PDB-6b0h: Crystal structure of Pfs25 in complex with the transmission block...

ID or keywords:

Entry

Database: PDB / ID: 6b0h

Title

Crystal structure of Pfs25 in complex with the transmission blocking antibody 1262

Components

1262 antibody, heavy chain
1262 antibody, light chain
Pfs25

Keywords

IMMUNE SYSTEM / Transmission blocking vaccine /

malaria /

antibody /

EGF-like domain

Function / homology

Function and homology information

side of membrane /

cell surface /

plasma membrane
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

McLeod, B. / Scally, S.W. / Bosch, A. / King, C.R. / Julien, J.P.

Citation

Journal: Nat Commun / Year: 2017
Title: Molecular definition of multiple sites of antibody inhibition of malaria transmission-blocking vaccine antigen Pfs25.
Authors: Scally, S.W. / McLeod, B. / Bosch, A. / Miura, K. / Liang, Q. / Carroll, S. / Reponen, S. / Nguyen, N. / Giladi, E. / Ramisch, S. / Yusibov, V. / Bradley, A. / Lemiale, F. / Schief, W.R. / ...

History

Deposition	Sep 14, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2017	Group: Database references / Category: citation 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	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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6b0h.cif.gz	471 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/6b0h ftp://data.pdbj.org/pub/pdb/validation_reports/b0/6b0h	HTTPS FTP

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Related structure data

Related structure data	6azzC 6b08C 6b0aC 6b0eC 6b0gC 1z27S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6jbt-d 7k0x-2 6xkp-1 3wd5-d 6phf-1 2ol3-d 5e9d-1 6u6u-d 6n5b-d 5du3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #75 - Mar 2006 Tissue Factor similarity (1)

Deposited unit

I: Pfs25

J: Pfs25

B: 1262 antibody, heavy chain

D: 1262 antibody, heavy chain

A: 1262 antibody, light chain

C: 1262 antibody, light chain

hetero molecules

134 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

I: Pfs25

D: 1262 antibody, heavy chain

C: 1262 antibody, light chain

hetero molecules

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

2

J: Pfs25

B: 1262 antibody, heavy chain

A: 1262 antibody, light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.110, 119.010, 165.010
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pfs25 Mass: 20104.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Production host: Homo sapiens (human) / References: UniProt: P13829*PLUS
#2: Antibody	1262 antibody, heavy chain Mass: 23548.393 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody	1262 antibody, light chain Mass: 23383.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.2 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium acetate and 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: 0.97949 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 14, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.7→48.262 Å / Num. obs: 36020 / % possible obs: 99.9 % / Redundancy: 7.4 % / R_pim(I) all: 0.089 / Net I/σ(I): 9.7
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3525 / R_pim(I) all: 0.434 / % 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: 1Z27, 1262 Fab

1z27

Resolution: 2.7→48.262 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57

	R_factor	Num. reflection	% reflection
R_free	0.2379	1800	5 %
R_work	0.1864	-	-
obs	0.1889	36005	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.7→48.262 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8921	0	12	443	9376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	9160
X-RAY DIFFRACTION	f_angle_d	0.649	12475
X-RAY DIFFRACTION	f_dihedral_angle_d	12.223	5576
X-RAY DIFFRACTION	f_chiral_restr	0.045	1434
X-RAY DIFFRACTION	f_plane_restr	0.005	1586

