PDB-7xsb: Crystal structure of SARS-CoV-2 spike receptor binding domain bou...

ID or keywords:

Entry

Database: PDB / ID: 7xsb

Title

Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab

Components

P5S-3B11 Heavy chain
P5S-3B11 Light chain
Spike protein S1

Keywords

VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex

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

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Wang, X. / Wang, Z. / Gao, M.

Funding support

1items

Citation

Journal: Nat.Immunol. / Year: 2023
Title: Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Authors: Ju, B. / Zhang, Q. / Wang, Z. / Aw, Z.Q. / Chen, P. / Zhou, B. / Wang, R. / Ge, X. / Lv, Q. / Cheng, L. / Zhang, R. / Wong, Y.H. / Chen, H. / Wang, H. / Shan, S. / Liao, X. / Shi, X. / Liu, ...

History

Deposition	May 13, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 10, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7xsb.cif.gz	941.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7xsb.ent.gz	787.6 KB	Display	PDB format
PDBx/mmJSON format	7xsb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7xsb_validation.pdf.gz	553.5 KB	Display	wwPDB validaton report
Full document	7xsb_full_validation.pdf.gz	616.3 KB	Display
Data in XML	7xsb_validation.xml.gz	84.5 KB	Display
Data in CIF	7xsb_validation.cif.gz	113.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xs/7xsb ftp://data.pdbj.org/pub/pdb/validation_reports/xs/7xsb	HTTPS FTP

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Related structure data

Related structure data	7xs8C 7xsaC 7xscC 6m0jS S: Starting model for refinement 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	#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) #21 - Sep 2001 Antibodies similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

E: Spike protein S1

A: Spike protein S1

B: Spike protein S1

C: Spike protein S1

H: P5S-3B11 Heavy chain

L: P5S-3B11 Light chain

D: P5S-3B11 Heavy chain

F: P5S-3B11 Light chain

G: P5S-3B11 Heavy chain

I: P5S-3B11 Light chain

J: P5S-3B11 Heavy chain

K: P5S-3B11 Light chain

295 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

E: Spike protein S1

H: P5S-3B11 Heavy chain

L: P5S-3B11 Light chain

defined by author
Evidence: gel filtration
73.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Spike protein S1

G: P5S-3B11 Heavy chain

I: P5S-3B11 Light chain

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

3

B: Spike protein S1

D: P5S-3B11 Heavy chain

F: P5S-3B11 Light chain

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

4

C: Spike protein S1

J: P5S-3B11 Heavy chain

K: P5S-3B11 Light chain

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

Unit cell

Length a, b, c (Å)	127.766, 85.732, 136.623
Angle α, β, γ (deg.)	90.00, 90.39, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Spike protein S1 Mass: 27234.678 Da / Num. of mol.: 4 / Fragment: receptor binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody	P5S-3B11 Heavy chain Mass: 23307.221 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody	P5S-3B11 Light chain Mass: 23186.502 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.79 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.05M Citric acid pH 4.4, 0.05M BIS-TRIS propane, 16% w/v Polyethylene glycol 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.987 Å

Detector

Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 23, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.987 Å / Relative weight: 1

Reflection

Resolution: 3.2→50 Å / Num. obs: 48152 / % possible obs: 98.5 % / Redundancy: 6.4 % / CC_1/2: 0.975 / CC star: 0.994 / R_merge(I) obs: 0.171 / R_pim(I) all: 0.107 / R_rim(I) all: 0.278 / Χ²: 1.025 / Net I/σ(I): 2.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.2-3.27	4.8	1.037	2992	0.639	0.883	0.477	1.147	0.75	92.3
3.27-3.36	5.3	0.915	3165	0.714	0.913	0.413	1.009	0.744	98.2
3.36-3.45	5.9	0.874	3217	0.814	0.947	0.383	0.957	0.784	99.1
3.45-3.55	6.3	0.786	3204	0.842	0.956	0.337	0.857	0.801	99.4
3.55-3.66	6.4	0.65	3214	0.878	0.967	0.274	0.707	0.83	98.9
3.66-3.79	6.1	0.582	3109	0.906	0.975	0.252	0.636	0.849	96.9
3.79-3.95	6.9	0.477	3250	0.951	0.987	0.194	0.515	0.92	99.8
3.95-4.13	7	0.383	3254	0.951	0.987	0.155	0.414	0.984	99.7
4.13-4.34	7	0.302	3213	0.968	0.992	0.122	0.326	1.076	99.3
4.34-4.61	6.9	0.246	3240	0.977	0.994	0.1	0.266	1.209	99.6
4.61-4.97	6.5	0.219	3208	0.977	0.994	0.092	0.238	1.189	98.2
4.97-5.47	7	0.211	3244	0.978	0.995	0.086	0.228	1.145	99.2
5.47-6.26	7	0.196	3251	0.98	0.995	0.079	0.212	1.08	99.4
6.26-7.88	6.5	0.143	3236	0.989	0.997	0.059	0.155	1.103	98
7.88-50	6.6	0.086	3355	0.993	0.998	0.036	0.093	1.635	98.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j

