PDB-8qh0: Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194

ID or keywords:

Entry

Database: PDB / ID: 8qh0

Title

Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194

Components

Cv2.3194 Heavy chain
IGK@ protein
Spike protein S1

Keywords

VIRAL PROTEIN / Coronavirus Neutralizing Antibody

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

Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...
Similarity search - Domain/homology

Biological species

Severe acute respiratory syndrome coronavirus 2

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Fernandez, I. / Rey, F.A.

Funding support

1items

Citation

Journal: To Be Published
Title: A broadly neutralizing antibody against SARS-CoV-2 Omicron variants
Authors: Planchais, C. / Fernandez, I. / Rey, F.A. / Mouquet, H.

History

Deposition	Sep 6, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qh0.cif.gz	314.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8qh0.ent.gz	209.9 KB	Display	PDB format
PDBx/mmJSON format	8qh0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qh0_validation.pdf.gz	824.3 KB	Display	wwPDB validaton report
Full document	8qh0_full_validation.pdf.gz	827.2 KB	Display
Data in XML	8qh0_validation.xml.gz	26.9 KB	Display
Data in CIF	8qh0_validation.cif.gz	39.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qh/8qh0 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/8qh0	HTTPS FTP

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Related structure data

Related structure data	18399C 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) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #21 - Sep 2001 Antibodies similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1)

Deposited unit

A: Spike protein S1

H: Cv2.3194 Heavy chain

L: IGK@ protein

hetero molecules

71 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)	54.388, 89.186, 174.471
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 2 types, 2 molecules AL

#1: Protein	Spike protein S1 Mass: 23068.695 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): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P0DTC2
#3: Protein	IGK@ protein Mass: 22821.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGK@ / Production host: Homo sapiens (human) / References: UniProt: Q6PJF2

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Antibody / Sugars , 2 types, 2 molecules H

#2: Antibody

Cv2.3194 Heavy chain

Mass: 24379.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): FreeStyle293 / Production host:

Homo sapiens (human)

#4: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

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Non-polymers , 3 types, 387 molecules

#5: Chemical	ChemComp-PRO / PROLINE Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₉NO₂
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 384 / 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: 3.01 Å³/Da / Density % sol: 59.15 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350, 0.2 M lithium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9198 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9198 Å / Relative weight: 1
Reflection	Resolution: 1.87→43.2 Å / Num. obs: 70747 / % possible obs: 99.5 % / Redundancy: 13.2 % / B_iso Wilson estimate: 37.05 Å² / CC_1/2: 0.999 / Net I/σ(I): 13.2
Reflection shell	Resolution: 1.87→1.94 Å / R_merge(I) obs: 1.5 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 6950 / CC_1/2: 0.613 / R_pim(I) all: 0.681 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.87→43.2 Å / SU ML: 0.2985 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2091	3401	4.81 %
R_work	0.1849	67346	-
obs	0.1861	70747	99.45 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 44.12 Å²

Refinement step

Cycle: LAST / Resolution: 1.87→43.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4723	0	47	384	5154

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	4880
X-RAY DIFFRACTION	f_angle_d	0.8139	6633
X-RAY DIFFRACTION	f_chiral_restr	0.0545	742
X-RAY DIFFRACTION	f_plane_restr	0.0061	851
X-RAY DIFFRACTION	f_dihedral_angle_d	11.9612	1740

