PDB-6phf: Pfs25 in complex with the human transmission blocking antibody 2587

ID or keywords:

Entry

Database: PDB / ID: 6phf

Title

Pfs25 in complex with the human transmission blocking antibody 2587

Components

25 kDa ookinete surface antigen
2587 Antibody Fab, Heavy Chain
2587 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6phf.cif.gz	452.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6phf.ent.gz	374.9 KB	Display	PDB format
PDBx/mmJSON format	6phf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6phf_validation.pdf.gz	467.2 KB	Display	wwPDB validaton report
Full document	6phf_full_validation.pdf.gz	476.2 KB	Display
Data in XML	6phf_validation.xml.gz	39.6 KB	Display
Data in CIF	6phf_validation.cif.gz	54.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ph/6phf ftp://data.pdbj.org/pub/pdb/validation_reports/ph/6phf	HTTPS FTP

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Related structure data

Related structure data	6phbC 6phcC 6phdC 6phgC 6phhC C: citing same article (ref.)
Similar structure data	3wd5-d 6jbt-d 5vke-d 7kmh-d 2ol3-d 3enh-1 6n5b-d 6j15-2 5vk6-d 7ch5-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

A: 2587 Antibody Fab, Heavy Chain

G: 25 kDa ookinete surface antigen

B: 2587 Antibody Fab, Light Chain

C: 2587 Antibody Fab, Heavy Chain

E: 25 kDa ookinete surface antigen

D: 2587 Antibody Fab, Light Chain

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

1

A: 2587 Antibody Fab, Heavy Chain

G: 25 kDa ookinete surface antigen

B: 2587 Antibody Fab, Light Chain

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

2

C: 2587 Antibody Fab, Heavy Chain

E: 25 kDa ookinete surface antigen

D: 2587 Antibody Fab, Light Chain

defined by author
67 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.236, 110.266, 147.097
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Antibody	2587 Antibody Fab, Heavy Chain Mass: 23951.740 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein	25 kDa ookinete surface antigen / Pfs25 Mass: 20233.270 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
#3: Antibody	2587 Antibody Fab, Light Chain Mass: 22776.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.2 M potassium thiocyanate, 20% (w/v) PEG 3350, and cryoprotected in 15% (v/v) ethylene glycol

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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: 25850 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC_1/2: 0.979 / R_merge(I) obs: 0.284 / R_pim(I) all: 0.119 / Net I/σ(I): 6.8
Reflection shell	Resolution: 3.1→3.2 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.784 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2305 / CC_1/2: 0.543 / R_pim(I) all: 0.334 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 3.1→39.752 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.07

	R_factor	Num. reflection	% reflection
R_free	0.2665	1291	5.01 %
R_work	0.2371	-	-
obs	0.2386	25791	99.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→39.752 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8766	0	0	0	8766

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	8971
X-RAY DIFFRACTION	f_angle_d	0.5	12215
X-RAY DIFFRACTION	f_dihedral_angle_d	10.446	5448
X-RAY DIFFRACTION	f_chiral_restr	0.043	1392
X-RAY DIFFRACTION	f_plane_restr	0.004	1562