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 (%)
2.7-2.773	0.3403	136	0.264	2589	X-RAY DIFFRACTION	100
2.773-2.8546	0.3527	137	0.2532	2592	X-RAY DIFFRACTION	100
2.8546-2.9467	0.3024	136	0.2477	2593	X-RAY DIFFRACTION	100
2.9467-3.052	0.3123	137	0.2442	2599	X-RAY DIFFRACTION	100
3.052-3.1742	0.3021	136	0.2483	2579	X-RAY DIFFRACTION	100
3.1742-3.3186	0.291	137	0.2127	2605	X-RAY DIFFRACTION	100
3.3186-3.4935	0.2514	138	0.194	2621	X-RAY DIFFRACTION	100
3.4935-3.7123	0.228	137	0.1824	2608	X-RAY DIFFRACTION	100
3.7123-3.9988	0.2098	138	0.1729	2615	X-RAY DIFFRACTION	100
3.9988-4.401	0.1959	139	0.1438	2648	X-RAY DIFFRACTION	100
4.401-5.0373	0.1675	140	0.1301	2659	X-RAY DIFFRACTION	100
5.0373-6.3442	0.1919	141	0.1535	2683	X-RAY DIFFRACTION	100
6.3442-48.2699	0.2291	148	0.1789	2814	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	4.4505	5.3275	1.7535	9.5702	2.4274	1.1257	0.137	-0.1904	-0.2159	0.1816	-0.1391	0.0814	0.0636	0.1293	-0.0192	0.2772	0.0267	0.0856	0.2732	0.049	0.2535	-34.4363	6.798	16.7613
2	5.2419	3.6023	0.0988	3.5667	-0.5163	7.5969	0.1844	-0.2028	-0.1886	0.1196	-0.0724	-0.2471	0.676	-0.4202	-0.0608	0.2198	0.0192	0.07	0.2549	0.0378	0.3309	-20.8033	10.6605	10.8352
3	5.7139	-0.0429	-1.5853	3.3998	-0.5184	4.4384	0.1867	-1.2579	0.4778	0.7643	-0.1277	0.0968	-0.5342	-0.0803	-0.1102	0.4689	-0.0519	-0.0283	0.4577	-0.0999	0.2862	-22.2667	23.9202	26.0657
4	9.6121	-3.3408	-8.0694	2.5626	4.0231	9.0896	0.0926	-0.7523	0.2168	-0.1278	0.3262	-0.1845	-0.3917	0.6078	-0.3774	0.3346	-0.0495	-0.0454	0.2121	-0.0538	0.3847	9.3345	12.1792	29.9571
5	8.2255	-3.4489	2.7179	6.5097	4.9735	9.9497	0.2097	0.1153	0.7186	-0.5362	0.1058	-0.0223	-0.5961	0.4915	-0.3192	0.2845	-0.0853	0.0746	0.2656	0.0623	0.3669	14.9098	9.7577	17.6268
6	6.78	-3.2624	-3.905	7.6064	2.33	6.444	0.4427	0.2586	0.1922	-0.5447	-0.1116	0.514	-0.4646	0.2199	-0.3342	0.2538	-0.1069	-0.0295	0.2702	-0.0023	0.2666	16.5084	2.1483	9.6783
7	8.835	-0.779	-6.6788	0.7939	0.7948	6.7793	-0.5117	1.1644	-0.2854	-0.1375	0.0509	0.0453	0.3033	-0.749	0.4817	0.3421	-0.0855	0.0005	0.3254	0.0003	0.4037	4.6133	-0.6166	13.0838
8	8.2248	-1.2016	0.0677	7.3405	-2.0178	3.615	0.347	-0	-0.1465	0.5087	-0.2448	0.5141	-0.3987	-0.0843	-0.1	0.241	-0.0201	0.0127	0.1905	-0.02	0.1966	-6.7242	5.8389	30.3539
9	6.7	6.3416	1.4495	7.5991	2.4363	8.2259	0.545	-1.8727	1.7081	1.0609	-0.511	-0.207	-0.5928	0.2659	-0.0167	0.5166	-0.0521	-0.0801	0.4904	-0.1438	0.3963	-1.423	17.4572	37.8422
10	8.7897	-7.3915	5.6131	9.5783	-6.343	5.8361	-0.9442	0.1161	2.6621	1.3135	0.238	-0.3983	-1.2344	0.5566	0.7081	0.6332	-0.0994	0.0849	0.6115	-0.1299	1.0916	10.7148	24.907	34.1047
11	8.2464	4.8958	3.8434	2.0385	2.6241	6.5327	-0.1011	0.7716	1.7437	-0.7819	0.6859	-0.1267	-1.3242	1.4644	-0.4834	0.7783	-0.2437	0.1602	0.5961	-0.1873	1.0601	8.9065	26.011	29.8242
12	3.8569	4.6077	-0.2313	6.0768	-2.1111	4.6838	-0.3884	0.2957	0.2405	-0.2107	0.6657	0.883	-0.0946	0.2979	-0.264	0.376	-0.0245	0.0791	0.2656	-0.1193	0.4346	-16.5343	-26.0569	14.7815
13	6.4505	2	0.5954	7.1381	2.7807	5.8977	-0.3655	0.3019	-0.4113	-0.5635	0.3542	-0.369	0.0288	0.332	0.0012	0.238	-0.0158	0.047	0.1941	-0.0736	0.2424	-11.5742	-17.8267	20.34
14	6.2945	2.6928	-0.0492	8.4303	1.5223	0.9195	-0.0806	0.5627	-0.6193	-0.3466	0.2988	-1.0305	0.2436	0.3218	-0.1846	0.3342	0.0305	0.0167	0.3463	-0.1123	0.3201	-8	-22.6107	19.6684
15	2.8758	2.9535	3.0126	8.2255	4.0939	3.2463	-0.3155	0.1715	0.0977	-0.6625	0.1547	0.4126	-0.2142	0.1739	0.1854	0.2222	-0.0073	0.0829	0.1843	0.0231	0.1969	-17.8366	-20.3171	21.0338
