	28.89	11037	1288	1286	0.057	99.8
	8.87		0.999	0.045	30.69	6739	784	770	0.047	98.2

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XDS		data reduction
PDB_EXTRACT	3.15	data extraction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4oox, 4x73

4oox

4x73
PDB Unreleased entry

Resolution: 2→46.93 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2176	2871	5 %
R_work	0.1661	54554	-
obs	0.1687	57425	99.77 %

Solvent computation

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

Displacement parameters

B_iso max: 99 Å² / B_iso mean: 34.8707 Å² / B_iso min: 13.31 Å²

Refinement step

Cycle: final / Resolution: 2→46.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6432	0	0	428	6860
B_iso mean	-	-	-	38.69	-
Num. residues	-	-	-	-	848

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6666
X-RAY DIFFRACTION	f_angle_d	1.213	9110
X-RAY DIFFRACTION	f_chiral_restr	0.054	1002
X-RAY DIFFRACTION	f_plane_restr	0.008	1202
X-RAY DIFFRACTION	f_dihedral_angle_d	13.263	2354

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2790	X-RAY DIFFRACTION	5.974	TORSIONAL
1	2	B	2790	X-RAY DIFFRACTION	5.974	TORSIONAL
2	1	C	954	X-RAY DIFFRACTION	5.974	TORSIONAL
2	2	D	954	X-RAY DIFFRACTION	5.974	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.0328	0.317	134	0.2499	2540	2674	100
2.0328-2.0678	0.3089	134	0.2369	2544	2678	100
2.0678-2.1054	0.2913	135	0.2297	2578	2713	99
2.1054-2.1459	0.2993	134	0.2302	2538	2672	100
2.1459-2.1897	0.2818	135	0.2147	2573	2708	100
2.1897-2.2374	0.2854	134	0.2162	2542	2676	100
2.2374-2.2894	0.2698	136	0.2129	2596	2732	100
2.2894-2.3467	0.269	135	0.2034	2557	2692	100
2.3467-2.4101	0.2389	136	0.1925	2583	2719	99
2.4101-2.481	0.2397	135	0.1886	2564	2699	100
2.481-2.5611	0.2617	136	0.1827	2579	2715	100
2.5611-2.6526	0.252	137	0.177	2604	2741	100
2.6526-2.7588	0.259	135	0.1773	2566	2701	100
2.7588-2.8844	0.2427	137	0.1759	2597	2734	100
2.8844-3.0364	0.2238	136	0.1707	2593	2729	100
3.0364-3.2266	0.2028	137	0.1582	2596	2733	99
3.2266-3.4756	0.2202	139	0.1519	2632	2771	100
3.4756-3.8253	0.1843	139	0.1457	2637	2776	100
3.8253-4.3784	0.174	138	0.1253	2634	2772	100
4.3784-5.515	0.1604	141	0.125	2686	2827	100
5.515-46.9396	0.1788	148	0.1614	2815	2963	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	1.2711	1.0395	-0.2482	4.1514	-1.459	2.0513	-0.0601	0.0295	-0.1254	-0.0585	0.1009	0.15	0.0715	-0.2155	-0.032	0.1862	0.0035	-0.0192	0.2119	-0.0089	0.2044	7.7949	0.5281	28.4509
2	1.3201	0.5652	-0.1715	0.819	-1.0367	5.8574	-0.0441	0.0054	-0.1067	-0.1844	0.2123	0.1904	0.7617	-0.3102	-0.1523	0.2735	-0.0546	0.0003	0.1722	0.0113	0.3247	4.8128	-15.1678	35.449
3	0.3704	0.1131	-0.3433	2.3989	-1.109	1.613	-0.0319	0.0501	-0.097	-0.2226	-0.0231	-0.1953	0.177	0.0494	0.0492	0.1587	-0.0046	-0.0068	0.2133	0.0104	0.1964	16.6457	6.6421	20.0081
4	1.2514	-1.2216	-0.2224	4.0604	1.1181	1.231	0.0435	-0.0362	-0.0594	-0.1489	0.027	-0.2752	-0.0595	0.1369	-0.0565	0.1776	-0.0229	-0.0012	0.2035	0.0466	0.1952	21.8849	3.157	45.4042
5	1.9949	-0.9658	-1.0584	3.2293	1.7005	4.9013	-0.096	-0.0609	-0.1389	0.1138	0.0719	-0.3718	0.4375	0.219	0.0329	0.1625	0.0332	0.0104	0.1775	0.0415	0.3469	27.2021	-12.8015	41.3691
6	0.3832	-0.3357	-0.4049	2.9903	0.7798	1.1132	-0.0037	-0.0225	-0.0827	0.162	-0.0312	0.1333	-0.0072	-0.0288	0.012	0.1697	0.01	-0.0244	0.1999	0.012	0.1786	12.5263	6.8094	52.7698
7	0.9776	-0.5716	-0.5092	3.3836	1.31	3.0614	0.1107	-0.0663	0.0831	-0.0844	-0.1592	0.2232	-0.211	-0.3198	-0.0416	0.1805	0.0235	0.0386	0.1717	0.027	0.1668	6.547	24.5536	54.4291
8	4.7697	1.9366	-0.2128	2.0034	2.6432	9.5394	0.513	0.1698	1.0843	-0.5917	-0.3216	0.381	-1.7209	-0.1211	-0.0968	0.8961	0.0987	0.1468	0.4269	0.0717	0.5022	17.499	42.8664	4.0461
9	4.6092	-2.4281	1.1836	8.9513	-3.6871	1.5252	0.1943	0.9193	0.567	-0.7035	-0.3015	-0.4285	-0.3214	0.1817	0.0894	0.4189	-0.0826	-0.0122	0.4145	0.1285	0.2782	23.85	36.9984	-17.3457
10	1.3836	0.0302	1.5982	2.7419	3.3528	5.8807	-0.4202	0.1216	-0.0941	0.6904	-0.0273	0.7212	-0.7162	0.7903	0.4316	0.5553	-0.0886	0.1774	0.3344	0.0162	0.4152	23.4298	39.2075	-0.3886
11	2.8709	1.0051	1.9239	4.158	0.1265	4.2773	0.3833	0.2691	0.3249	-0.0428	-0.0524	0.126	-0.265	-0.0646	-0.3131	0.2667	0.0056	0.0771	0.3329	0.0319	0.2425	17.7235	33.344	4.4222