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 (%)
3.1-3.2241	0.395	140	0.3571	2669	X-RAY DIFFRACTION	100
3.2241-3.3708	0.3331	141	0.3312	2666	X-RAY DIFFRACTION	100
3.3708-3.5484	0.3085	142	0.2889	2703	X-RAY DIFFRACTION	100
3.5484-3.7705	0.2999	142	0.2666	2683	X-RAY DIFFRACTION	100
3.7705-4.0614	0.2406	142	0.2353	2706	X-RAY DIFFRACTION	100
4.0614-4.4696	0.2435	143	0.1962	2710	X-RAY DIFFRACTION	100
4.4696-5.1152	0.2101	143	0.1848	2724	X-RAY DIFFRACTION	100
5.1152-6.4402	0.2576	145	0.2147	2757	X-RAY DIFFRACTION	100
6.4402-39.7554	0.2533	153	0.2168	2882	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	8.3082	3.6015	-1.3873	3.7587	-0.2825	1.8339	-0.0732	1.4875	1.0534	0.2558	0.5203	-0.1123	-0.4505	0.0169	-0.3152	0.6776	-0.0247	0.0338	0.3526	0.0557	0.2635	-51.4674	39.8475	163.447
2	5.6567	-2.1829	0.6997	2.9206	-0.206	2.2111	-0.0402	-0.7414	-0.0077	0.044	0.3894	-0.2166	-0.6436	-0.0924	0.0858	0.4296	0.1434	0.0077	0.1779	0.0106	0.2602	-57.5922	40.2178	173.4118
3	4.1196	-0.367	-2.0684	4.5591	0.872	1.7989	0.3079	-0.4005	0.3983	0.4761	-0.3424	0.1349	-0.0976	-0.0579	-0.0266	0.7795	0.1667	-0.0731	0.2165	-0.1139	0.342	-53.5165	45.4428	172.743
4	0.367	-0.5386	-0.372	0.6555	0.8282	2.698	-0.2382	-0.168	-0.1057	-0.0502	0.0802	0.1638	0.1251	-0.1158	0.0949	0.3812	0.0362	0.0005	0.2067	0.0532	0.2862	-50.453	27.5468	159.8439
5	6.5894	-2.7274	4.4641	2.6063	0.0652	5.9347	-0.1471	0.1785	-0.3048	-0.3486	-0.0381	-0.1876	0.0606	0.0195	0.1197	0.5336	-0.0744	0.0312	0.2057	-0.0011	0.2367	-44.2879	21.2188	157.7123
6	1.8118	-0.6927	0.4267	0.9458	0.8441	2.4415	0.0022	0.1302	-0.1823	-0.0084	-0.0778	1.0543	-0.0845	0.0737	0.0898	0.536	0.1847	0.0124	0.0894	0.1206	0.5686	-53.0741	17.5152	149.2429
7	1.6408	0.3421	-0.1346	1.1923	-2.2763	4.5473	-0.2293	0.1518	-0.2025	-0.5434	-0.1308	-0.1258	1.0507	0.2767	-3.7323	0.6195	0.0378	-0.1884	0.2809	0.2751	0.0865	-50.3805	22.3848	144.0311
8	7.565	-0.3734	-2.6439	4.4426	3.6894	4.0542	0.4272	0.0988	1.2332	1.0786	-0.4796	-0.2489	1.5216	-0.03	0.1307	0.9491	0.2156	0.3388	0.7691	0.2741	0.7401	-80.9438	38.5275	206.9946
9	2.7029	1.558	4.5431	8.1116	1.6071	7.7879	-1.3614	-1.3862	-0.0297	0.6112	1.2495	0.1944	0.4218	-0.0344	0.1317	0.6454	0.2966	0.1312	0.739	-0.0965	0.422	-78.7884	42.3363	198.9447
10	7.1005	-5.7833	7.5445	6.5853	-5.7604	8.067	0.1897	0.9848	-0.7791	0.5625	-0.3331	0.9559	0.4545	-0.2821	0.1598	0.4238	0.0278	0.102	1.3119	-0.0715	0.6888	-91.8758	46.0999	204.0611
11	4.2745	-2.1243	-1.1373	4.1653	3.1986	4.8609	0.9246	0.2155	1.4412	0.5504	0.2997	0.1732	-1.1018	-1.683	-0.9562	1.0195	0.1067	0.6174	1.5019	-0.1688	1.5997	-99.0322	54.4921	208.7177
12	3.6281	4.3619	-2.8597	7.4522	-1.6016	3.7542	1.0064	-0.0752	2.8851	0.5728	0.1664	1.7608	-1.1688	-0.6833	-1.0524	0.7591	0.1632	0.1475	1.1772	-0.4044	1.2918	-85.3262	58.0571	204.3476
13	7.9095	-1.2982	-2.1476	4.6295	4.2364	3.9944	0.4277	-1.7637	1.0348	0.3297	0.4452	-1.0589	-2.0769	1.3392	-1.0416	0.7471	-0.0943	0.1546	0.9332	-0.2197	0.8154	-71.5839	55.6685	201.4153
14	4.7079	0.2194	0.8312	0.835	-1.764	4.0797	0.5042	-1.8024	1.6506	0.4697	0.0701	-0.0933	-1.271	0.9376	0.1459	0.4372	-0.1779	0.1018	0.45	-0.3038	0.666	-68.7928	50.5198	193.627
15	2.7364	-0.0017	-0.6219	3.6156	3.2332	6.1504	0.5681	-0.5754	0.5425	0.4454	-0.3327	0.6631	0.0669	0.1819	-0.1244	0.5611	0.099	0.0977	0.4466	-0.0135	0.4505	-71.3191	40.4408	192.7415
16	6.7461	-4.4785	-2.589	8.2984	-1.184	2.5829	-0.5458	0.0359	-1.354	-0.177	-0.2781	1.6321	0.5883	-0.8307	0.7517	0.918	-0.1481	0.0639	0.5752	-0.1219	0.5374	-79.513	37.1139	191.1753
17	4.5196	-4.1136	5.1704	6.5809	-6.1992	6.7023	1.3618	-1.623	0.0793	-0.6389	0.826	0.9118	0.2682	-1.274	-1.3877	0.8651	-0.2131	0.3457	1.1788	-0.0965	1.0649	-88.367	25.5367	189.1842
18	2.3165	-2.7806	-0.5843	4.8365	0.7834	3.0866	-0.1302	0.0514	-0.2022	0.2581	0.0554	0.1515	0.2058	-0.2117	0.085	0.4245	-0.01	-0.0002	0.2289	0.0071	0.2716	-56.5657	22.9881	184.605
19	1.8541	1.2887	-1.1018	3.8841	-2.7534	7.1101	-0.0783	-0.4173	-0.1977	0.3663	0.2593	-0.1602	-0.0124	0.1003	-0.1792	0.6908	0.1254	-0.0056	0.2222	0.0276	0.3334	-35.9315	10.2718	155.5876
