PDB-6phb: Pfs25 in complex with the human transmission blocking antibody 2530

ID or keywords:

Entry

Database: PDB / ID: 6phb

Title

Pfs25 in complex with the human transmission blocking antibody 2530

Components

25 kDa ookinete surface antigen
2530 Antibody Fab, Heavy Chain
2530 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

Plasmodium falciparum (malaria parasite P. falciparum)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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	Oct 11, 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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Download

PDBx/mmCIF format	6phb.cif.gz	491.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6phb.ent.gz	402 KB	Display	PDB format
PDBx/mmJSON format	6phb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6phb_validation.pdf.gz	472 KB	Display	wwPDB validaton report
Full document	6phb_full_validation.pdf.gz	476.1 KB	Display
Data in XML	6phb_validation.xml.gz	54 KB	Display
Data in CIF	6phb_validation.cif.gz	78.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ph/6phb ftp://data.pdbj.org/pub/pdb/validation_reports/ph/6phb	HTTPS FTP

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Related structure data

Related structure data	6phcC 6phdC 6phfC 6phgC 6phhC 5uqyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6xc4-2 3c09-1 7bwj-d 7c01-2 2zuq-1 6b0a-d 6hhc-d 6wo4-d 7aud-5 7kmi-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: 25 kDa ookinete surface antigen

C: 2530 Antibody Fab, Light Chain

D: 2530 Antibody Fab, Heavy Chain

E: 25 kDa ookinete surface antigen

A: 2530 Antibody Fab, Light Chain

B: 2530 Antibody Fab, Heavy Chain

hetero molecules

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

1

I: 25 kDa ookinete surface antigen

C: 2530 Antibody Fab, Light Chain

D: 2530 Antibody Fab, Heavy Chain

hetero molecules

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

2

E: 25 kDa ookinete surface antigen

A: 2530 Antibody Fab, Light Chain

B: 2530 Antibody Fab, Heavy Chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	114.599, 114.599, 98.181
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: 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
#2: Antibody	2530 Antibody Fab, Light Chain Mass: 23625.131 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	2530 Antibody Fab, Heavy Chain Mass: 23309.992 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 Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1057 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.2 M lithium sulfate, 0.1 M Tris, pH 7.0, and 2.0 M ammonium sulfate

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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: 2→40 Å / Num. obs: 96360 / % possible obs: 98.8 % / Redundancy: 4.1 % / CC_1/2: 0.997 / R_merge(I) obs: 0.106 / R_pim(I) all: 0.059 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 4 % / R_merge(I) obs: 0.512 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 13044 / CC_1/2: 0.759 / R_pim(I) all: 0.288 / % possible all: 98.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5UQY

5uqy

Resolution: 2→37.511 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.2

	R_factor	Num. reflection	% reflection
R_free	0.2091	1867	1.94 %
R_work	0.1772	-	-
obs	0.1778	96331	98.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→37.511 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9071	0	64	1057	10192

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9322
X-RAY DIFFRACTION	f_angle_d	1.147	12645
X-RAY DIFFRACTION	f_dihedral_angle_d	13.637	5696
X-RAY DIFFRACTION	f_chiral_restr	0.044	1448
X-RAY DIFFRACTION	f_plane_restr	0.004	1616