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 (%)
1.87-1.9	0.5729	136	0.4812	2659	X-RAY DIFFRACTION	96.61
1.9-1.92	0.4421	140	0.4205	2759	X-RAY DIFFRACTION	99.21
1.92-1.95	0.3458	132	0.3486	2750	X-RAY DIFFRACTION	98.94
1.95-1.99	0.3821	136	0.3076	2768	X-RAY DIFFRACTION	99.15
1.99-2.02	0.3078	159	0.2689	2770	X-RAY DIFFRACTION	99.32
2.02-2.06	0.2634	145	0.2361	2758	X-RAY DIFFRACTION	99.45
2.06-2.1	0.2649	142	0.2303	2788	X-RAY DIFFRACTION	99.09
2.1-2.14	0.2475	153	0.2175	2724	X-RAY DIFFRACTION	99.28
2.14-2.19	0.2745	133	0.2331	2799	X-RAY DIFFRACTION	99.36
2.19-2.24	0.2766	133	0.2407	2782	X-RAY DIFFRACTION	99.35
2.24-2.29	0.2921	140	0.2065	2779	X-RAY DIFFRACTION	99.83
2.29-2.36	0.2674	138	0.191	2799	X-RAY DIFFRACTION	99.73
2.36-2.42	0.245	159	0.1924	2800	X-RAY DIFFRACTION	99.87
2.42-2.5	0.2417	142	0.1867	2785	X-RAY DIFFRACTION	99.69
2.5-2.59	0.2138	124	0.1827	2822	X-RAY DIFFRACTION	99.97
2.59-2.7	0.2191	124	0.1918	2840	X-RAY DIFFRACTION	99.9
2.7-2.82	0.2384	148	0.1895	2815	X-RAY DIFFRACTION	99.93
2.82-2.97	0.2257	133	0.1855	2813	X-RAY DIFFRACTION	99.86
2.97-3.15	0.1828	136	0.1786	2849	X-RAY DIFFRACTION	99.97
3.15-3.4	0.1945	145	0.1718	2854	X-RAY DIFFRACTION	99.93
3.4-3.74	0.1774	150	0.1676	2841	X-RAY DIFFRACTION	99.87
3.74-4.28	0.1586	155	0.1492	2849	X-RAY DIFFRACTION	99.6
4.28-5.39	0.1504	136	0.1425	2917	X-RAY DIFFRACTION	99.8
5.39-43.2	0.1982	162	0.182	3026	X-RAY DIFFRACTION	99.1