Resolution: 3.2→46.82 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3243	2377	4.95 %
R_work	0.2576	-	-
obs	0.2609	48035	97.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.2→46.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18496	0	0	0	18496

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	19410
X-RAY DIFFRACTION	f_angle_d	1.235	26472
X-RAY DIFFRACTION	f_dihedral_angle_d	16.584	6872
X-RAY DIFFRACTION	f_chiral_restr	0.064	2928
X-RAY DIFFRACTION	f_plane_restr	0.009	3412

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 (%)
3.2-3.27	0.4504	117	0.3666	2390	X-RAY DIFFRACTION	88
3.27-3.34	0.4541	152	0.3499	2625	X-RAY DIFFRACTION	97
3.34-3.42	0.3873	152	0.3403	2700	X-RAY DIFFRACTION	99
3.42-3.5	0.4133	119	0.3213	2681	X-RAY DIFFRACTION	99
3.5-3.6	0.356	126	0.3166	2729	X-RAY DIFFRACTION	99
3.6-3.7	0.3766	145	0.2876	2646	X-RAY DIFFRACTION	98
3.7-3.82	0.325	154	0.2727	2631	X-RAY DIFFRACTION	97
3.82-3.96	0.3017	118	0.2549	2742	X-RAY DIFFRACTION	100
3.96-4.12	0.3465	148	0.2553	2731	X-RAY DIFFRACTION	100
4.12-4.3	0.315	137	0.2359	2713	X-RAY DIFFRACTION	99
4.3-4.53	0.2726	143	0.2127	2717	X-RAY DIFFRACTION	100
4.53-4.81	0.3338	161	0.2128	2701	X-RAY DIFFRACTION	99
4.81-5.19	0.2914	155	0.2327	2661	X-RAY DIFFRACTION	98
5.19-5.71	0.2967	155	0.2295	2742	X-RAY DIFFRACTION	99
5.71-6.53	0.326	144	0.2492	2722	X-RAY DIFFRACTION	99
6.53-8.22	0.2727	111	0.2606	2753	X-RAY DIFFRACTION	98
8.22-46.82	0.2974	140	0.2453	2774	X-RAY DIFFRACTION	97