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 (%)
2-2.0541	0.3117	146	0.2536	7258	X-RAY DIFFRACTION	98
2.0541-2.1145	0.2538	144	0.2412	7173	X-RAY DIFFRACTION	98
2.1145-2.1828	0.2984	142	0.2273	7249	X-RAY DIFFRACTION	98
2.1828-2.2608	0.2494	136	0.2161	7267	X-RAY DIFFRACTION	98
2.2608-2.3513	0.2402	148	0.2075	7197	X-RAY DIFFRACTION	99
2.3513-2.4583	0.2273	133	0.2061	7234	X-RAY DIFFRACTION	99
2.4583-2.5879	0.3031	140	0.2084	7295	X-RAY DIFFRACTION	99
2.5879-2.75	0.2459	144	0.1984	7269	X-RAY DIFFRACTION	99
2.75-2.9622	0.2211	150	0.1932	7293	X-RAY DIFFRACTION	99
2.9622-3.2602	0.2199	144	0.1772	7315	X-RAY DIFFRACTION	99
3.2602-3.7315	0.1992	148	0.1564	7274	X-RAY DIFFRACTION	99
3.7315-4.6999	0.1565	150	0.1295	7333	X-RAY DIFFRACTION	100
4.6999-37.5179	0.1463	142	0.1524	7307	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	4.0076	1.2203	-1.4934	5.259	-1.7832	6.2106	0.0805	0.6647	-0.0777	-0.6857	-0.0603	0.2136	-0.0777	0.018	-0.0557	0.4122	0.0246	0.0634	0.4538	0.0531	0.4631	33.8128	150.3768	-16.5343
2	2.7248	-1.5956	-0.2202	4.6061	0.4048	0.7972	-0.2567	-0.3208	0.0856	0.3922	0.2168	0.1627	-0.1192	0.0102	0.0547	0.3709	0.0715	0.0495	0.3146	0.0675	0.367	39.0885	150.7029	-10.7658
3	5.3127	1.6828	-0.3632	2.3442	-0.5693	5.1594	-0.216	-0.1731	-0.4622	0.0001	0.1712	0.064	0.2563	0.3982	0.0834	0.3599	0.0275	0.0384	0.2394	0.0916	0.3708	56.1543	137.296	-10.8321
4	5.8496	-2.2587	-1.5049	4.7498	1.4512	3.4831	-0.1358	0.0066	-0.0351	-0.1057	0.224	0.0306	-0.0795	0.1714	-0.0806	0.2809	-0.0004	-0.0072	0.2806	0.0617	0.2623	57.3518	142.1327	-18.1869
5	3.9298	-0.7929	-0.6093	6.9543	-0.6655	2.3214	-0.0921	-0.4078	0.143	0.2406	-0.0795	-0.4772	-0.2401	0.3582	0.1218	0.3273	-0.0064	-0.0397	0.3476	0.0445	0.3029	51.9537	155.1382	-18.5965
6	2.9205	0.4622	-0.6852	2.8764	1.1418	5.3715	0.1538	-0.234	0.5275	0.2328	0.0454	0.0942	-0.6737	0.1982	-0.1827	0.453	0.012	0.0002	0.261	-0.0307	0.4583	43.2028	165.0182	-18.2527
7	2.4353	2.1025	0.767	5.2715	-0.7263	1.2284	0.1569	-0.2985	1.5885	0.1853	0.0497	0.3224	-1.1395	0.0151	-0.2679	0.9102	-0.0761	0.0002	0.3506	-0.1046	0.9439	42.6835	175.5975	-14.2004
8	6.8297	5.1459	-0.432	6.8483	0.1769	1.9469	0.8858	-0.8002	0.9344	1.1067	-0.4779	0.8484	0.0275	-0.0277	-0.3985	0.6838	0.0215	0.1582	0.6018	-0.0878	0.6376	28.9605	157.6888	-3.269
9	1.0247	0.409	1.0171	0.1713	0.496	2.0284	0.2201	-1.0389	0.3078	0.709	0.2916	-0.2607	-0.789	-0.0932	-0.4323	1.2369	-0.081	0.087	0.9492	-0.1696	0.6728	27.092	152.5605	7.5987
10	1.9384	-0.8896	-0.515	4.2621	0.5519	1.7144	0.0658	0.1359	0.0027	-0.1189	-0.0534	0.4121	0.0258	-0.2423	0.0006	0.1986	-0.0102	-0.0321	0.221	0.0276	0.2157	51.2275	115.5147	-7.3553
11	1.0186	-0.4413	0.2761	1.3785	-0.4103	0.8616	0.069	-0.0354	-0.0326	-0.0005	-0.0411	-0.0351	0.1126	0.0621	-0.0272	0.1801	-0.0221	0.0019	0.2197	-0.0041	0.1718	65.9583	102.4936	5.9487
12	1.4442	-0.2946	0.215	1.6929	-0.5823	3.5186	-0.0144	-0.0693	0.1488	0.1962	-0.0275	0.0533	-0.2586	0.0837	0.0244	0.2243	-0.0047	0.0103	0.172	0.0152	0.2211	55.855	130.9642	7.6715
13	2.9011	-1.1863	-0.7059	2.3661	-0.2835	1.6123	0.1453	0.0486	0.1645	-0.1057	-0.1461	-0.4714	-0.0698	0.2388	-0.0203	0.1868	-0.0281	0.0059	0.2211	0.0215	0.2493	76.0776	109.5303	15.3467
14	5.7786	0.0384	-2.1738	3.1303	0.5196	6.4053	-0.0353	-0.3836	0.1	0.7746	0.0702	0.0269	-0.1269	-0.0979	0.0109	0.4841	0.0084	0.0998	0.3791	0.0358	0.4983	82.0849	178.2245	-3.4583
15	4.5495	-1.7887	-1.1526	1.5795	-0.4312	1.185	0.2293	0.0783	0.3928	-0.5217	-0.0849	0.1051	-0.0908	-0.2517	-0.1383	0.4345	0.0749	0.0391	0.3474	0.0143	0.4307	75.9086	178.7951	-9.4107
16	6.1604	0.0031	0.669	5.6847	0.4948	7.3736	0.3196	0.2873	0.1807	-0.765	-0.1197	-0.3106	-0.519	0.1189	-0.2495	0.4047	0.0716	0.1151	0.2628	-0.005	0.3742	82.4859	168.679	-9.0378
17	4.0936	2.1848	-0.6909	4.4931	-1.5499	6.4439	-0.0074	-0.0657	-0.2996	-0.4123	-0.1154	-0.4221	0.5714	-0.0248	0.0746	0.3018	0.0616	0.103	0.3007	-0.0417	0.3503	82.2269	152.3262	-9.1671
18	2.8942	-0.5704	0.6005	7.8784	-1.5281	2.9017	0.1359	-0.242	0.0969	-0.0564	-0.0737	0.0974	0.0968	-0.2068	-0.055	0.2726	-0.0053	0.0615	0.2819	-0.0361	0.252	77.4433	153.7201	-1.8079
19	6.9211	-1.4507	-0.2728	6.7065	0.6655	4.1905	-0.081	0.297	-0.2407	-0.2594	0.0442	0.4859	0.2478	-0.4495	0.0607	0.3096	-0.0114	0.0143	0.3602	-0.0546	0.2885	68.7716	164.9205	-1.3645
20	3.497	-0.087	0.943	3.101	-1.2444	6.2179	0.0251	0.2353	0.3699	-0.2661	0.0663	0.388	-0.2509	-0.8213	-0.1171	0.2848	0.0899	-0.0107	0.3897	-0.0159	0.4271	64.6778	177.4287	-1.7574
21	1.5482	0.6431	-1.2586	1.3192	0.1353	2.59	0.314	1.3031	1.1968	-0.4393	0.0706	0.5477	-0.5434	-0.6838	-0.2856	0.5431	0.1381	-0.0074	0.6813	0.1684	0.7486	70.5434	185.1769	-13.0388
22	0.1417	0.3612	0.4296	1.0979	0.5292	3.1099	-0.1264	1.3596	0.2299	-0.5626	0.3965	0.4651	-0.7983	-0.6268	-0.121	1.0885	-0.0315	-0.1509	1.3242	0.155	0.4754	83.1227	186.9109	-27.8737
23	3.147	-1.6505	0.1884	3.2765	-0.4457	1.6627	-0.0205	-0.0714	0.3382	0.2106	0.0362	-0.1551	-0.1207	0.1069	-0.0261	0.1934	-0.007	0.0148	0.1974	-0.0428	0.2017	103.5414	145.7133	-12.6323
24	0.7986	-0.5621	-0.3618	1.7981	0.4196	0.7643	-0.0578	-0.0595	0.0693	0.1929	0.0475	0.1098	0.0132	0.0244	0.0226	0.1701	-0.0225	0.0106	0.1988	0.0003	0.1816	101.87	137.0918	-16.6904
25	1.2201	0.1296	0.5297	1.3679	1.0113	4.6475	-0.0132	0.1143	-0.0794	-0.0669	0.0668	-0.1354	-0.0144	0.1138	-0.047	0.2219	-0.0149	0.0044	0.1795	-0.0055	0.2	112.0383	120.6669	-30.8842
26	1.4968	0.0354	0.6208	1.9453	2.354	3.89	0.0733	0.3472	-0.4028	-0.0723	0.0862	-0.0701	0.279	0.4026	-0.1845	0.3032	0.0116	0.0199	0.3044	-0.062	0.272	113.3324	111.8276	-38.7609
27	1.3612	-0.3113	-0.4397	1.791	0.5564	3.3244	0.0136	0.1427	0.0889	-0.0952	-0.0435	0.106	-0.0358	-0.2818	0.0048	0.1713	0.0155	0.0175	0.2021	0.0025	0.206	87.8498	149.3781	-27.6546
28	1.6004	-0.5281	-0.2435	3.4932	-0.3505	1.4589	-0.0699	0.0472	-0.3393	0.1577	0.0868	0.3848	0.1845	-0.1731	-0.017	0.182	-0.0323	0.0183	0.2115	-0.0056	0.2418	96.2956	121.202	-35.3489

