PDB-6phd: Pfs25 in complex with the human transmission blocking antibody 2586

ID or keywords:

Entry

Database: PDB / ID: 6phd

Title

Pfs25 in complex with the human transmission blocking antibody 2586

Components

25 kDa ookinete surface antigen
2586 Antibody Fab, Heavy Chain
2586 Antibody Fab, Light Chain

Keywords

IMMUNE SYSTEM / Fab / Complex / Antigen / Immunoglobulin

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: 3.1 Å

Authors

McLeod, B.R. / Julien, J.P.

Funding support

Canada, 1items

Citation

Journal: Nat Commun / Year: 2019
Title: Potent antibody lineage against malaria transmission elicited by human vaccination with Pfs25.
Authors: McLeod, B. / Miura, K. / Scally, S.W. / Bosch, A. / Nguyen, N. / Shin, H. / Kim, D. / Volkmuth, W. / Ramisch, S. / Chichester, J.A. / Streatfield, S. / Woods, C. / Schief, W.R. / Emerling, D. ...

History

Deposition	Jun 25, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Apr 3, 2024	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 1.3	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	6phd.cif.gz	241.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6phd.ent.gz	194.6 KB	Display	PDB format
PDBx/mmJSON format	6phd.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/ph/6phd ftp://data.pdbj.org/pub/pdb/validation_reports/ph/6phd	HTTPS FTP

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Related structure data

Related structure data	6phbC 6phcC 6phfC 6phgC 6phhC C: citing same article (ref.)
Similar structure data	3u4e-2 6phf-2 4dqo-d 4g7v-d 7kfv-2 7kfw-2 4g7y-d 1mb2-3 4msw-d 6xxv-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) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #75 - Mar 2006 Tissue Factor similarity (1)

Deposited unit

H: 2586 Antibody Fab, Heavy Chain

L: 2586 Antibody Fab, Light Chain

C: 25 kDa ookinete surface antigen

68 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)	156.545, 156.545, 85.667
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Antibody	2586 Antibody Fab, Heavy Chain Mass: 24773.803 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	2586 Antibody Fab, Light Chain Mass: 22980.316 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: 20233.270 Da / Num. of mol.: 1 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
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: 3.86 Å³/Da / Density % sol: 68.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5, 30 % (w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 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: 3.1→40 Å / Num. obs: 19905 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC_1/2: 0.986 / R_merge(I) obs: 0.293 / R_pim(I) all: 0.084 / Net I/σ(I): 8.3
Reflection shell	Resolution: 3.1→3.2 Å / Redundancy: 12.7 % / R_merge(I) obs: 0.792 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1770 / CC_1/2: 0.698 / R_pim(I) all: 0.23 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 3.1→39.947 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.78

	R_factor	Num. reflection	% reflection
R_free	0.2314	994	5.01 %
R_work	0.2131	-	-
obs	0.214	19851	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→39.947 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4481	0	0	0	4481

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	4587
X-RAY DIFFRACTION	f_angle_d	0.47	6245
X-RAY DIFFRACTION	f_dihedral_angle_d	10.22	2788
X-RAY DIFFRACTION	f_chiral_restr	0.042	710
X-RAY DIFFRACTION	f_plane_restr	0.005	800