20	8.4893	-2.9408	-1.8529	2.1511	0.821	1.5539	-0.8607	-0.8156	-0.1374	0.6627	0.7437	0.0553	-0.409	0.6029	0.1424	0.9192	0.0436	0.0629	0.4558	0.0051	0.2265	-31.963	37.5475	198.8048
21	4.2672	1.005	-1.0851	6.1713	0.4172	4.0772	-0.165	0.0618	0.295	0.1094	0.1165	0.2144	-0.4343	0.5847	0.0586	0.4426	-0.0199	-0.0613	0.4182	-0.0094	0.2169	-27.3994	41.5799	187.5177
22	2.5075	-0.1798	-3.1351	1.2655	0.1943	3.6077	-0.0111	-0.248	0.0527	0.3281	0.0333	-0.1452	-0.1464	0.4191	-0.0938	0.4362	-0.0291	-0.0956	0.3539	-0.0189	0.1981	-30.1459	38.459	192.5888
23	2.3611	2.2544	-0.007	2.1678	0.0803	0.8467	0.1507	-0.3136	-0.6443	-0.6825	-0.024	-1.1288	-0.0057	0.2513	-0.1758	0.6925	-0.0171	0.1918	0.1408	-0.2771	0.2818	-37.0833	16.8964	210.4742
24	4.8736	-4.3871	-5.0996	4.0657	4.5539	5.4025	0.473	0.313	-0.2352	-0.7523	-0.0943	-0.4599	0.0474	0.2682	-0.2849	0.5552	-0.0334	0.0165	0.5943	0.0489	0.5084	-4.3788	41.0018	160.3893
25	3.417	-0.125	0.7379	4.626	1.1544	2.288	0.1606	0.3308	0.6508	-0.6417	0.2007	-1.0749	-0.2193	-0.0309	-0.2596	0.6147	0.0313	0.0887	0.6794	0.1653	0.9647	6.7316	55.6063	157.9199
26	5.2894	1.4154	-1.7013	3.0302	-3.5567	5.3909	0.2516	0.3346	0.3003	-0.2547	-0.8835	-0.2519	-0.0375	0.2728	0.5625	0.4223	0.0196	-0.0933	0.2539	-0.0125	0.4323	-16.2107	52.6611	167.1403
27	8.767	0.3843	-0.9632	5.7375	2.5754	7.9176	-0.227	-0.1011	-1.251	-0.427	0.4907	-1.2209	1.0439	1.1674	-0.1291	0.5185	0.0212	0.0623	0.452	0.117	0.611	-5.7889	33.0088	168.9105
28	3.7153	-1.4549	4.4243	8.2745	0.3171	7.0147	0.9438	0.8833	-0.7439	0.2148	0.3832	1.9467	0.3504	-0.2427	-1.4402	0.7825	0.0761	-0.1662	0.6429	0.2839	0.9038	4.5066	26.3866	173.043
29	2.0094	2.4271	-0.456	3.5632	-0.9833	0.9522	-0.1676	0.0161	-0.003	-0.107	0.0864	0.0822	0.3939	0.2438	0.0864	0.5181	0.1119	0.0151	0.1986	0.0704	0.2828	-28.723	22.7173	176.6113
30	2.1199	-0.6464	-1.2084	2.6197	1.3452	2.5833	-0.0493	-0.1203	-0.0679	0.0021	-0.1255	0.0279	-0.1351	-0.0836	0.1452	0.5658	0.0175	0.0032	0.0934	0.0298	0.2858	-50.3058	8.7119	205.2239

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 164 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 165 through 184 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 185 through 210 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 211 through 221 )
8	X-RAY DIFFRACTION	8	chain 'G' and (resid 1 through 11 )
9	X-RAY DIFFRACTION	9	chain 'G' and (resid 12 through 25 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 26 through 44 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 45 through 54 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 55 through 89 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 90 through 108 )
14	X-RAY DIFFRACTION	14	chain 'G' and (resid 109 through 121 )
15	X-RAY DIFFRACTION	15	chain 'G' and (resid 122 through 150 )
16	X-RAY DIFFRACTION	16	chain 'G' and (resid 151 through 158 )
17	X-RAY DIFFRACTION	17	chain 'G' and (resid 159 through 173 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 2 through 112 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 113 through 208 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 1 through 17 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 18 through 68 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 69 through 126 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 127 through 221 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 1 through 25 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 26 through 89 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 90 through 134 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 135 through 158 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 159 through 173 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 1 through 112 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 113 through 208 )

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Movie

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Structure viewers

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Open data

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Validation report

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Assembly

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi