PDB-6b0s: Crystal structure of circumsporozoite protein aTSR domain in comp...

ID or keywords:

Entry

Database: PDB / ID: 6b0s

Title

Crystal structure of circumsporozoite protein aTSR domain in complex with 1710 antibody

Components

(1710 antibody, ...) x 2
Circumsporozoite protein

Keywords

IMMUNE SYSTEM / Malaria / Circumsporozoite protein / alpha thrombospondin type-1 repeat

Function / homology

Function and homology information

side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Scally, S.W. / Murugan, R. / Bosch, A. / Triller, G. / Wardemann, H. / Julien, J.P.

Citation

Journal: J. Exp. Med. / Year: 2018
Title: Rare PfCSP C-terminal antibodies induced by live sporozoite vaccination are ineffective against malaria infection.
Authors: Scally, S.W. / Murugan, R. / Bosch, A. / Triller, G. / Costa, G. / Mordmuller, B. / Kremsner, P.G. / Sim, B.K.L. / Hoffman, S.L. / Levashina, E.A. / Wardemann, H. / Julien, J.P.

History

Deposition	Sep 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 10, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6b0s.cif.gz	208.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6b0s.ent.gz	166 KB	Display	PDB format
PDBx/mmJSON format	6b0s.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6b0s_validation.pdf.gz	455.6 KB	Display	wwPDB validaton report
Full document	6b0s_full_validation.pdf.gz	456.9 KB	Display
Data in XML	6b0s_validation.xml.gz	23.3 KB	Display
Data in CIF	6b0s_validation.cif.gz	33.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/6b0s ftp://data.pdbj.org/pub/pdb/validation_reports/b0/6b0s	HTTPS FTP

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Related structure data

Related structure data	6b0wC 3vdjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4aei-2 4aei-1 4dn4-d 3a1p-d 4lmq-2 4aei-3 4lmq-1 6z7z-2 6a77-d 4rqq-2 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

H: 1710 antibody, heavy chain

L: 1710 antibody, light chain

C: Circumsporozoite protein

hetero molecules

56.5 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)	70.487, 70.683, 96.283
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules C

#3: Protein	Circumsporozoite protein Mass: 9431.616 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: csp / Production host: Homo sapiens (human) / References: UniProt: M1V0B0

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Antibody , 2 types, 2 molecules HL

#1: Antibody	1710 antibody, heavy chain Mass: 23940.674 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	1710 antibody, light chain Mass: 22629.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 382 molecules

#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.14 Å³/Da / Density % sol: 42.56 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2, 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97948 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 14, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97948 Å / Relative weight: 1
Reflection	Resolution: 1.95→40 Å / Num. obs: 35815 / % possible obs: 100 % / Redundancy: 7.4 % / R_pim(I) all: 0.062 / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.95→2.05 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4909 / R_pim(I) all: 0.295 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XPREP		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1710 Fab, 3VDJ

3vdj

Resolution: 1.95→39.789 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2238	1797	5.03 %
R_work	0.1804	-	-
obs	0.1826	35752	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→39.789 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3692	0	34	376	4102

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3814
X-RAY DIFFRACTION	f_angle_d	0.653	5192
X-RAY DIFFRACTION	f_dihedral_angle_d	12.633	2293
X-RAY DIFFRACTION	f_chiral_restr	0.048	581
X-RAY DIFFRACTION	f_plane_restr	0.005	661

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 (%)
1.95-2.0027	0.3041	133	0.2551	2572	X-RAY DIFFRACTION	100
2.0027-2.0617	0.286	137	0.2393	2579	X-RAY DIFFRACTION	100
2.0617-2.1282	0.2739	134	0.2192	2593	X-RAY DIFFRACTION	100
2.1282-2.2043	0.2954	134	0.2091	2570	X-RAY DIFFRACTION	100
2.2043-2.2925	0.2609	136	0.2062	2567	X-RAY DIFFRACTION	100
2.2925-2.3968	0.2668	136	0.1927	2571	X-RAY DIFFRACTION	100
2.3968-2.5232	0.238	138	0.2034	2606	X-RAY DIFFRACTION	100
2.5232-2.6812	0.2475	138	0.188	2600	X-RAY DIFFRACTION	100
2.6812-2.8882	0.2293	140	0.1746	2602	X-RAY DIFFRACTION	100
2.8882-3.1787	0.214	139	0.171	2608	X-RAY DIFFRACTION	100
3.1787-3.6384	0.211	139	0.154	2637	X-RAY DIFFRACTION	100
3.6384-4.583	0.1689	145	0.143	2666	X-RAY DIFFRACTION	100
4.583-39.7976	0.201	148	0.1766	2784	X-RAY DIFFRACTION	100

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	4.2688	-0.7938	-1.4893	5.1444	-1.1815	6.3809	-0.0353	-0.8894	0.2681	0.554	-0.2258	0.3295	0.1197	-0.8808	0.1718	0.2278	-0.083	-0.009	0.503	-0.0739	0.3168	-44.7637	-10.2807	9.1444
2	3.6318	-0.9779	-2.6954	3.5319	-1.3333	3.3037	-0.1876	-0.5576	0.5213	0.1117	-0.0891	0.6271	0.0513	-0.8153	0.0472	0.2104	-0.0199	-0.0021	0.4238	-0.17	0.3786	-40.4154	-2.0155	13.655
3	5.2846	-0.2203	-0.7157	1.5578	1.8038	2.1946	-0.0061	0.1	0.0534	0.0955	-0.1062	0.0542	-0.0715	0.0115	0.1682	0.17	-0.0169	-0.0088	0.1685	0.0182	0.1952	-27.4053	-8.0173	5.786
4	3.8394	-1.0088	-3.9783	2.1268	-0.2376	5.0149	0.2228	-0.9748	-0.0954	0.234	-0.2986	0.4871	-0.1492	-0.2189	0.0681	0.2375	-0.0917	0.0396	0.5844	-0.1392	0.3099	-40.4783	-7.1225	16.785
5	2.7087	-2.7196	-1.6406	7.9921	5.3117	5.5357	0.3607	0.33	0.0405	-0.969	-0.4266	0.0443	-0.5724	-0.2898	0.0756	0.1118	-0.0242	0.0091	0.24	0.0294	0.1467	-27.7833	-16.4724	-24.954
6	1.2548	0.8024	0.3936	6.687	1.8617	3.4224	0.0585	0.0037	0.0946	-0.0379	-0.079	-0.122	-0.0668	0.1159	0.0055	0.1268	-0.0034	-0.0024	0.1782	0.0187	0.1436	-28.9323	-11.1971	-15.4742
7	4.8915	1.8026	2.2067	1.6066	0.9549	3.5043	0.2206	-0.017	-0.1682	0.1844	-0.1226	-0.1044	0.3657	0.0015	-0.1293	0.1649	0.0113	0.0194	0.1543	-0.0112	0.1448	-30.0618	-19.3911	-10.4857
8	3.9837	0.0564	1.0595	6.5798	1.646	2.5621	0.0513	-0.0785	-0.2075	0.085	-0.0223	-0.2904	0.2564	0.2416	-0.0126	0.1357	0.0278	0.0091	0.1505	0.0057	0.0891	-23.4306	-18.9689	-13.0907
9	3.5572	-0.8128	0.9487	1.5574	2.3499	5.0514	0.3485	-0.0592	-0.4362	0.3459	-0.0279	-0.41	0.3881	0.1417	-0.3145	0.1595	0.0064	-0.003	0.1892	0.03	0.1566	-24.9353	-22.4315	-19.8435
10	1.0639	-0.8394	0.0482	1.8594	1.0004	0.9016	0.1691	-0.0226	0.0175	-0.0904	-0.1739	-0.0803	-0.1349	-0.1945	0.0208	0.1615	-0.0253	0.0075	0.1916	-0.0042	0.1854	-36.4467	-12.3325	-11.4701
11	1.3672	0.1317	1.2284	1.187	-1.4418	3.1761	0.0111	0.2473	-0.0501	-0.1661	0.0041	-0.1521	0.7037	0.3853	0.0022	0.2247	0.0302	0.0198	0.1852	-0.0189	0.1351	-28.6741	-25.2129	-34.4101
12	2.0832	-0.3216	-0.7257	3.5343	0.685	4.0164	0.1552	0.2852	-0.1229	-0.2288	-0.0805	0.3173	-0.0283	-0.1729	-0.0792	0.1291	0.0056	-0.0117	0.2027	-0.0047	0.2158	-41.798	-15.6441	-49.3284
13	2.1031	0.0456	0.2736	2.9343	-0.9675	3.1511	-0.0777	-0.056	0.3231	-0.0275	0.0268	0.1566	-0.4194	-0.2173	0.0407	0.2141	0.0231	-0.0335	0.1844	-0.0105	0.1908	-42.1748	-12.801	-43.0238
14	5.9031	-1.644	2.2138	5.9364	-2.9039	5.6442	-0.1444	0.5161	0.3425	0.0587	-0.1856	-0.05	-0.5053	0.3541	0.428	0.1823	-0.0407	-0.0145	0.1791	0.0046	0.1847	-33.8849	-11.3757	-46.1145
15	2.4951	0.7825	-0.5473	2.6845	-0.3636	2.2301	-0.086	0.0981	0.0341	-0.1138	0.1038	0.1196	-0.0964	0.0341	-0.0107	0.1417	-0.0166	-0.0028	0.1574	0.005	0.1465	-50.6214	-17.2806	-10.911
16	2.9639	-0.8416	-2.7828	0.5252	0.4734	4.6476	0.015	-0.278	0.0667	-0.0009	0.0105	0.0144	-0.1485	0.0859	-0.0113	0.1378	0.0003	-0.0139	0.168	-0.0064	0.157	-51.6209	-22.0158	-46.9521
17	2.7099	-0.0583	0.1387	2.8431	1.5326	3.4817	0.099	-0.2119	0.0154	0.0002	-0.0226	-0.0572	-0.0732	-0.0464	-0.0732	0.1328	-0.0077	0.0132	0.1906	0.0202	0.1911	-49.6671	-26.3172	-47.1364
18	4.0321	-1.2373	-4.9072	2.2654	2.004	7.5797	-0.1944	0.504	-0.1449	-0.1146	0.1587	0.1435	0.2068	-0.5156	0.0068	0.1695	-0.0298	-0.0263	0.2368	0.031	0.2261	-57.1281	-25.0665	-53.535

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 310 through 322 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 323 through 346 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 347 through 359 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 360 through 374 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 1 through 17 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 18 through 39 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 40 through 59 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 60 through 75 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 76 through 87 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 88 through 106 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 107 through 119 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 120 through 145 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 146 through 194 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 195 through 214 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 2 through 107 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 108 through 151 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 152 through 188 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 189 through 212 )

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