PDB-7nkt: RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226

ID or keywords:

Entry

Database: PDB / ID: 7nkt

Title

RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226

Components

Spike protein S1
neutralizing nanobody NM1226

Keywords

VIRAL PROTEIN / RBD /

SARS-CoV2 / neutralizing nanobody /

complex / NM1226

Function / homology

Function and homology information

Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...
Similarity search - Function

Biological species

Severe acute respiratory syndrome coronavirus 2

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Ostertag, E. / Zocher, G. / Stehle, T.

Citation

Journal: Embo Rep. / Year: 2021
Title: NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies.
Authors: Wagner, T.R. / Ostertag, E. / Kaiser, P.D. / Gramlich, M. / Ruetalo, N. / Junker, D. / Haering, J. / Traenkle, B. / Becker, M. / Dulovic, A. / Schweizer, H. / Nueske, S. / Scholz, A. / Zeck, ...

History

Deposition	Feb 18, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 12, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 19, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Jan 31, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7nkt.cif.gz	142.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7nkt.ent.gz		Display	PDB format
PDBx/mmJSON format	7nkt.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/nk/7nkt ftp://data.pdbj.org/pub/pdb/validation_reports/nk/7nkt	HTTPS FTP

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Related structure data

Related structure data	7b27C 6xc4S 6z1zS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4uy2-2 5h4s-d 5h7n-1 6eev-d 4uy2-1 3tgx-3 3afg-1 6eeu-d 3tgx-8 5a7y-1 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	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (2) #264 - Dec 2021 SARS-CoV-2 Spike Variants similarity (1) #246 - Jun 2020 SARS-CoV-2 Spike similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

AAA: Spike protein S1

BBB: neutralizing nanobody NM1226

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	128.093, 128.093, 77.676
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	80
Space group name H-M	I4₁

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Protein / Antibody / Sugars , 3 types, 3 molecules AAABBB

#1: Protein

Spike protein S1

Mass: 25951.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): Expi293F GnTI- / Production host:

Homo sapiens (human) / References: UniProt: P0DTC2

#2: Antibody

neutralizing nanobody NM1226

Mass: 15960.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vicugna pacos (alpaca) / Production host:

Escherichia coli (E. coli)

#3: 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 , 3 types, 141 molecules

#4: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.8 Å³/Da / Density % sol: 67.64 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 50mM K2HPO4, 20% (w/v) PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2020
Radiation	Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2.297→46.103 Å / Num. obs: 28115 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC_1/2: 0.999 / Net I/σ(I): 19.5
Reflection shell	Resolution: 2.297→2.44 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4500 / CC_1/2: 0.484 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6Z1Z, 6XC4

6z1z

6xc4

Resolution: 2.3→46.103 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.946 / SU B: 12.113 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2239	1687	6 %
R_work	0.1843	26428	-
all	0.187	-	-
obs	-	28115	99.908 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 59.942 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.682 Å²	-0 Å²	-0 Å²
2-	-	0.682 Å²	-0 Å²
3-	-	-	-1.364 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→46.103 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2503	0	40	137	2680

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	2629
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2286
X-RAY DIFFRACTION	r_angle_refined_deg	1.463	1.656	3570
X-RAY DIFFRACTION	r_angle_other_deg	1.262	1.578	5306
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.715	5	323
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.612	21.986	141
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.138	15	384
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.526	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	324
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2994
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	608
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	411
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	2123
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1232
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1246
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	136
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.223	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.207	0.2	21
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.142	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	3.653	7.343	1288
X-RAY DIFFRACTION	r_mcbond_other	3.64	7.342	1287
X-RAY DIFFRACTION	r_mcangle_it	5.262	9.601	1608
X-RAY DIFFRACTION	r_mcangle_other	5.264	9.603	1609
X-RAY DIFFRACTION	r_scbond_it	3.99	8.056	1341
X-RAY DIFFRACTION	r_scbond_other	3.87	8.038	1338
X-RAY DIFFRACTION	r_scangle_it	5.482	10.305	1961
X-RAY DIFFRACTION	r_scangle_other	5.426	10.281	1956
X-RAY DIFFRACTION	r_lrange_it	8.57	43.873	2812
X-RAY DIFFRACTION	r_lrange_other	8.578	43.61	2793

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
2.297-2.357	0.415	122	0.415	1922	0.415	2063	0.564	0.542	99.079	0.408
2.357-2.421	0.361	122	0.35	1902	0.351	2024	0.717	0.736	100	0.333
2.421-2.491	0.375	116	0.303	1825	0.307	1941	0.823	0.833	100	0.274
2.491-2.567	0.298	114	0.26	1780	0.263	1894	0.884	0.873	100	0.222
2.567-2.651	0.224	111	0.23	1744	0.229	1855	0.895	0.904	100	0.193
2.651-2.744	0.26	107	0.214	1676	0.216	1784	0.899	0.921	99.9439	0.174
2.744-2.847	0.232	103	0.198	1616	0.2	1719	0.921	0.926	100	0.163
2.847-2.963	0.253	100	0.195	1559	0.199	1660	0.921	0.928	99.9398	0.161
2.963-3.094	0.211	96	0.187	1503	0.188	1599	0.938	0.943	100	0.157
3.094-3.245	0.258	91	0.186	1429	0.19	1520	0.927	0.948	100	0.164
3.245-3.419	0.217	87	0.193	1371	0.194	1458	0.951	0.953	100	0.177
3.419-3.625	0.238	83	0.193	1294	0.195	1377	0.932	0.951	100	0.178
3.625-3.874	0.213	77	0.179	1208	0.181	1286	0.943	0.956	99.9222	0.165
3.874-4.182	0.19	73	0.149	1136	0.151	1209	0.954	0.964	100	0.137
4.182-4.577	0.153	67	0.127	1062	0.129	1129	0.968	0.975	100	0.12
4.577-5.111	0.183	60	0.13	933	0.133	993	0.967	0.975	100	0.127
5.111-5.89	0.215	54	0.161	847	0.164	901	0.946	0.966	100	0.153
5.89-7.184	0.246	46	0.18	719	0.184	765	0.936	0.956	100	0.176
7.184-10.039	0.212	36	0.152	565	0.155	601	0.945	0.966	100	0.161
10.039-46.103	0.197	22	0.213	337	0.212	360	0.953	0.942	99.7222	0.22

