PDB-6b0a: Crystal structure of Pfs25 in complex with the transmission block...

ID or keywords:

Entry

Database: PDB / ID: 6b0a

Title

Crystal structure of Pfs25 in complex with the transmission blocking antibody 1269

Components

1269 antibody, heavy chain
1269 antibody, light chain
25 kDa ookinete surface antigen

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

Homo sapiens (human)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Scally, S.W. / McLeod, B. / 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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Validation report

Summary document	6b0a_validation.pdf.gz	452.5 KB	Display	wwPDB validaton report
Full document	6b0a_full_validation.pdf.gz	456.9 KB	Display
Data in XML	6b0a_validation.xml.gz	21.8 KB	Display
Data in CIF	6b0a_validation.cif.gz	29.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/6b0a ftp://data.pdbj.org/pub/pdb/validation_reports/b0/6b0a	HTTPS FTP

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Related structure data

Related structure data	6azzC 6b08C 6b0eC 6b0gC 6b0hC 1z27S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6u6u-d 7dpm-3 1sy6-d 7dpm-1 6zlr-2 6phb-1 6azz-1 1kg0-d 6xc4-2 6wo4-d 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

H: 1269 antibody, heavy chain

L: 1269 antibody, light chain

A: 25 kDa ookinete surface antigen

hetero molecules

67.5 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)	82.100, 39.503, 101.845
Angle α, β, γ (deg.)	90.00, 94.70, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	1269 antibody, heavy chain Mass: 24012.631 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	1269 antibody, light chain Mass: 23179.652 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	25 kDa ookinete surface antigen / Pfs25 Mass: 20104.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate NF54 / Production host: Homo sapiens (human) / References: UniProt: P13829
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.45 Å³/Da / Density % sol: 49.71 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M di-ammonium hydrogen citrate, 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: Sep 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.5→40 Å / Num. obs: 23042 / % possible obs: 99.6 % / Redundancy: 3.7 % / R_pim(I) all: 0.03 / Net I/σ(I): 17.4
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2539 / R_pim(I) all: 0.294 / % possible all: 99.9

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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, 1269 Fab

1z27

Resolution: 2.5→39.073 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.59

	R_factor	Num. reflection	% reflection
R_free	0.2485	1162	5.05 %
R_work	0.2173	-	-
obs	0.2189	22998	99.52 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→39.073 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4366	0	12	15	4393

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	4470
X-RAY DIFFRACTION	f_angle_d	0.467	6081
X-RAY DIFFRACTION	f_dihedral_angle_d	10.81	2701
X-RAY DIFFRACTION	f_chiral_restr	0.04	702
X-RAY DIFFRACTION	f_plane_restr	0.004	779

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 (%)
2.5001-2.6138	0.4698	150	0.3642	2710	X-RAY DIFFRACTION	100
2.6138-2.7516	0.3865	134	0.3143	2668	X-RAY DIFFRACTION	99
2.7516-2.9239	0.3493	156	0.2857	2711	X-RAY DIFFRACTION	100
2.9239-3.1496	0.3464	136	0.2866	2714	X-RAY DIFFRACTION	100
3.1496-3.4664	0.2728	139	0.2472	2715	X-RAY DIFFRACTION	100
3.4664-3.9675	0.2464	153	0.2201	2726	X-RAY DIFFRACTION	99
3.9675-4.9971	0.2037	145	0.1664	2748	X-RAY DIFFRACTION	99
4.9971-39.0774	0.1865	149	0.1831	2844	X-RAY DIFFRACTION	99