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 (%)
3.1-3.2634	0.3421	139	0.3132	2645	X-RAY DIFFRACTION	100
3.2634-3.4677	0.3192	140	0.2766	2639	X-RAY DIFFRACTION	100
3.4677-3.7353	0.2698	140	0.2462	2657	X-RAY DIFFRACTION	100
3.7353-4.1109	0.2498	138	0.2203	2652	X-RAY DIFFRACTION	100
4.1109-4.7049	0.2076	142	0.1734	2688	X-RAY DIFFRACTION	100
4.7049-5.9246	0.1816	144	0.1791	2717	X-RAY DIFFRACTION	100
5.9246-39.9504	0.1886	151	0.1928	2859	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	4.989	1.8679	1.6373	2.8955	-0.3913	1.4367	0.1591	0.1539	0.7936	-0.2357	-0.6695	0.2808	-0.1085	-0.8116	0.3853	0.3827	0.0186	0.0248	0.5506	0.1059	0.5031	3.5727	42.1376	-6.8561
2	6.5545	2.1267	6.7494	1.5775	2.2635	9.1516	-0.6101	0.7575	1.0074	-0.5475	-0.1409	0.2518	-0.9291	1.0273	0.7365	0.4619	0.0277	-0.0067	0.4053	0.0729	0.5493	14.0411	45.3957	0.5055
3	1.5791	-2.4152	-0.8604	4.3895	-0.3601	6.2489	-0.2057	0.1894	0.2562	0.3681	0.0693	0.2039	-0.4552	-0.5583	0.1062	0.3309	-0.0454	0.0116	0.4662	-0.0685	0.3303	5.9439	33.2902	1.1539
4	6.7021	-0.2486	0.7959	4.4945	0.9191	5.7153	-0.9252	-1.0152	-0.1101	-0.1931	0.6343	-1.1761	-0.471	0.666	0.1985	0.3814	-0.0853	0.0042	0.4598	-0.0041	0.4462	22.5518	36.1548	1.1331
5	6.5801	-1.7248	3.1988	5.6081	-0.0594	1.6537	1.6088	0.7559	-1.1901	-0.6405	-0.1446	1.7407	1.5503	1.2892	-1.1218	0.59	0.0395	-0.0744	0.548	-0.0857	0.5395	10.9803	25.9374	-6.4064
6	0.4324	0.0643	0.0862	1.9684	2.1112	3.9841	-0.2748	-0.2515	0.715	-1.7032	0.0613	-1.6496	-1.3483	-0.6686	0.2401	0.5974	0.1322	-0.003	0.3696	-0.0135	0.6199	16.9364	42.0901	-5.3346
7	3.5039	1.2792	0.8722	3.6378	3.6959	3.923	-0.5298	0.689	0.6082	-1.0487	0.6286	-0.1041	-1.2144	0.3766	-0.1759	0.477	-0.0867	-0.0576	0.4338	0.1236	0.4777	12.3728	41.5645	-6.7728
8	3.4409	-0.2027	0.8658	0.4605	-1.4149	5.1121	-0.0587	-0.115	0.2628	-0.0173	-0.1385	0.425	-0.0591	-1.4595	0.2745	0.2247	-0.0102	-0.0077	0.5081	0.0354	0.371	4.945	34.365	-3.8068
9	7.2427	-3.7136	-0.8905	4.7918	-2.8002	4.0518	-0.747	-0.2073	0.3718	0.6826	-0.0813	-1.3753	-0.396	0.0288	0.964	0.5259	-0.07	-0.1404	0.4182	-0.023	0.4925	22.0226	38.9133	14.3411
10	5.2406	-0.5426	2.7403	1.1778	-1.5493	5.0114	-0.3582	-0.0209	0.0922	-0.2108	0.2581	0.2606	-0.6536	-0.9431	-0.0909	0.2892	0.0169	0.0538	0.4394	-0.0162	0.3345	2.9216	38.5015	-0.0126
11	8.5609	4.0234	-2.5729	6.4564	-0.6585	3.0235	-0.8565	-0.5622	-0.2845	-1.3512	0.0935	0.4757	0.8949	1.002	0.5768	0.4286	0.1315	-0.1061	0.6216	0.0798	0.5112	-21.8647	26.9537	-17.0676
12	6.8564	2.2741	-4.1702	6.0968	0.2735	6.9113	0.1348	0.9938	-0.3801	0.0832	0.0186	0.499	-0.6443	-1.1581	0.11	0.4458	0.1726	-0.0078	0.3933	-0.1356	0.5677	-32.1359	21.2251	-4.6964
13	3.6555	0.9566	-2.119	2.3229	-1.5811	4.0553	0.3298	0.039	0.2008	0.0934	-0.0499	0.6343	-1.6009	0.6187	-0.1997	0.3787	-0.1419	-0.0754	0.432	-0.1267	0.3941	-28.4556	33.0657	-8.8649
14	5.8898	-1.9437	-1.7592	4.7117	-4.8917	8.0389	0.2189	2.1825	0.6142	-0.9318	-0.0449	0.4488	1.7106	0.973	0.035	0.2904	-0.0746	-0.08	0.7398	-0.0882	0.4611	-15.2268	28.2357	-9.0638
15	0.0633	0.0362	0.2843	3.2744	-2.1197	4.6909	0.187	-0.0332	-0.0105	-0.0497	0.0119	0.8521	-0.0868	-0.3648	-0.2585	0.4094	-0.0203	0.0352	0.398	-0.0748	0.6177	-34.8511	27.5979	-8.8325
16	4.2344	-0.2896	1.312	1.2304	1.1666	5.0967	-0.0935	0.2244	0.9526	-0.8071	0.1799	1.8419	0.1083	-0.3973	0.2125	0.4277	0.0267	-0.1169	0.4233	-0.1596	0.4178	-33.4957	25.9701	-16.2361
17	6.0507	-0.0856	-1.3221	1.7191	0.1713	2.2592	-0.0325	-0.4262	0.3507	0.2843	-0.025	-0.0533	-0.0721	-0.2924	0.0453	0.3436	0.0607	0.0108	0.5287	-0.0991	0.2668	1.6201	32.0927	19.1591
18	1.611	-0.1187	1.2469	0.5328	0.0029	-0.246	-0.1293	-0.3247	0.0083	0.0642	0.032	0.1035	-0.0036	-0.0623	0.1413	0.4297	0.0514	0.0593	0.5398	-0.0579	0.3499	-11.3528	25.1517	7.1989
19	3.544	0.0997	0.552	3.6146	1.5696	4.0491	0.0682	-0.5063	-0.2546	-0.2042	-0.1239	-0.3697	0.2791	0.3902	0.1136	0.5038	0.097	0.0492	0.5629	0.0791	0.3583	-19.297	16.6647	0.0716
