PDB-7usv: Plasmodium falciparum protein Pfs230 D1 in complex with nanobody F10

ID or keywords:

Entry

Database: PDB / ID: 7usv

Title

Plasmodium falciparum protein Pfs230 D1 in complex with nanobody F10

Components

Gametocyte surface protein P230
Nanobody F10

Keywords

PROTEIN BINDING/IMMUNE SYSTEM / 6-cysteine protein / s48/45 domain / Plasmodium / nanobody / PROTEIN BINDING / PROTEIN BINDING-IMMUNE SYSTEM complex

Function / homology

Function and homology information

cell surface / plasma membrane
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Dietrich, M.H. / Tham, W.H.

Funding support

Australia,

United Kingdom, 2items

Citation

Journal: Biochem.J. / Year: 2022
Title: Nanobodies against Pfs230 block Plasmodium falciparum transmission.
Authors: Dietrich, M.H. / Gabriela, M. / Reaksudsan, K. / Dixon, M.W.A. / Chan, L.J. / Adair, A. / Trickey, S. / O'Neill, M.T. / Tan, L.L. / Lopaticki, S. / Healer, J. / Keremane, S. / Cowman, A.F. / Tham, W.H.

History

Deposition	Apr 25, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 28, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2023	Group: Data collection / Database references / Category: citation / citation_author / diffrn_source Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7usv.cif.gz	232.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7usv.ent.gz	185.5 KB	Display	PDB format
PDBx/mmJSON format	7usv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7usv_validation.pdf.gz	463.9 KB	Display	wwPDB validaton report
Full document	7usv_full_validation.pdf.gz	468.4 KB	Display
Data in XML	7usv_validation.xml.gz	24.8 KB	Display
Data in CIF	7usv_validation.cif.gz	35.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/us/7usv ftp://data.pdbj.org/pub/pdb/validation_reports/us/7usv	HTTPS FTP

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Related structure data

Related structure data	7usrSC 7ussC 7ustC 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	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Gametocyte surface protein P230

B: Gametocyte surface protein P230

D: Nanobody F10

C: Nanobody F10

hetero molecules

63 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gametocyte surface protein P230

C: Nanobody F10

hetero molecules

defined by author&software
Evidence: gel filtration
31.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Gametocyte surface protein P230

D: Nanobody F10

hetero molecules

defined by author&software
31.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.083, 101.221, 148.185
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Gametocyte surface protein P230 Mass: 16800.465 Da / Num. of mol.: 2 / Fragment: Domain 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate 3D7 / Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P68874
#2: Antibody	Nanobody F10 Mass: 14290.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.9 Å³/Da / Density % sol: 57.58 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, and 25% PEG 4000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX2 / Wavelength: 0.953732 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.953732 Å / Relative weight: 1

Reflection

Resolution: 2.1→47.894 Å / Num. obs: 43202 / % possible obs: 99.5 % / Redundancy: 9.782 % / B_iso Wilson estimate: 40.777 Å² / CC_1/2: 0.98 / R_merge(I) obs: 0.227 / R_rim(I) all: 0.242 / Χ²: 0.77 / Net I/σ(I): 11.83 / Num. measured all: 422617

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.1-2.22	9.734	1.358	1.76	65033	6897	6681	0.683	1.434	96.9
2.22-2.38	9.48	0.909	2.7	61497	6490	6487	0.835	0.961	100
2.38-2.56	9.908	0.602	4.28	60210	6078	6077	0.92	0.636	100
2.56-2.81	10.176	0.39	7.04	57180	5620	5619	0.963	0.413	100
2.81-3.14	9.965	0.259	11.16	50560	5075	5074	0.981	0.275	100
3.14-3.62	9.3	0.188	18.92	42223	4543	4540	0.977	0.201	99.9
3.62-4.43	10.186	0.18	29.32	39430	3871	3871	0.962	0.192	100
4.43-6.24	9.678	0.157	32.51	29490	3048	3047	0.973	0.169	100
6.24-47.894	9.41	0.099	33.92	16994	1813	1806	0.996	0.106	99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.15_3459	refinement
XSCALE		data scaling
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7USR