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	2.2569	2.7038	-3.1982	4.0507	-4.527	5.1379	-0.0942	-1.106	-0.4668	-0.9379	-0.0066	0.2742	0.6719	-0.4636	-0.1006	0.7899	0.0096	0.0007	0.8914	0.0411	1.2577	-17.2797	-27.4301	-81.6204
2	6.5718	-2.7488	-1.4118	5.1644	-2.965	7.9885	-0.2493	0.8346	-0.3099	-0.6212	0.0003	0.237	0.6682	0.0895	0.2646	0.5622	-0.0287	-0.0124	0.6605	-0.0102	0.803	-20.2784	-13.6005	-74.2493
3	4.0889	-0.879	-1.5492	5.025	-2.7256	3.2558	-0.594	0.837	-0.3474	0.2434	0.1962	0.1025	0.4758	-0.4364	0.2794	0.575	0.0396	-0.0412	0.6481	-0.0395	0.9059	-16.5326	-5.5389	-67.2592
4	7.9441	5.994	-6.4444	7.6091	-5.7836	5.8447	-0.0907	-0.1498	1.1356	0.2253	0.3902	-0.8976	-0.3298	0.2334	-0.4492	0.5451	0.0889	0.0198	0.4922	0.016	0.9492	-15.0308	6.572	-68.7552
5	9.0036	1.4873	-1.9027	1.6873	1.7948	7.7827	-0.152	0.735	0.2385	-0.3661	-0.2561	-0.1448	0.0492	0.3017	0.1967	0.6143	0.0706	0.0073	0.7267	0.132	1.0183	3.8392	1.5553	-84.5267
6	1.3963	0.7936	-1.5913	2.1249	-0.5597	6.2805	0.1665	0.0507	-0.1712	-0.0452	-0.0853	0.0518	0.3154	-0.2412	-0.092	0.3772	-0.0117	-0.0748	0.2695	-0.0008	0.6641	-27.2803	-8.1731	-48.9811
7	0.4482	0.221	0.6784	1.0911	0.5606	3.1561	0.0877	-0.2557	0.084	0.0255	-0.2991	-0.0064	0.1186	-0.5109	0.2185	0.3429	-0.0521	-0.0676	0.5308	0.001	0.8407	-29.1165	0.4303	-35.8182
8	4.9711	-2.9023	-0.7051	6.1426	3.7474	8.6796	0.1977	-0.4265	0.5567	0.0331	-0.7149	0.381	-0.7001	-1.2774	0.4498	0.4883	-0.0846	-0.0291	0.8642	-0.0447	0.6992	-35.359	8.8465	-17.5045
9	5.1849	0.9393	0.6551	2.9563	2.8787	7.3441	0.103	-0.589	-0.3564	-0.1119	0.3972	-1.1587	0.3197	1.0957	-0.3951	0.4561	0.0097	-0.1229	0.6738	0.0473	0.9603	-4.3059	-0.1417	-39.4528
10	5.2469	0.378	0.4342	4.1547	2.8829	8.3316	0.2698	-0.1252	0.2849	0.0064	-0.2939	-0.3386	0.0283	-0.2217	0.1046	0.394	-0.0279	-0.0439	0.3706	0.0843	0.7942	-14.5745	3.3165	-45.4986
11	3.4872	1.6917	0.9808	2.3695	2.4292	6.2951	0.2167	-0.0839	0.0955	-0.1704	-0.1665	-0.4623	-0.277	0.6052	-0.109	0.4254	-0.004	-0.0103	0.5313	0.1021	0.8464	-8.9485	4.928	-44.8256
12	1.844	3.6943	3.7174	7.8045	7.5719	7.5576	0.6691	-0.804	0.1428	0.5889	0.2496	-1.3014	0.3198	0.8704	-0.9347	0.5975	-0.2035	-0.0403	0.8792	-0.139	0.8048	-9.5778	11.6687	-23.5733
13	2.9052	1.0028	-1.0914	4.7549	-0.654	6.9585	0.1572	-0.4779	0.495	0.3811	-0.0948	-0.0795	0.1972	-0.1135	0.1237	0.4555	-0.1623	-0.083	0.8962	-0.0082	0.5011	-24.2216	3.9428	-10.2237
14	2.4092	1.3068	-1.0805	6.004	-2.8846	9.2588	0.2519	-0.3979	-0.0528	1.2776	0.1489	-0.447	-0.5936	0.1577	0.2317	0.6436	-0.0039	-0.1496	0.7795	0.0041	0.7564	-21.451	-4.8179	-8.9813
15	4.4708	-0.0494	-0.422	9.3925	-0.8356	7.9851	-0.1761	-1.4919	0.9987	-0.967	0.4599	-1.1335	-0.567	0.0006	0.0555	0.6467	-0.209	-0.0006	0.8169	-0.0089	0.877	-17.2826	12.3496	-24.3877
16	1.8809	0.5143	-1.3101	4.2965	-0.866	6.0381	-0.3617	-0.9706	-0.131	0.5767	-0.4943	0.1299	0.9965	0.4162	0.2028	0.8627	-0.2013	-0.0093	1.1408	0.0785	0.7071	-26.3191	-2.2349	-3.9187
17	0.5416	0.7461	1.0473	4.4177	-0.0651	3.4283	0.1551	-1.619	-0.3202	0.6372	-0.524	-0.8938	0.0424	1.2214	0.0798	0.7336	-0.1787	-0.187	1.2363	0.0911	0.6897	-16.4369	6.8233	-3.8198
18	3.7115	-0.2811	-2.2323	2.9232	2.9948	4.2474	-0.3248	-0.0292	-0.1087	0.3454	0.4086	-0.1273	0.0157	-0.1675	-0.1257	0.489	0.0705	0.004	0.5664	0.0062	0.7896	-2.6165	-7.3831	-76.8713
19	0.9195	2.6053	0.2916	7.2424	0.6744	6.5608	-0.372	1.3505	-0.3618	-0.3989	0.1617	-0.7238	1.4847	-0.2576	0.2754	0.5485	-0.0843	0.1732	0.8966	-0.165	1.0213	-8.162	-17.7469	-84.4943

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 44 through 73 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 74 through 89 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 90 through 109 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 110 through 132 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 133 through 172 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 1 through 73 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 74 through 177 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 178 through 227 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 1 through 30 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 31 through 49 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 50 through 100 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 101 through 111 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 112 through 148 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 149 through 161 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 162 through 172 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 173 through 195 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 196 through 211 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 2 through 25 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 26 through 43 )

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