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'I' and (resid -2 through 11 )
2	X-RAY DIFFRACTION	2	chain 'I' and (resid 12 through 38 )
3	X-RAY DIFFRACTION	3	chain 'I' and (resid 39 through 48 )
4	X-RAY DIFFRACTION	4	chain 'I' and (resid 49 through 73 )
5	X-RAY DIFFRACTION	5	chain 'I' and (resid 74 through 89 )
6	X-RAY DIFFRACTION	6	chain 'I' and (resid 90 through 119 )
7	X-RAY DIFFRACTION	7	chain 'I' and (resid 120 through 132 )
8	X-RAY DIFFRACTION	8	chain 'I' and (resid 133 through 158 )
9	X-RAY DIFFRACTION	9	chain 'I' and (resid 159 through 172 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 48 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 49 through 215 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 110 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 111 through 220 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid -2 through 11 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 12 through 25 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 26 through 38 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 39 through 48 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 49 through 73 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 74 through 89 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 90 through 119 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 120 through 158 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 159 through 173 )
23	X-RAY DIFFRACTION	23	chain 'A' and (resid 1 through 48 )
24	X-RAY DIFFRACTION	24	chain 'A' and (resid 49 through 129 )
25	X-RAY DIFFRACTION	25	chain 'A' and (resid 130 through 175 )
26	X-RAY DIFFRACTION	26	chain 'A' and (resid 176 through 215 )
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 1 through 110 )
28	X-RAY DIFFRACTION	28	chain 'B' and (resid 111 through 220 )

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

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Yorodumi