16	7.9215	2.5652	1.7194	4.1396	-0.7369	8.6833	-0.2727	-0.038	-0.8224	0.6204	-0.3027	1.194	-0.5293	-1.4489	0.5407	0.301	0.0344	0.0647	0.3712	0.022	0.565	-52.3918	-28.627	16.6697
17	8.0049	-2.059	-0.1657	0.5622	-0.208	0.6963	0.3129	-0.0835	0.499	-0.286	-0.0665	-0.3685	0.0888	-0.019	-0.2459	0.4708	-0.0718	-0.0042	0.2588	-0.0243	0.3631	-43.2486	-30.4272	16.2537
18	1.6758	-1.495	-0.6012	1.1732	0.4646	0.2164	0.0973	-0.223	0.3347	-0.0818	0.185	-0.7335	-0.2729	0.0158	-0.2482	0.4182	-0.0439	-0.0174	0.2019	-0.0813	0.5922	-37.5341	-23.2635	14.3714
19	4.2239	-0.2808	1.1206	0.9641	-1.0082	4.8043	0.2311	-0.2906	-0.7836	0.1536	0.2485	0.5514	0.2185	-0.2571	-0.4365	0.3471	-0.0526	0.0443	0.1629	-0.012	0.3829	-41.8001	-29.0871	19.2567
20	6.8278	-4.8263	2.6391	7.2068	-0.8856	9.1233	0.639	0.7591	0.0171	-0.5683	-0.2198	0.1456	-0.1413	-0.3808	-0.3977	0.4116	-0.0494	-0.0102	0.2667	-0.0093	0.3201	-42.5299	-27.2053	7.4209
21	3.4589	-1.3665	-2.3363	2.4061	2.4205	5.9429	-0.0823	0.1082	-0.4285	0.0877	-0.1599	0.4502	0.3876	-0.1817	0.2044	0.2315	-0.0446	0.003	0.1482	-0.0346	0.3922	-10.7775	2.7459	-10.4871
22	4.0005	-2.1095	-1.769	1.0476	0.677	0.4831	-0.0114	-0.2026	-0.1029	-0.0042	-0.0529	0.034	0.1073	0.1407	0.064	0.2245	0.006	-0.0096	0.1842	0.0012	0.2394	7.9092	2.7537	-11.8189
23	5.2695	0.6472	2.0353	2.5402	-0.1354	3.5214	0.1089	-0.0995	-0.4459	-0.0536	-0.0421	-0.0833	0.3488	0.0678	-0.0859	0.2576	-0.0084	0.0306	0.1404	-0.0326	0.2188	20.0856	-3.7524	-14.7412
24	8.2373	0.486	-0.2744	2.9409	-0.0586	1.4373	0.0545	-0.4218	-0.1054	0.3318	-0.1231	0.1363	0.1356	-0.2123	0.0736	0.3243	-0.044	0.0436	0.1962	-0.0594	0.2027	-22.6042	-10.2921	36.0648
25	3.4078	1.909	0.8433	6.4757	2.4682	3.4929	0.259	-0.4717	-0.2057	1.0312	-0.5428	1.0099	0.5779	-0.5148	0.2989	0.4046	-0.1074	0.119	0.3826	0.0112	0.534	-49.4874	-33.2142	27.0548
26	7.2166	-3.3416	1.3884	2.9251	-1.9595	1.6998	0.6748	0.1362	0.5811	0.0293	-0.3143	-0.1071	-0.0118	-0.0023	-0.3466	0.3786	-0.0131	0.0118	0.1835	-0.024	0.2761	2.1891	26.5692	-6.5391
27	6.8003	-2.7936	-1.8269	4.6815	-0.0715	3.1225	-0.0062	0.4212	0.4924	0.133	0.0205	0.2289	0.2328	-0.306	0.0037	0.2975	-0.025	0.0125	0.2055	-0.0035	0.3375	-7.6372	21.6387	-2.2684
28	9.6392	-0.4331	0.0742	0.7363	-0.4967	3.1888	-0.0151	-0.3407	0.1986	-0.0097	-0.0997	-0.2896	0.0502	0.0064	0.131	0.2173	-0.0331	0.0045	0.1355	0.0096	0.2103	-0.1011	19.9644	2.4299
29	5.7766	1.9502	5.1811	4.082	0.3125	7.1844	0.2776	0.2869	-0.2649	-0.2454	0.0315	-0.3809	0.2383	0.4871	-0.3115	0.1968	-0.0217	0.0483	0.1715	0.0051	0.2534	7.3124	19.0352	-1.836
30	9.8882	-1.0499	-2.019	0.857	0.4837	1.4826	-0.141	-0.001	1.1322	-0.1089	0.1728	-0.0168	-0.1418	0.1085	-0.0088	0.2718	-0.0263	-0.0435	0.1534	-0.0431	0.2292	3.7093	19.9031	-7.8401
31	6.4652	2.4658	3.437	9.1981	1.2258	7.6139	0.0697	0.9482	-0.1521	0.1129	-0.1142	-0.4224	1.1248	0.8809	0.0642	0.3169	0.0733	0.1248	0.27	-0.1351	0.4427	29.2139	-1.6015	-24.0109
32	4.8914	-4.2106	-4.1839	7.9113	8.8784	2.1647	0.119	0.1946	0.4426	-0.4756	-0.0565	0.4281	-0.1135	-0.37	0.0172	0.297	0.0419	0.0103	0.3136	0.0706	0.2577	26.0267	12.25	-21.0114
33	6.7518	1.7732	-5.1583	2.697	-1.0474	7.2878	0.722	0.322	1.2284	-0.0882	0.0417	-0.1637	-1.2986	0.3444	-0.7455	0.4091	-0.0378	0.1172	0.2924	0.0507	0.5287	25.432	10.9403	-30.0106
34	6.1183	-6.003	-2.122	9.1565	7.563	9.9625	-0.6852	-0.9684	-0.0192	0.8029	0.2196	0.2534	2.2433	0.3379	0.4063	0.5153	0.0469	0.0926	0.3578	0.0171	0.361	19.3689	13.7468	-7.4376
35	5.8284	-1.2211	-1.1298	4.2961	2.8259	4.4663	0.0881	0.4244	0.1766	-0.7129	0.121	-0.4365	-0.3263	0.403	-0.2034	0.3121	0.02	0.1074	0.271	0.076	0.2433	32.3137	7.8431	-27.0824