12	6.3474	0.6569	2.4703	2.0761	-0.0961	4.2093	-0.1408	0.2453	0.7737	-0.4074	-0.109	0.3985	0.166	-1.0279	0.2439	0.3382	-0.0498	-0.0025	0.5072	0.0578	0.3346	12.7031	28.6793	-5.3765
13	2.7006	-0.6218	-1.1387	4.2389	-2.3246	2.1031	-0.2286	-0.0822	-0.2373	-0.853	-0.2701	0.0008	0.6126	0.0913	0.3876	0.3338	0.0012	0.0798	0.2607	0.0024	0.373	23.1742	24.7141	-3.3071
14	8.1211	-1.4171	-5.028	7.0541	-2.1878	4.8005	0.0646	-1.1985	0.4074	0.3156	-0.0712	-0.5177	-0.5957	1.2356	0.0849	0.2348	-0.0972	0.0411	0.4784	-0.0242	0.3146	26.2672	35.0745	-0.2086
15	2.6638	-1.1755	-3.3306	4.4965	0.372	4.4651	0.6412	0.2373	-0.9278	-0.9151	-0.3335	0.8352	0.5504	-0.3594	-0.1117	0.5664	-0.0889	-0.1415	0.3025	0.0062	0.4	20.2178	29.7627	-16.4807
16	0.1598	-0.3023	0.6131	0.6761	-1.2255	2.2521	0.0484	0.0807	0.1628	0.024	0.1806	0.3141	-0.4008	-0.5793	-0.2467	0.2921	-0.0022	0.0125	0.3496	0.0878	0.2288	14.9663	34.2529	2.2167
17	3.7904	1.9218	-2.0531	2.2295	-0.8112	1.1395	0.1876	0.1535	0.4633	-0.0098	-0.028	-0.1108	-0.4653	-0.3567	-0.2101	0.2319	0.0676	0.0403	0.1658	0.02	0.2558	12.0538	34.2642	12.7764
18	7.2512	-1.4392	4.1033	9.1004	-3.8136	3.3438	0.5918	0.3328	0.2936	0.0831	-0.1083	0.0795	-0.3426	-1.2531	-0.5995	0.3541	-0.0395	0.0037	0.4317	0.0719	0.2685	17.163	38.0416	-15.0778
19	1.6081	-1.0044	1.2461	2.2569	-0.8115	1.5744	0.0464	-0.0146	0.313	-0.3116	0.0013	-0.1479	-0.6041	-0.6655	0.0396	0.3574	0.0545	0.0621	0.2321	-0.0656	0.4028	2.3913	43.0862	73.9479
20	0.6241	1.0273	0.4417	3.0138	2.7643	3.4073	0.3014	0.1063	0.2086	-0.1682	-0.1034	-0.2815	-0.1443	0.2925	-0.2259	0.238	0.0217	0.0807	0.2872	-0.0569	0.2934	9.3063	35.3412	68.383
21	1.0773	1.0192	0.205	1.7198	2.7343	9.3015	-0.0359	-0.1036	0.0636	0.1174	-0.1251	0.1182	0.7947	-0.1667	0.195	0.2581	-0.0039	0.0427	0.1974	-0.0015	0.2312	2.1865	28.4207	72.9816
22	9.1491	-1.2878	0.5252	8.5776	-6.6816	5.2016	0.3864	0.328	-0.1989	-0.9982	0.4239	0.4986	0.2032	-0.6291	-0.7834	0.3756	0.0038	0.0029	0.2886	-0.021	0.2617	-3.3787	38.6378	68.3548
23	0.0631	0.258	0.2803	1.9439	2.2179	2.673	0.226	-0.0111	0.1194	-0.271	0.1171	-0.1555	-0.5256	0.1571	-0.3845	0.2503	0.0606	0.0202	0.2736	-0.0485	0.2783	7.7573	36.7436	73.4089
24	5.1116	-1.6532	-5.3939	0.9273	1.2761	6.1802	0.4487	-0.1795	0.5326	-0.6975	0.4089	-0.5318	-1.4109	0.5601	-0.9331	0.4047	0.0108	0.0847	0.1898	0.0235	0.3649	12.3167	38.1501	57.3966
25	7.0775	1.3958	2.2166	2.03	0.8436	5.2721	-0.0126	-0.7939	0.9518	0.5813	0.2798	0.1299	-0.6653	-0.0393	-0.378	0.369	-0.0094	0.0202	0.3692	-0.1037	0.3841	7.3355	42.3492	85.1159

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 224 through 323 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 324 through 380 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 381 through 530 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 224 through 323 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 324 through 380 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 381 through 513 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 514 through 530 )	B
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 7 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 8 through 17 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 18 through 26 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 27 through 39 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 40 through 52 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 53 through 70 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 71 through 82 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 83 through 90 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 91 through 100 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 101 through 113 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 114 through 119 )	C
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1 through 26 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 27 through 52 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 53 through 70 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 71 through 82 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 83 through 100 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 101 through 113 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 114 through 120 )	D

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