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	1.4547	0.0785	-0.0139	1.2003	-0.1325	1.1419	0.1701	-0.2837	-0.1865	-0.1661	0.2701	0.2566	0.8061	-0.3109	0.2614	0.6832	-0.0102	-0.0557	0.7099	0.1647	0.4368	23.1976	1.5935	32.0745
2	0.7375	-0.0799	-0.7725	1.0738	0.21	0.9369	-0.4604	0.5053	0.1204	-0.2587	0.6543	0.153	-0.043	-0.0848	0.6262	0.711	-0.1869	0.0126	0.9811	0.0678	0.3799	42.0999	2.2208	-8.9172
3	0.7561	-0.3567	-0.4708	0.6737	0.332	0.8243	-0.1077	-0.4578	0.3434	0.0298	0.1069	-0.0444	-0.0624	-0.0978	0.0019	0.5502	0.019	0.0191	0.9116	0.0021	0.4369	44.0691	1.5439	77.6713
4	0.4825	-0.3794	0.2147	0.9879	-0.8489	1.133	-0.068	-0.0118	0.0613	-0.0087	-0.0511	-0.0606	-0.1689	0.8147	-0.0304	0.5221	-0.0833	0.0514	0.7537	-0.0049	0.3221	49.1543	19.3717	37.3885
5	0.3525	-0.0596	-0.127	0.5899	0.3977	0.3384	-0.0368	-0.0539	0.2389	0.2032	0.2308	-0.1708	0.2252	-0.1355	0.6916	0.4197	-0.1021	-0.0619	0.4086	0.0965	0.4304	6.6945	24.951	9.4603
6	0.0222	-0.0125	0.0927	0.4642	0.5151	0.687	-0.1203	0.2757	-0.1192	0.2669	0.206	0.1726	0.299	-0.2486	0.474	0.2931	0.0265	0.1621	0.6323	0.0756	0.425	12.6768	45.0065	-13.1812
7	0.4494	0.0456	0.4432	0.5927	-0.0409	0.5739	0.3518	0.0099	-0.0534	-0.2196	0.1822	0.0235	0.1987	0.2526	2.7678	0.3339	-0.0567	0.0461	0.2117	0.0235	0.1713	28.7561	22.1407	10.5705
8	0.1208	0.025	-0.1087	0.2406	-0.1782	0.3729	-0.2045	0.3046	0.1548	0.0934	0.3875	0.1003	-0.1126	-0.2939	1.4416	0.3617	0.227	0.1207	-0.1703	0.4921	0.5575	25.2173	55.4215	-9.0424
9	0.337	0.1228	0.4526	0.7555	0.1304	0.6025	0.1747	0.1469	0.4129	-0.0957	0.1276	-0.59	-0.012	0.4665	1.074	0.4203	-0.155	0.1253	0.7505	-0.036	0.498	63.8097	23.6305	99.6255
10	0.725	-0.4373	-0.1941	0.3938	0.1097	0.0539	-0.0039	0.1479	0.4389	-0.2943	0.3062	-0.5405	-0.0521	0.6546	1.0928	0.544	-0.6521	0.3366	1.4811	0.2418	0.1438	60.7224	42.5584	123.8239
11	0.2511	0.1016	0.0456	0.2732	0.0682	0.0057	0.0807	0.0399	0.0819	-0.0809	0.2315	0.1445	-0.1633	-0.1104	1.5771	0.462	-0.1094	0.024	0.4155	0.0807	0.1899	41.3953	22.8582	99.4852
12	-0.0095	0.0611	-0.003	0.1591	0.0753	0.062	0.1874	-0.421	0.4787	-0.2742	0.2527	-0.4454	-0.314	0.4696	1.1416	0.2998	-0.5764	0.381	0.5575	-0.0657	0.5858	49.1552	54.3799	121.7051
13	0.2758	0.0536	-0.443	0.5888	-0.4066	0.8863	-0.8754	0.9566	0.1048	-0.349	0.3714	-0.3948	-0.1293	0.6049	-0.447	0.7064	-0.3805	-0.0106	0.7447	0.0181	0.5191	15.8199	-8.6242	-32.0829
14	-0.0347	0.0088	0.0403	0.27	0.3385	0.4169	-0.03	0.1611	-0.0634	0.2238	-0.3516	0.2423	0.2238	-0.2316	-0.1267	0.8069	0.3074	-0.4872	0.4531	-0.0585	2.1226	-19.4045	9.3383	-38.3243
15	0.6241	0.1955	-0.0598	0.2904	-0.3579	1.1651	0.0035	-0.2813	0.216	0.1178	0.2283	0.3122	-0.781	-0.7439	0.3635	1.4541	-0.3656	-0.4934	0.8748	0.6025	0.5874	20.2328	13.1731	-29.5073
16	0.4129	-0.2013	-0.0416	0.3049	-0.0214	0.0692	-0.4037	0.1977	0.3062	0.2592	0.1271	0.4041	0.1624	0.0826	-0.176	2.0858	-0.1716	-0.5187	0.6796	-0.059	1.5489	-11.5691	15.541	-24.98
17	0.32	0.4454	0.0889	1.6326	-0.4502	0.769	-0.1577	-0.3349	0.3764	0.2796	0.284	0.5604	-0.8925	0.2786	0.2197	0.7525	0.0763	-0.0682	0.3566	-0.1077	0.1799	35.4918	43.3214	61.8587
18	0.0023	-0.0291	0.0637	0.0798	-0.2559	1.1073	-0.5103	-0.1593	0.114	0.2012	-0.2257	0.491	-0.935	-0.4209	-0.2117	1.4912	0.5725	-0.0721	0.8321	-0.249	2.0766	-2.4164	43.5778	73.264
19	0.4066	-0.1585	0.0559	0.3573	-0.0183	0.0295	-0.0383	0.2341	-0.0922	-0.0753	0.4084	0.2062	-0.3231	-0.0834	2.1425	0.3695	0.0244	0.1481	0.5093	0.0567	0.1935	29.2424	21.7883	60.8134
20	0.1	0.011	0.0825	0.0471	0.0553	0.0462	-0.3844	0.1454	-0.208	-0.8115	0.1671	0.2019	-0.866	-0.1281	-0.0014	1.5924	0.0809	-0.3559	1.3505	0.2339	1.4642	0.2527	33.9051	59.8224

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain E
2	X-RAY DIFFRACTION	2	chain A
3	X-RAY DIFFRACTION	3	chain B
4	X-RAY DIFFRACTION	4	chain C
5	X-RAY DIFFRACTION	5	chain H and resid 1:117
6	X-RAY DIFFRACTION	6	chain H and resid 121:217
7	X-RAY DIFFRACTION	7	chain L and resid 2:110
8	X-RAY DIFFRACTION	8	chain L and resid 115:213
9	X-RAY DIFFRACTION	9	chain D and resid 1:117
10	X-RAY DIFFRACTION	10	chain D and resid 121:217
11	X-RAY DIFFRACTION	11	chain F and resid 2:110
12	X-RAY DIFFRACTION	12	chain F and resid 115:213
13	X-RAY DIFFRACTION	13	chain G and resid 1:117
14	X-RAY DIFFRACTION	14	chain G and resid 121:217
15	X-RAY DIFFRACTION	15	chain I and resid 2:110
16	X-RAY DIFFRACTION	16	chain I and resid 115:213
17	X-RAY DIFFRACTION	17	chain J and resid 1:117
18	X-RAY DIFFRACTION	18	chain J and resid 121:216
19	X-RAY DIFFRACTION	19	chain K and resid 2:110
20	X-RAY DIFFRACTION	20	chain K and resid 115:213

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