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'I' and (resid 1 through 73 )
2	X-RAY DIFFRACTION	2	chain 'I' and (resid 74 through 108 )
3	X-RAY DIFFRACTION	3	chain 'I' and (resid 109 through 172 )
4	X-RAY DIFFRACTION	4	chain 'J' and (resid 2 through 25 )
5	X-RAY DIFFRACTION	5	chain 'J' and (resid 26 through 43 )
6	X-RAY DIFFRACTION	6	chain 'J' and (resid 44 through 56 )
7	X-RAY DIFFRACTION	7	chain 'J' and (resid 57 through 96 )
8	X-RAY DIFFRACTION	8	chain 'J' and (resid 97 through 129 )
9	X-RAY DIFFRACTION	9	chain 'J' and (resid 130 through 139 )
10	X-RAY DIFFRACTION	10	chain 'J' and (resid 140 through 150 )
11	X-RAY DIFFRACTION	11	chain 'J' and (resid 151 through 172 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1 through 17 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 18 through 52 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 53 through 96 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 97 through 119 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 120 through 135 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 136 through 146 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 147 through 166 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 167 through 190 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 191 through 215 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 2 through 96 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 97 through 135 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 136 through 217 )
24	X-RAY DIFFRACTION	24	chain 'A' and (resid 1 through 113 )
25	X-RAY DIFFRACTION	25	chain 'A' and (resid 114 through 213 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 1 through 25 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 26 through 38 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 39 through 75 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 76 through 89 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 90 through 113 )
31	X-RAY DIFFRACTION	31	chain 'C' and (resid 114 through 128 )
32	X-RAY DIFFRACTION	32	chain 'C' and (resid 129 through 150 )
33	X-RAY DIFFRACTION	33	chain 'C' and (resid 151 through 163 )
34	X-RAY DIFFRACTION	34	chain 'C' and (resid 164 through 174 )
35	X-RAY DIFFRACTION	35	chain 'C' and (resid 175 through 213 )

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