PDB-8owv: H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD

ID or keywords:

Entry

Database: PDB / ID: 8owv

Title

H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD

Components

F2
H6
Spike glycoproteinSpike protein

Keywords

VIRAL PROTEIN /

Nanobody /

Complex /

Receptor binding domain /

SARS-CoV-2

Function / homology

Function and homology information

endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane /

viral envelope / host cell plasma membrane / virion membrane /

membrane
Similarity search - Function

Biological species

Severe acute respiratory syndrome coronavirus 2

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Mikolajek, H. / Naismith, J.H. / Owens, R.J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Trimeric nanobodies potently neutralize Omicron variants of SARS-CoV-2
Authors: Cornish, K.A.S. / Mikolajek, H. / Naismith, J.H. / Owens, R.J.

History

Deposition	Apr 28, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8owv.cif.gz	188.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8owv.ent.gz		Display	PDB format
PDBx/mmJSON format	8owv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ow/8owv ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8owv	HTTPS FTP

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Related structure data

Related structure data	17296C 8owtC 8oyuC C: citing same article (ref.)
Similar structure data	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)

Deposited unit

EEE: Spike glycoprotein

BBB: F2

FFF: H6

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.775, 59.438, 145.624
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Antibody , 2 types, 2 molecules BBBFFF

#2: Antibody	F2 Mass: 14962.622 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody	H6 Mass: 14588.144 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Protein / Sugars , 2 types, 2 molecules EEE

#1: Protein

Spike glycoprotein /

Spike protein

Mass: 23638.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Severe acute respiratory syndrome coronavirus 2
Production host:

Homo sapiens (human) / References: UniProt: A0A8A5XRG7

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 2 types, 219 molecules

#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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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: 47.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 10, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.73→59.52 Å / Num. obs: 53452 / % possible obs: 100 % / Redundancy: 12.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.105 / R_pim(I) all: 0.031 / Net I/σ(I): 11.5
Reflection shell	Resolution: 1.73→1.76 Å / Num. unique obs: 2634 / CC_1/2: 0.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
DIALS		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→59.438 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.954 / SU B: 7.878 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2234	2623	4.927 %
R_work	0.1972	50615	-
all	0.199	-	-
obs	-	53238	99.979 %

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 38.513 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.963 Å²	-0 Å²	0 Å²
2-	-	-0.016 Å²	-0 Å²
3-	-	-	-0.948 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→59.438 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3512	0	32	216	3760

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	3669
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	3289
X-RAY DIFFRACTION	r_angle_refined_deg	1.403	1.656	4999
X-RAY DIFFRACTION	r_angle_other_deg	1.263	1.581	7563
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.303	5	458
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.388	21.487	195
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.143	15	547
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.145	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	465
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4240
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	940
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	559
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.177	0.2	3098
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1768
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	1742
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	203
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.128	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.169	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.18	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	1.007	1.379	1805
X-RAY DIFFRACTION	r_mcbond_other	1.006	1.378	1804
X-RAY DIFFRACTION	r_mcangle_it	1.582	2.06	2254
X-RAY DIFFRACTION	r_mcangle_other	1.581	2.06	2255
X-RAY DIFFRACTION	r_scbond_it	1.715	1.594	1864
X-RAY DIFFRACTION	r_scbond_other	1.716	1.596	1865
X-RAY DIFFRACTION	r_scangle_it	2.525	2.307	2739
X-RAY DIFFRACTION	r_scangle_other	2.524	2.31	2740
X-RAY DIFFRACTION	r_lrange_it	5.461	16.552	3977
X-RAY DIFFRACTION	r_lrange_other	5.461	16.569	3978

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.73-1.775	0.435	157	0.427	3700	0.428	3865	0.485	0.507	99.793	0.422
1.775-1.823	0.386	193	0.38	3606	0.381	3800	0.562	0.527	99.9737	0.377
1.823-1.876	0.321	182	0.313	3490	0.313	3672	0.755	0.752	100	0.303
1.876-1.934	0.279	173	0.266	3422	0.267	3595	0.801	0.829	100	0.253
1.934-1.997	0.253	170	0.239	3277	0.24	3447	0.893	0.877	100	0.217
1.997-2.067	0.253	173	0.214	3213	0.216	3386	0.905	0.909	100	0.19
2.067-2.145	0.233	139	0.205	3086	0.206	3225	0.913	0.917	100	0.18
2.145-2.233	0.214	171	0.19	2956	0.191	3127	0.931	0.938	100	0.163
2.233-2.332	0.222	123	0.192	2875	0.193	2998	0.936	0.935	100	0.163
2.332-2.446	0.24	151	0.199	2733	0.201	2884	0.925	0.937	100	0.165
2.446-2.578	0.26	126	0.196	2622	0.199	2748	0.91	0.936	100	0.163
2.578-2.734	0.212	153	0.188	2447	0.189	2600	0.938	0.948	100	0.157
2.734-2.922	0.2	141	0.19	2315	0.191	2456	0.949	0.952	100	0.16
2.922-3.155	0.24	120	0.193	2184	0.195	2304	0.935	0.946	100	0.169
3.155-3.456	0.284	90	0.193	2033	0.196	2123	0.921	0.946	100	0.174
3.456-3.862	0.212	107	0.188	1817	0.189	1924	0.95	0.957	100	0.171
3.862-4.456	0.187	92	0.15	1628	0.152	1720	0.968	0.974	100	0.141
4.456-5.45	0.159	78	0.145	1398	0.146	1476	0.973	0.977	100	0.14
5.45-7.675	0.233	43	0.189	1127	0.19	1170	0.959	0.967	100	0.176
7.675-59.438	0.128	39	0.186	667	0.183	706	0.984	0.971	100	0.182