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	1.99965033585	0.275378204522	0.644676636815	0.997966687422	-0.180103671292	2.40482323405	0.244318421857	0.00511718683238	0.234769638267	0.119745556731	-0.0583469820407	0.0354193483281	-0.0169559070618	0.048860594014	-0.133174668307	0.33564376498	-0.0305522631436	-0.0151232950573	0.298963442583	-0.000760151430098	0.302774748397	20.327	-4.481	72.518
2	2.63733993668	-0.506625880987	2.43368856075	0.106910161264	-0.4967746931	2.30066865263	-0.150162103938	-0.0566730174621	0.467317790842	0.100150193118	0.0386807160654	0.0289235075714	-0.0850573326537	0.00792445527265	0.149058396481	0.470804050558	0.00970614577662	-0.0292312723821	0.365473050151	-0.0259521199826	0.477528433371	19.996	1.462	81.415
3	4.52489426043	-5.35435759799	2.00487613937	8.21282256616	-0.906480333242	5.34939669605	-0.827369859458	-1.58302786028	-0.0330910064105	1.56882017488	0.677245779837	-0.1163689461	-0.119090918642	-0.635820860528	0.18538287734	0.58123384327	-0.0355906185736	0.000505548595869	0.511565125178	-0.00713281054342	0.364554085075	18.934	-2.912	85.474
4	2.388129257	-0.318597863257	0.382994092403	2.44603577911	0.39171839412	3.01574511019	-0.157366493322	0.914553218146	-0.253652375287	-0.161807285959	-0.157327907065	-0.167659906148	0.205411988839	1.04037428625	0.171652409125	0.336501128637	0.0569677270357	0.0311119894015	0.596435443628	0.0890926815228	0.317900647229	22.314	-3.55	42.126
5	5.89838484092	1.04818186959	1.52174488242	4.03914489216	1.52617070259	4.62085943952	-0.0593923732893	1.15271234232	-0.148041209695	-0.648216070913	-0.101888445861	0.209730840486	0.00997322804759	0.521430633816	0.229461678839	0.367949864519	0.0299681369814	0.00448881104556	0.60426983221	0.0574197825204	0.329397088944	12.833	-0.65	35.535
6	3.48655216902	-0.352009206421	-1.14003459487	2.41774783766	-2.33233647413	2.88833951763	0.0345630163716	0.558622940465	0.307345885832	-0.0696742918958	-0.225686697844	-0.192012975536	-0.145506663139	0.511209678668	0.179680622832	0.301962265022	-0.0408298934044	-0.00382033025382	0.542115631246	0.106889374148	0.382288260863	17.185	6.913	38.444
7	2.47103069123	-0.905911025031	1.57402110952	1.26357379271	-1.0020745501	1.53033568966	-0.00353652708762	0.631079122811	0.245836090064	-0.00483135522615	-0.142855564655	-0.126609706008	-0.154062210288	0.503150552477	0.145843282004	0.311671394607	-0.0365376868771	0.0180327872158	0.505801294136	0.0523752360041	0.331396772381	22.021	0.063	47.124
8	2.36187101447	1.00081804249	-0.639231520375	2.8637404983	-1.26203038022	1.71810377756	0.00759099421359	-0.0147300780984	-0.080164029592	0.0975150457837	0.078066601406	0.0200319202442	0.00348878230442	0.105393519404	-0.0887441658686	0.265957196894	-0.00693350851916	-0.0299949598355	0.318767593329	0.0207980416631	0.306251798276	20.982	-16.698	70.501
9	2.9752593003	0.918390140382	-1.79527518474	3.84402492995	-2.05769967379	3.11508036291	-0.0734884441071	-0.0326291177081	-0.246910630841	0.169390917111	0.00921035040416	-0.201793269878	0.173361653032	0.108323280471	0.0318351264378	0.320829019593	-0.0505084283601	-0.0670183477457	0.30547356973	-0.0175846438794	0.242739100454	24.267	-17.4	70.143
10	5.65093774335	1.6600744176	1.78860013718	2.20178106348	1.52056192736	4.25156662638	0.0573760057029	0.29528316668	-0.428446717817	-0.0614772643284	-0.146891138446	0.247056947309	0.52406290957	-0.275758051997	0.0516396738687	0.397656366022	-0.013164080464	-0.0264447339028	0.28365341287	-0.0296789272954	0.363723741403	-19.257	-2.074	10.773
11	1.46003023692	0.659361769951	1.0254781274	2.47985702392	1.33653722837	3.23093206564	0.0538379720045	0.0671745845636	0.00267919163887	0.093883389692	-0.0902433157794	0.0133496001264	0.120376650063	-0.0147877201443	0.0257347648341	0.315123783184	0.0105672756383	-0.0191234753905	0.267865054907	0.0354063781476	0.292928078161	-8.89	6.641	22.805
12	8.68535693967	-4.63498355201	2.00002959038	4.23390375828	2.00003318901	1.99998590265	-0.678400940659	7.06149181687	5.80056992491	-0.133123139088	0.249418187564	-7.66710825743	-2.29074395733	5.82681333209	0.403801755508	0.939963593023	-0.375925489999	-0.0551657048859	0.692432240346	0.0570119879306	1.54005738365	-29.399	-8.293	2.829
13	2.60364103707	-0.950596007592	0.69832157138	4.38748787486	-1.35747533047	5.41838712053	0.110257500368	-0.703467165317	0.158015441451	0.759171095743	-0.306451410957	-0.131963118978	-0.670253528676	0.234447190538	0.187171183187	0.277573540182	0.0352047952227	-0.0465584306218	0.336283768287	-0.0573049116226	0.225872532483	-1.987	8.641	58.276
14	0.501019433781	-0.0750272450416	0.869703884312	1.84299269362	-1.79435166915	3.65239600307	-0.0281628522184	-0.112144714292	0.165757561404	0.205473098275	-0.0118706553134	0.191377028799	-0.496932257876	-0.108114456795	0.0579475718828	0.34093845829	-0.0196691875692	-0.00459915469871	0.304700372357	0.00841706066689	0.349890360785	-2.73	11.448	48.045
15	4.74661959545	-0.212903589828	0.467274249165	0.802109229338	1.02379115031	1.42492102942	0.00335406391731	-0.563898182742	-0.674146200666	-0.0647895397264	0.211804863056	0.124192999209	0.358632009183	-0.0778982810142	-0.209399454214	0.331895530788	-0.00345988520551	0.0284964060682	0.319050061908	0.0533666882252	0.316189366497	1.658	-0.14	48.382
16	1.16302152806	-0.353431461529	1.42515384905	1.12530899344	-2.28424563468	5.12806826173	0.093792242407	-0.036895404599	-0.152437382312	-0.158080368828	0.0240108178162	0.098250814232	0.371962741541	-0.24590921567	-0.0699882204934	0.323301088412	-0.0320299820968	0.0284224655885	0.264031051148	0.0165828853189	0.327810642623	-8.557	2.79	41.902
17	2.10136659146	0.771873312622	0.140847400061	5.8532951834	-1.70963288197	3.80752974169	-0.0287661092023	-0.118459753087	0.120175152273	-0.0368664009275	0.0580856912998	0.284040598061	-0.308733746979	-0.307964722796	-0.0341647011404	0.314718976639	0.0129572118269	0.00880926075014	0.337298375681	0.00252001092285	0.331089488692	-9.549	9.433	50.302
18	1.63761018783	-0.605752308034	-0.257643022114	0.66389334517	-1.03931810863	3.20307460897	-0.0223017625127	-0.0259093188608	0.0949876251678	-0.0948076806629	-0.0655538627578	-0.024704625811	-0.00629101208778	0.122531162257	0.120084323298	0.309223485515	-0.0308668544853	-0.0237851199223	0.247720950401	0.0135286450326	0.29443370756	1.267	5.398	49.61
19	3.38168693497	1.25393561771	0.779962148519	1.28670786532	-0.128103553052	4.02742456924	0.0908341874577	-0.652275569123	-0.38916505029	0.0353846806755	0.150864735086	-0.0164081992168	0.125165767048	-0.313239146157	-0.230635199549	0.299800941963	-0.027835762281	0.0218584875794	0.201319423524	0.00161708385894	0.257523101889	12.434	-7.166	76.872
20	2.85395158583	0.215449319343	0.977026138695	1.13619675451	-0.26497976235	2.03464199704	-0.139441057125	0.108584355303	0.0955360072823	0.147361572497	0.174785163409	0.058230461743	-0.015033565398	-0.11318807076	-0.102618087261	0.364375946924	-0.0270349115034	-0.0215015907896	0.341934064182	0.0154355610419	0.310608978327	16.625	-2.029	75.61