7usr

Resolution: 2.1→47.894 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2354	2154	5 %
R_work	0.198	40912	-
obs	0.1999	43066	99.82 %

Solvent computation

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

Displacement parameters

B_iso max: 135.41 Å² / B_iso mean: 43.5588 Å² / B_iso min: 19.33 Å²

Refinement step

Cycle: final / Resolution: 2.1→47.894 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4100	0	40	349	4489
B_iso mean	-	-	81.02	47.54	-
Num. residues	-	-	-	-	537

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.1-2.1489	0.3452	139	0.2917	2644	99
2.1489-2.2026	0.287	142	0.2745	2691	100
2.2026-2.2622	0.3342	141	0.2543	2689	100
2.2622-2.3287	0.2902	142	0.2532	2687	100
2.3287-2.4039	0.295	142	0.2394	2702	100
2.4039-2.4898	0.2937	141	0.2224	2681	100
2.4898-2.5895	0.2971	143	0.2211	2713	100
2.5895-2.7073	0.2499	143	0.2187	2702	100
2.7073-2.85	0.244	144	0.2177	2735	100
2.85-3.0286	0.2403	142	0.2142	2713	100
3.0286-3.2624	0.2659	144	0.1992	2725	100
3.2624-3.5906	0.2343	144	0.1951	2734	100
3.5906-4.1099	0.2057	146	0.1719	2777	100
4.1099-5.177	0.1735	147	0.1408	2792	100
5.177-47.89	0.201	154	0.1936	2927	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	5.2143	-0.1814	-0.3625	3.724	-2.1197	3.4917	0.0268	0.2683	0.1422	0.226	0.0403	0.4016	-0.1805	-0.1984	0.0525	0.31	0.0082	0.0494	0.3407	-0.0297	0.3108	-15.8698	13.2033	-11.0183
2	4.7579	-3.7371	0.6967	3.3474	0.2857	2.0317	-0.1725	0.2457	0.5353	-0.2533	0.4783	-0.8117	-0.4895	0.4789	-0.1762	0.3082	-0.055	0.0485	0.3069	-0.0387	0.4031	-6.4915	11.0323	-9.2755
3	2.7149	-1.6662	-0.0469	6.6428	-0.2013	0.991	0.16	-0.0191	-0.2555	-0.7277	-0.0148	0.7824	-0.0603	-0.001	-0.1895	0.3718	0.0267	0.0054	0.3216	-0.03	0.2889	-15.8513	13.5613	-17.9534
4	2.6246	-0.5316	-0.2366	5.4736	1.1165	4.9922	0.2552	0.0484	0.2864	-0.1239	-0.2106	-0.5012	-0.4505	0.1614	-0.0517	0.6043	-0.0615	0.1209	0.3369	0.0629	0.3638	-3.9364	18.2169	-22.6657
5	5.7851	-1.9318	-0.3178	7.65	-1.3777	0.3184	0.0593	0.1973	0.3039	0.3089	-0.3937	-1.0509	0.1525	0.4401	0.4493	0.6209	-0.0405	0.1644	0.412	-0.0183	0.3701	2.7662	15.6346	-24.2223
6	5.9148	-1.2868	-0.7549	2.8874	0.5076	2.0637	0.1652	0.6259	-0.8324	-0.6254	-0.1894	0.386	0.0973	-0.3224	0.0526	0.6022	0.0078	-0.0431	0.3366	-0.0426	0.299	-10.8753	8.2811	-28.6869
7	1.8712	-0.5472	-0.1886	3.5627	0.634	3.1228	-0.0423	0.1112	0.0187	-0.2245	0.0555	-0.1641	-0.0723	0.5512	-0.0166	0.3358	-0.0051	0.0592	0.3687	-0.016	0.3048	-2.9478	8.347	-19.7845
8	4.1673	-1.1029	0.5144	7.308	0.7432	5.7274	0.093	-0.7048	0.6552	0.4592	0.4785	0.6025	0.074	-0.5719	-0.4888	0.4962	0.0769	0.1344	0.5306	-0.0351	0.5143	-19.9977	28.9185	-9.9301
9	3.4564	0.2157	-3.119	3.7357	3.4401	6.3392	-0.1897	-0.8191	0.8026	0.5221	0.6563	-1.2753	0.049	0.9232	-0.2474	0.2499	-0.0116	0.0063	0.4034	-0.0608	0.3335	-0.891	8.6818	-13.7438
10	4.3983	2.2766	-1.356	5.8481	-1.2917	3.9755	0.3302	-0.215	0.3154	-0.5252	-0.4056	-0.7562	-0.3428	0.4339	0.1475	0.4048	0.0224	0.1208	0.2963	0.0411	0.3875	15.2216	15.0419	-54.8545
11	2.2484	1.5765	1.2153	2.648	-1.0865	2.8031	0.0366	-0.179	0.6348	-0.1077	-0.0407	0.702	-0.4145	-0.181	-0.1589	0.2622	0.0347	-0.0018	0.2299	0.0245	0.3001	5.7781	11.4099	-55.2366