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	6.0941	3.1142	-2.0147	4.432	-0.8029	2.1494	-0.1107	-0.6775	-0.2847	0.1657	-0.0853	-0.4361	0.448	0.8179	0.196	0.2987	0.1456	0.0012	0.3531	0.0482	0.34	53.639	-3.759	-41.207
2	6.8336	1.1889	3.0734	11.0137	5.5001	4.6669	-0.2391	-0.2811	0.5896	0.0772	0.2893	-0.0873	-0.2331	0.2314	-0.0502	0.3661	-0.0644	0.0466	0.2388	-0.0728	0.4432	51.946	12.333	-39.035
3	6.2869	2.7501	-1.0865	3.7692	0.0327	2.0239	-0.1155	0.7466	0.4223	-0.2248	0.1179	0.2067	0.0068	-0.0355	-0.0025	0.2025	-0.014	0.0304	0.1281	0.0291	0.2593	45.248	2.164	-49.55
4	4.7854	-0.0506	-1.8542	1.02	0.4495	2.7933	-0.064	-0.1049	0.1011	-0.0319	0.0828	-0.3474	0.0967	0.5035	-0.0188	0.1977	0.0044	-0.004	0.1246	-0.0095	0.2646	50.415	2.102	-43.045
5	2.507	-0.5771	1.8452	2.4628	-2.3599	6.229	-0.0085	0.1175	-0.0469	0.0178	-0.0303	0.5123	0.1367	-0.6813	0.0388	0.2264	-0.0283	0.0498	0.2087	-0.066	0.312	15.302	0.616	-34.544
6	0.8691	0.0458	0.549	2.7535	0.7243	2.0508	-0.01	0.015	0.0115	0.1671	-0.0326	0.1194	0.0256	-0.1115	0.0426	0.2316	-0.0071	0.0197	0.0102	0.0102	0.1438	26.571	0.617	-32.2
7	1.3595	0.1296	-0.6354	1.5866	-0.0242	5.2373	-0.0394	-0.299	-0.1085	0.7688	-0.0255	0.2452	0.3937	-0.2642	0.0649	0.6662	-0.0403	0.1041	0.1097	0.0474	0.1959	23.531	-8.012	-9.143
8	0.6916	0.192	0.2054	3.6709	0.9278	1.4772	-0.0321	-0.0223	-0.0316	0.2076	0.0131	0.104	-0.024	-0.0519	0.019	0.1597	0.0134	0.033	0.0219	0.0124	0.1623	24.362	0.854	-30.798
9	3.155	1.2981	1.801	4.886	1.8021	2.1856	0.0939	-0.5757	-0.0071	0.2465	-0.0048	-0.1632	0.1268	-0.0363	-0.0891	0.708	0.0324	-0.0763	0.2943	0.0051	0.1745	47.149	-1.589	0.65
10	4.7365	3.9982	-1.5517	6.7137	3.6072	8.8247	0.1436	-0.379	0.4379	0.0897	-0.048	0.0497	0.0777	-0.1449	-0.0955	0.4383	0.0172	0.0021	0.649	-0.1987	0.4986	38.538	9.412	7.446
11	2.0056	0.7378	1.5413	0.6945	0.8653	2.4557	0.0266	-0.223	0.1711	0.4185	0.0206	-0.0934	0.0898	0.1522	-0.0472	0.7839	0.0468	-0.1101	0.1503	-0.02	0.2102	44.254	2.374	-4.122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Selection details
1	X-RAY DIFFRACTION	1	ALL	{ BBB\|3-38 }
2	X-RAY DIFFRACTION	2	ALL	{ BBB\|39-48 }
3	X-RAY DIFFRACTION	3	ALL	{ BBB\|49-71 }
4	X-RAY DIFFRACTION	4	ALL	{ BBB\|72-127 }
5	X-RAY DIFFRACTION	5	ALL	{ EEE\|331-357 }
6	X-RAY DIFFRACTION	6	ALL	{ EEE\|358-452 }
7	X-RAY DIFFRACTION	7	ALL	{ EEE\|453-491 }
8	X-RAY DIFFRACTION	8	ALL	{ EEE\|491-528 }
9	X-RAY DIFFRACTION	9	ALL	{ FFF\|2-42 }
10	X-RAY DIFFRACTION	10	ALL	{ FFF\|43-47 }
11	X-RAY DIFFRACTION	11	ALL	{ FFF\|48-127 }

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