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN H AND RESID 162:192 )	H	162 - 192
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 193:207 )	H	193 - 207
3	X-RAY DIFFRACTION	3	( CHAIN H AND RESID 208:219 )	H	208 - 219
4	X-RAY DIFFRACTION	4	( CHAIN L AND RESID 2:18 )	L	2 - 18
5	X-RAY DIFFRACTION	5	( CHAIN L AND RESID 19:39 )	L	19 - 39
6	X-RAY DIFFRACTION	6	( CHAIN L AND RESID 40:76 )	L	40 - 76
7	X-RAY DIFFRACTION	7	( CHAIN L AND RESID 77:114 )	L	77 - 114
8	X-RAY DIFFRACTION	8	( CHAIN L AND RESID 115:164 )	L	115 - 164
9	X-RAY DIFFRACTION	9	( CHAIN L AND RESID 165:214 )	L	165 - 214
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 333:393 )	A	333 - 393
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 394:526 )	A	394 - 526
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 601:601 )	A	601
13	X-RAY DIFFRACTION	13	( CHAIN H AND RESID 1:17 )	H	1 - 17
14	X-RAY DIFFRACTION	14	( CHAIN H AND RESID 18:39 )	H	18 - 39
15	X-RAY DIFFRACTION	15	( CHAIN H AND RESID 40:51 )	H	40 - 51
16	X-RAY DIFFRACTION	16	( CHAIN H AND RESID 52:63 )	H	52 - 63
17	X-RAY DIFFRACTION	17	( CHAIN H AND RESID 64:82 )	H	64 - 82
18	X-RAY DIFFRACTION	18	( CHAIN H AND RESID 83:113 )	H	83 - 113
19	X-RAY DIFFRACTION	19	( CHAIN H AND RESID 114:138 )	H	114 - 138
20	X-RAY DIFFRACTION	20	( CHAIN H AND RESID 139:161 )	H	139 - 161

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