PDB-8fdo: SARS-CoV-2 fusion peptide epitope scaffold FP15 bound to DH1058

ID or keywords:

Entry

Database: PDB / ID: 8fdo

Title

SARS-CoV-2 fusion peptide epitope scaffold FP15 bound to DH1058

Components

DH1058 Heavy chain
DH1058 Light chain
FP15

Keywords

IMMUNE SYSTEM / antibody / Fab / Spike / fusion peptide

Biological species

Homo sapiens (human)

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Kapingidza, A.B. / Marston, D.J. / Wrapp, D. / Winters, K. / Azoitei, M.L.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Engineered immunogens to elicit antibodies against conserved coronavirus epitopes.
Authors: Kapingidza, A.B. / Marston, D.J. / Harris, C. / Wrapp, D. / Winters, K. / Mielke, D. / Xiaozhi, L. / Yin, Q. / Foulger, A. / Parks, R. / Barr, M. / Newman, A. / Schafer, A. / Eaton, A. / ...

History

Deposition	Dec 4, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8fdo.cif.gz	237.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8fdo.ent.gz	190.5 KB	Display	PDB format
PDBx/mmJSON format	8fdo.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/fd/8fdo ftp://data.pdbj.org/pub/pdb/validation_reports/fd/8fdo	HTTPS FTP

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Related structure data

Related structure data	8f5hC 8f5iC 5yo4S 7towS S: Starting model for refinement C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: DH1058 Heavy chain

B: DH1058 Light chain

C: FP15

65.2 kDa, 3 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)	48.390, 50.580, 146.240
Angle α, β, γ (deg.)	90.00, 96.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	DH1058 Heavy chain Mass: 25669.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	DH1058 Light chain Mass: 23555.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein	FP15 Mass: 15933.106 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.73 Å³/Da / Density % sol: 54.89 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.39 Å / Num. obs: 35552 / % possible obs: 98.18 % / Redundancy: 7.5 % / CC_1/2: 0.501 / CC star: 0.817 / Net I/σ(I): 23.64
Reflection shell	Resolution: 2.2→2.279 Å / Mean I/σ(I) obs: 2.26 / Num. unique obs: 3518 / CC_1/2: 0.529

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Processing

Software

Name	Version	Classification
PHENIX	dev-3758-000	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7TOW, 5YO4

7tow

5yo4

Resolution: 2.2→48.39 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2292	1671	4.72 %
R_work	0.1892	-	-
obs	0.1911	35398	98.19 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→48.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4264	0	0	189	4453

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4354
X-RAY DIFFRACTION	f_angle_d	0.834	5905
X-RAY DIFFRACTION	f_dihedral_angle_d	35.764	600
X-RAY DIFFRACTION	f_chiral_restr	0.05	656
X-RAY DIFFRACTION	f_plane_restr	0.005	765

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 (%)
2.2-2.26	0.352	138	0.2774	2743	X-RAY DIFFRACTION	98
2.26-2.34	0.3008	148	0.25	2824	X-RAY DIFFRACTION	98
2.34-2.42	0.2813	148	0.2437	2755	X-RAY DIFFRACTION	97
2.42-2.52	0.2597	158	0.226	2652	X-RAY DIFFRACTION	95
2.52-2.63	0.2656	141	0.2113	2791	X-RAY DIFFRACTION	99
2.63-2.77	0.283	109	0.2125	2865	X-RAY DIFFRACTION	99
2.77-2.95	0.2435	140	0.2101	2847	X-RAY DIFFRACTION	99
2.95-3.17	0.2495	116	0.2051	2852	X-RAY DIFFRACTION	99
3.17-3.49	0.2162	132	0.1923	2826	X-RAY DIFFRACTION	98
3.49-4	0.2	112	0.1659	2827	X-RAY DIFFRACTION	98
4-5.03	0.1792	152	0.1431	2864	X-RAY DIFFRACTION	99
5.04-48.39	0.221	177	0.1768	2881	X-RAY DIFFRACTION	98