20	4.8448	2.0683	-0.008	3.9703	1.3632	2.5127	0.2422	-0.3347	-0.0367	0.4243	-0.0533	0.2541	0.2894	0.0493	-0.2627	0.3889	-0.0946	-0.0085	0.4581	-0.0244	0.3198	30.4261	29.0247	31.3524
21	5.7962	-0.3826	-1.1148	1.5401	-0.944	4.3408	0.0647	-0.0157	0.3773	-0.3087	0.0163	-0.2177	-0.1012	0.1528	-0.0423	0.4837	0.013	0.0355	0.3489	-0.1004	0.362	43.105	35.4277	35.1408
22	0.7067	-0.9224	1.6156	5.0585	0.2434	5.2144	-1.2001	-1.0722	1.2902	-0.6959	0.7673	-0.7579	0.1144	-0.259	0.2611	0.4048	-0.1088	-0.1075	0.8959	-0.2602	0.5773	52.5049	33.5062	35.5238
23	1.9467	-0.89	-2.4862	6.3224	0.2956	9.2427	-0.0221	-0.8138	-0.1711	-1.2625	0.1245	-0.8033	0.492	1.0481	-0.0929	0.6412	0.0357	0.1301	0.5251	-0.0192	0.6376	60.256	31.0525	31.3358
24	5.4377	2.8087	1.7978	2.8631	-1.1913	5.3561	-0.066	0.1933	-0.4396	-0.0142	-0.0039	-0.3092	0.6001	0.4746	0.0981	0.4384	0.0157	0.0407	0.3243	-0.058	0.3042	43.3355	26.4733	19.7579
25	9.0228	-6.8406	-1.8186	5.2796	2.2856	6.6318	0.3393	-0.2031	-1.9476	0.5384	-0.1394	1.5672	0.6372	0.4821	-0.2757	0.725	-0.204	-0.0965	0.5377	0.0188	0.7258	36.6509	13.6192	21.8291
26	3.328	-1.9308	0.883	1.4917	-1.4147	1.7188	-0.2074	-0.0782	0.0129	0.0268	0.3113	-0.0268	0.2842	-0.2616	-0.1814	0.4274	-0.0561	-0.023	0.2997	-0.0416	0.3713	28.9591	26.1548	11.0854
27	6.1724	-1.038	4.2868	4.1025	-3.1585	4.5201	0.2386	-0.1848	0.2956	0.9862	0.1138	0.1926	-1.4261	-1.9679	-0.265	0.3663	-0.0977	0.1943	0.8773	-0.0401	0.3832	18.6113	32.1816	30.1319
28	5.7362	-0.45	-0.1021	1.5551	0.3507	2.0333	-1.0029	-0.6989	1.6077	1.1559	0.7533	-0.1396	-0.0828	-0.6562	0.4003	0.7924	0.0671	-0.1209	0.7629	-0.1706	0.5046	22.898	37.8606	27.5028
29	9.3169	6.8689	3.0582	6.0636	3.1744	1.82	-0.4043	-1.4983	1.6545	1.2494	-0.2039	0.1944	0.4827	0.7115	0.8656	1.0019	0.1822	-0.1241	1.3561	-0.2019	0.9829	18.862	46.3952	35.1784

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 33 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 34 through 51 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 52 through 62 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 63 through 69 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 70 through 78 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 79 through 85 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 86 through 102 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 103 through 113 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 114 through 128 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 129 through 139 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 140 through 158 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 159 through 180 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 181 through 192 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 193 through 218 )
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 219 through 229 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 5 through 69 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 70 through 154 )
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 155 through 213 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 2 through 25 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 26 through 44 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 45 through 56 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 57 through 73 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 74 through 101 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 102 through 109 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 110 through 132 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 133 through 144 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 145 through 158 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 159 through 172 )

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