12	4.4638	1.9428	-0.1	7.3219	-0.0798	2.7132	0.3191	0.3186	0.2615	1.0757	0.1542	-0.6623	-0.5117	0.1966	-0.4388	0.4625	-0.0391	0.0819	0.2982	0.0197	0.3236	14.811	14.6509	-46.9929
13	7.8883	0.2106	-0.927	1.8506	-0.1838	7.573	-0.053	-0.341	0.6358	0.5417	0.5521	-0.2644	-0.3318	0.2727	-0.4478	0.6147	0.0439	0.1161	0.4257	-0.071	0.3825	7.5919	18.6281	-39.5299
14	1.8657	2.669	0.3971	5.3265	-3.2069	2.0132	-0.1041	0.489	1.4267	-0.2251	-0.5088	1.2024	-1.077	-0.6985	0.2863	0.8082	0.1881	0.1161	0.5772	0.0203	0.5506	-3.6926	18.6501	-45.4488
15	5.1124	2.3812	-1.8256	3.2444	0.8007	1.8662	-0.0135	0.5474	0.3823	-0.2918	-0.1756	-0.2224	-0.8602	-1.0462	0.3142	0.8106	0.1501	0.1727	0.3728	0.0919	0.4257	-3.2579	15.384	-40.1834
16	7.1395	1.2359	-0.878	2.5949	-0.0144	2.5359	0.1939	0.807	-0.6172	0.7052	-0.0937	-0.2852	-0.0325	0.3233	0.0294	0.6596	0.0327	-0.0162	0.4259	0.0609	0.3548	5.0472	5.2522	-35.884
17	4.6862	1.1053	-1.1704	4.3098	-0.6304	3.2745	0.026	-0.3457	-0.0476	0.5866	0.0728	-0.1135	-0.1145	-0.0242	-0.1378	0.4178	0.0494	0.0581	0.3126	0.0201	0.2487	7.1043	10.2138	-42.1537
18	2.7067	1.3892	-0.8644	6.2989	-1.027	3.1789	0.1393	0.8097	1.0906	-0.1933	0.4392	0.3861	-0.7523	-0.382	-0.2391	0.4974	0.085	0.1585	0.2983	0.1062	0.5482	8.6393	19.5203	-53.4111
19	3.5491	-0.2678	-1.0243	3.9996	0.2233	1.9467	0.1306	1.0472	-0.7512	-0.205	-0.1184	0.2382	0.1716	0.3648	0.1482	0.2456	-0.0408	0.0333	0.3504	-0.0833	0.295	13.2855	-8.8847	-73.3728
20	9.6048	-2.9677	4.5926	7.555	-6.9286	7.7764	-0.1756	0.484	-0.1097	0.7135	0.0686	0.768	0.4278	-1.2182	0.0808	0.3808	-0.084	0.0119	0.2687	-0.066	0.3533	9.6851	-10.3043	-69.9975
21	2.5826	0.773	-0.5712	0.4412	0.7423	3.6477	0.1896	-0.0313	-0.5286	0.0109	-0.2769	-0.0496	0.5156	0.3858	0.1471	0.1945	0.052	0.0243	0.3297	0.0222	0.3072	13.7289	-6.8319	-60.3468
22	6.3658	0.7586	-5.4547	0.737	-1.0789	8.5273	0.2167	0.2565	0.1286	-0.2504	-0.2478	-0.026	-0.2049	-0.4123	0.0386	0.2092	0.0422	-0.0053	0.3502	0.0563	0.2782	16.1008	4.2079	-70.1749
23	2.1939	-0.8611	-0.1526	0.6967	1.062	1.5949	-0.0513	0.2748	0.1323	0.1364	-0.0299	0.1745	-0.2621	0.0822	0.0525	0.1928	-0.0659	0.0014	0.3292	0.0181	0.2336	4.7042	0.009	-64.1388
24	2.3041	-0.443	0.1591	0.469	0.408	4.3936	-0.1094	0.5533	-0.0726	-0.2784	-0.1472	0.0118	0.5354	-0.2846	0.2154	0.23	-0.0435	0.0511	0.433	-0.0106	0.3443	7.2809	-4.8315	-71.9906
25	0.9543	-0.7619	-0.2741	0.9912	1.2333	2.0894	-0.0764	0.2554	-0.0836	0.1253	0.1278	-0.1465	-0.1576	0.0134	-0.0783	0.2468	-0.0269	0.0065	0.3352	0.0678	0.2727	15.7443	1.8967	-61.728
26	3.1024	0.2467	1.4049	1.7175	0.9533	5.458	0.0522	0.2751	-0.2771	-0.0526	0.0224	-0.1809	0.3632	-0.0385	-0.0485	0.2201	-0.0709	0.0509	0.361	0.0253	0.366	17.564	-4.0661	-70.4539
27	3.3343	1.1968	-0.5704	3.0014	1.6478	4.5933	0.0104	-0.1018	-0.519	0.0492	0.0029	-0.1287	0.3783	-0.4337	0.0029	0.215	0.0094	0.0008	0.1924	0.013	0.3214	-12.381	-10.9714	2.7829
28	2.6958	0.1544	-0.8214	0.4018	-0.5808	1.5343	-0.0149	-0.0705	0.0721	0.0177	0.0294	-0.1137	0.1038	-0.0037	-0.0462	0.2079	0.0005	-0.0118	0.2716	-0.0381	0.287	-8.9495	-1.5154	3.34
29	1.0533	0.1118	-1.1085	1.9602	-0.9122	3.9891	-0.0425	0.0357	-0.0426	-0.0632	0.1407	0.1798	0.1987	-0.0933	-0.0665	0.1353	0.005	0.0141	0.2672	-0.0781	0.2663	-16.6636	-1.6583	1.0947