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	8.674	-3.1633	2.7042	5.6608	-0.3758	4.0113	0.1429	-0.0595	0.2678	0.3774	0.3076	-0.8827	0.5595	1.4721	-0.036	0.314	0.0391	-0.052	0.6661	-0.0197	0.3532	19.236	-20.333	3.443
2	1.9405	-0.0323	-1.3375	4.1236	1.3658	5.9133	-0.1267	-0.1873	0.7535	0.4428	0.1002	-0.3588	-0.6163	-0.0749	-0.1072	0.2775	-0.0664	0.0013	0.2494	-0.0484	0.3471	13.021	8.172	29.433
3	1.6926	-0.4559	-0.0851	3.8873	1.1907	4.3946	0.1446	-0.1025	0.1452	0.0227	-0.0745	0.0233	-0.3344	-0.3813	-0.0371	0.1447	0.0104	-0.0123	0.2238	0.0247	0.2415	10.424	1.533	21.761
4	0.6757	-1.1415	-1.1179	3.8367	2.4607	5.9252	-0.0318	-0.2219	-0.0578	0.1311	0.0649	-0.4031	0.4391	0.4772	-0.1836	0.1694	-0.0006	-0.027	0.2383	0.0269	0.3216	19.473	-9.889	19.916
5	0.8966	-0.1501	0.2064	3.3634	-0.276	3.0686	0.0351	-0.4119	0.0043	1.6329	-0.0453	0.0834	-0.2041	-0.3946	0.0628	0.8234	-0.1189	0.0184	0.4612	0.0029	0.1795	9.931	1.23	45.036
6	0.2764	-0.4025	-0.3666	1.4028	-0.319	3.7285	0.3253	-0.3744	0.0347	2.1059	-0.3094	-0.1028	-0.7558	0.4481	0.1293	1.6525	-0.2194	-0.1937	0.7587	0.0397	0.3725	12.792	7.939	58.876
7	2.9025	-1.2923	1.5347	0.825	-0.8733	5.5132	-0.023	-0.0448	-0.0784	1.0149	-0.0736	0.2372	0.5486	-0.6091	0.0397	0.9527	-0.281	-0.0467	0.5754	0.1614	0.3654	8.822	-20.766	39.042
8	2.7011	1.0571	1.2215	1.8118	1.0884	0.9227	0.132	-0.2437	-0.2895	0.1591	0.1406	0.3406	1.4081	-0.7044	-0.1317	0.6488	-0.2822	-0.1287	0.3619	0.1268	0.3517	9.458	-20.545	28.853
9	1.9632	-1.0504	-0.5388	2.5271	-0.849	4.0784	0.1935	-0.2774	-0.2294	0.409	0.0554	-0.0944	0.8614	0.0771	-0.2	0.5357	-0.0585	-0.1016	0.271	0.0523	0.2943	17.36	-19.137	33.389
10	0.477	0.0704	-0.452	1.3213	-1.1433	5.8115	0.0562	-0.3062	-0.1184	0.6304	-0.0931	0.0264	0.0355	-0.1751	-0.1822	0.5247	-0.1642	-0.0434	0.3942	0.0916	0.3073	9.15	-15.273	38.935
11	0.762	-1.1263	0.5426	6.4509	0.9875	2.376	0.4103	-0.3978	0.4393	1.5929	-0.3369	1.7676	-0.3995	-0.8929	-0.4378	1.8789	-0.197	0.5764	0.8825	0.0528	0.673	0.491	-1.062	62.529
12	2.8218	0.3583	0.1174	3.0416	-3.9685	5.2748	0.4988	-0.7743	-0.0733	0.5772	0.2979	1.5363	-0.459	-1.2024	-0.986	1.035	-0.1561	0.3263	1.0586	-0.0186	0.9771	-7.484	-2.856	58.092
13	5.5854	-2.6579	-0.0215	5.6749	0.6665	2.8471	0.6838	0.0468	1.2258	1.2572	-0.3114	-0.0365	-0.3515	-0.1884	-0.2511	1.2345	-0.2187	0.2411	0.6252	0.0489	0.5109	4.196	-2.466	58.081
14	3.477	-1.9123	-0.6716	1.7024	1.6843	2.5057	0.3956	-1.032	0.4638	1.3675	0.1663	0.8422	-0.1948	-1.3602	0.2274	2.4288	-0.0277	1.3202	1.1603	-0.0329	0.8624	-5.381	-4.794	67.971
15	8.108	-0.5774	-1.5618	3.0467	0.2955	3.2229	0.4247	0.1272	-0.221	0.1788	-0.3276	0.1125	-0.5137	-0.2006	-0.0936	0.2172	-0.0339	-0.037	0.2021	0.0214	0.2056	5.442	-8.189	7.931
16	4.5153	-2.8844	-2.2447	4.5798	1.6381	4.3716	-0.1046	-0.1086	0.3531	-0.0982	0.157	-0.4058	-0.1261	0.3081	-0.0038	0.1572	-0.0269	-0.0206	0.2371	0.024	0.2469	6.621	-9.71	-0.963
17	4.2767	-3.0599	-2.9139	5.4918	1.4402	4.7722	0.0434	0.3294	-0.4047	-0.2066	-0.3201	-0.078	-0.0426	0.2384	0.2275	0.2038	-0.0181	-0.0188	0.2588	0.004	0.2297	8.088	-18.599	-5.365
18	7.4196	-4.6391	-0.9487	5.7503	1.0666	2.4998	-0.0342	-0.4368	-0.1974	0.1687	-0.0313	0.4957	0.1667	-0.2696	0.1356	0.2681	-0.0713	0.0144	0.3746	-0.0228	0.4007	-3.008	-16.953	5.59

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN C AND RESID 103:110 )	C	103 - 110
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 1:17 )	A	1 - 17
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 18:87 )	A	18 - 87
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 88:100 )	A	88 - 100
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 101:145 )	A	101 - 145
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 146:213 )	A	146 - 213
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 1:18 )	B	1 - 18
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 19:38 )	B	19 - 38
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 39:90 )	B	39 - 90
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 91:113 )	B	91 - 113
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 114:150 )	B	114 - 150
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 151:163 )	B	151 - 163
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 164:186 )	B	164 - 186
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 187:213 )	B	187 - 213
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 2:23 )	C	2 - 23
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 24:49 )	C	24 - 49
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 50:81 )	C	50 - 81
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 82:102 )	C	82 - 102

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