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	1.5262	2.9238	-4.7456	16.6277	-11.5694	18.2101	0.1191	0.0135	-0.278	0.3179	0.0662	-0.373	-0.1528	-0.2562	-0.1854	0.4335	0.043	-0.0576	0.4185	0.0203	0.461	24.7403	-8.044	40.7998
2	4.2219	-3.7277	-0.8394	10.608	1.2311	4.5501	-0.0464	-0.6413	0.6095	0.5957	0.0648	-0.3732	-0.6014	0.5923	-0.0184	0.1393	-0.0965	-0.0064	0.4361	-0.0514	0.1008	23.9572	-14.8402	21.3555
3	6.9856	-1.0741	-0.4644	2.4046	-1.1267	0.9887	-0.2849	-1.4964	-0.1441	0.7676	0.2626	-0.0037	-0.2944	0.4509	0.0223	0.3633	0.1163	0.0487	0.7664	0.0231	0.1247	13.7579	-15.415	32.6247
4	1.9108	-1.8625	-2.2153	6.677	-1.8632	5.9312	0.0973	0.0693	-0.284	-0.2742	0.1147	0.9369	0.0086	-0.1752	-0.212	0.0322	-0.0044	-0.029	0.2111	0.0777	0.1565	12.8601	-22.6064	16.0379
5	3.6899	-1.2248	-2.4261	3.986	0.5622	3.1607	-0.0179	-0.181	-0.2505	-0.2997	0.0782	0.1789	0.0846	0.1419	-0.0603	0.0345	-0.0323	-0.0232	0.1668	0.0517	0.0612	20.0492	-24.4321	11.5165
6	12.0814	-9.978	7.4581	10.3439	-8.1377	7.5142	0.4075	0.2237	-0.4344	-0.0487	-0.3395	0.3838	0.1348	0.5722	-0.068	0.333	-0.0388	0.0094	0.3606	0.0246	0.3568	-8.7025	-23.0787	21.386
7	0.0357	0.1838	0.3533	10.6456	0.2039	3.9138	0.0158	-0.0421	-0.0052	-0.802	-0.2325	-0.364	0.1613	-0.3335	0.2167	0.2189	-0.0498	-0.0145	0.4439	0.0738	0.5037	-25.3223	-8.7817	11.4117
8	6.8955	-1.6268	2.5108	3.0393	-1.9169	7.3259	-0.0162	-0.3073	-0.6898	-0.2387	0.1384	0.828	0.6238	-0.4557	-0.1222	0.2498	-0.0648	-0.0174	0.1856	0.0451	0.4722	-10.6009	-14.8753	19.0229
9	4.3288	2.5009	0.6741	2.4838	3.4791	9.4146	-0.3539	0.5706	-0.1705	-0.2859	0.1752	-0.0233	-0.2466	-0.1779	0.1787	0.3655	0.0213	0.0191	0.4057	-0.046	0.4025	-7.7277	-11.7587	2.9823
10	4.8472	-2.9861	1.8932	3.3067	-0.9542	3.3453	-0.0415	-0.3161	-0.4977	-0.2156	0.0463	0.6933	0.0922	-0.3661	-0.0048	0.1423	-0.0537	-0.0078	0.1896	0.0375	0.3242	-9.336	-7.9494	18.4019
11	12.0046	1.5633	3.4826	1.6903	-1.302	7.6274	0.0733	-0.3773	-1.4718	-0.376	0.1285	0.4084	0.5417	-0.5917	-0.2018	0.3254	-0.0735	-0.1231	0.202	-0.0554	0.7015	-11.249	-16.0966	11.9725

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	332 - 335
2	X-RAY DIFFRACTION	2	ALL	AAA	336 - 356
3	X-RAY DIFFRACTION	3	ALL	AAA	357 - 396
4	X-RAY DIFFRACTION	4	ALL	AAA	397 - 415
5	X-RAY DIFFRACTION	5	ALL	AAA	416 - 518
6	X-RAY DIFFRACTION	6	ALL	BBB	1 - 6
7	X-RAY DIFFRACTION	7	ALL	BBB	7 - 17
8	X-RAY DIFFRACTION	8	ALL	BBB	18 - 40
9	X-RAY DIFFRACTION	9	ALL	BBB	41 - 45
10	X-RAY DIFFRACTION	10	ALL	BBB	46 - 109
11	X-RAY DIFFRACTION	11	ALL	BBB	110 - 125

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