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 587 through 607 )	A	587 - 607
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 608 through 615 )	A	608 - 615
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 616 through 639 )	A	616 - 639
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 640 through 656 )	A	640 - 656
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 657 through 666 )	A	657 - 666
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 667 through 686 )	A	667 - 686
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 687 through 707 )	A	687 - 707
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 708 through 719 )	A	708 - 719
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 720 through 731 )	A	720 - 731
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 588 through 607 )	B	588 - 607
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 608 through 615 )	B	608 - 615
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 616 through 639 )	B	616 - 639
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 640 through 648 )	B	640 - 648
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 649 through 656 )	B	649 - 656
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 657 through 666 )	B	657 - 666
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 667 through 676 )	B	667 - 676
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 677 through 707 )	B	677 - 707
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 708 through 731 )	B	708 - 731
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1 through 17 )	D	1 - 17
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 18 through 24 )	D	18 - 24
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 25 through 39 )	D	25 - 39
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 40 through 51 )	D	40 - 51
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 52 through 73 )	D	52 - 73
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 74 through 91 )	D	74 - 91
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 92 through 109 )	D	92 - 109
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 110 through 124 )	D	110 - 124
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 1 through 32 )	C	1 - 32
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 33 through 91 )	C	33 - 91
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 92 through 124 )	C	92 - 124

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