PDB-6phc: Pfs25 in complex with the human transmission blocking antibody 2544

ID or keywords:

Entry

Database: PDB / ID: 6phc

Title

Pfs25 in complex with the human transmission blocking antibody 2544

Components

25 kDa ookinete surface antigen
2544 Antibody Fab, Heavy Chain
2544 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: 2.9 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	6phc.cif.gz	463.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6phc_validation.pdf.gz	474.8 KB	Display	wwPDB validaton report
Full document	6phc_full_validation.pdf.gz	483.1 KB	Display
Data in XML	6phc_validation.xml.gz	40.2 KB	Display
Data in CIF	6phc_validation.cif.gz	54.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ph/6phc ftp://data.pdbj.org/pub/pdb/validation_reports/ph/6phc	HTTPS FTP

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Related structure data

Related structure data	6phbC 6phdC 6phfC 6phgC 6phhC C: citing same article (ref.)
Similar structure data	5sx5-2 5ogk-2 4zs7-d 6qsk-3 6qsk-1 4lvh-4 5sx4-2 7aas-3 5vag-d 6b0g-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

A: 2544 Antibody Fab, Heavy Chain

B: 2544 Antibody Fab, Light Chain

E: 25 kDa ookinete surface antigen

C: 2544 Antibody Fab, Heavy Chain

D: 2544 Antibody Fab, Light Chain

hetero molecules

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

1

I: 25 kDa ookinete surface antigen

A: 2544 Antibody Fab, Heavy Chain

B: 2544 Antibody Fab, Light Chain

hetero molecules

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

2

E: 25 kDa ookinete surface antigen

C: 2544 Antibody Fab, Heavy Chain

D: 2544 Antibody Fab, Light Chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	141.220, 141.220, 164.370
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#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	2544 Antibody Fab, Heavy Chain Mass: 24460.242 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	2544 Antibody Fab, Light Chain Mass: 23834.557 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
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: 3.45 Å³/Da / Density % sol: 64.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.1 M HEPES NaOH, pH 7.5, 20 % (w/v) PEG 4000, 10 % (v/v) 2-propanol

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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: 2.9→40 Å / Num. obs: 42529 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC_1/2: 0.993 / R_merge(I) obs: 0.236 / R_pim(I) all: 0.088 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.9→3 Å / Redundancy: 10.4 % / R_merge(I) obs: 0.832 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4085 / CC_1/2: 0.533 / R_pim(I) all: 0.249 / % 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: 2.9→39.568 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.06

	R_factor	Num. reflection	% reflection
R_free	0.238	2124	5 %
R_work	0.2003	-	-
obs	0.2022	42482	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.9→39.568 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8976	0	24	0	9000

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9202
X-RAY DIFFRACTION	f_angle_d	0.582	12519
X-RAY DIFFRACTION	f_dihedral_angle_d	12.189	5579
X-RAY DIFFRACTION	f_chiral_restr	0.043	1419
X-RAY DIFFRACTION	f_plane_restr	0.004	1611

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 (%)
2.9001-2.9675	0.3066	141	0.2826	2661	X-RAY DIFFRACTION	100
2.9675-3.0417	0.3217	139	0.2761	2654	X-RAY DIFFRACTION	100
3.0417-3.1239	0.3046	140	0.2709	2658	X-RAY DIFFRACTION	100
3.1239-3.2158	0.3278	140	0.2626	2661	X-RAY DIFFRACTION	100
3.2158-3.3195	0.3009	140	0.2356	2655	X-RAY DIFFRACTION	100
3.3195-3.4381	0.2789	142	0.2179	2691	X-RAY DIFFRACTION	100
3.4381-3.5757	0.2536	139	0.2104	2638	X-RAY DIFFRACTION	100
3.5757-3.7383	0.2421	141	0.2036	2698	X-RAY DIFFRACTION	100
3.7383-3.9352	0.2446	142	0.1981	2688	X-RAY DIFFRACTION	100
3.9352-4.1815	0.2286	140	0.1676	2654	X-RAY DIFFRACTION	100
4.1815-4.5039	0.1964	140	0.158	2681	X-RAY DIFFRACTION	100
4.5039-4.9564	0.1735	142	0.1567	2703	X-RAY DIFFRACTION	100
4.9564-5.6718	0.2181	144	0.1871	2738	X-RAY DIFFRACTION	100
5.6718-7.1391	0.2522	143	0.2193	2722	X-RAY DIFFRACTION	100
7.1391-39.5716	0.2262	151	0.2017	2856	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	5.108	0.0242	-1.2255	6.8098	1.3448	5.0514	0.1316	-0.1558	-0.2411	0.8969	-0.1016	0.5493	0.1765	-0.438	-0.1635	0.5285	-0.0011	0.0936	0.5045	0.0802	0.6223	39.9247	16.9258	45.6647
2	3.3828	-1.7004	-0.3461	2.5632	-1.4843	2.1779	-0.0417	-0.5937	0.106	0.7405	0.1493	1.2242	-0.1659	-1.4512	-0.0679	0.7903	0.1203	0.2671	0.9788	0.0334	0.9539	27.5839	22.7017	55.6532
3	4.7791	-2.0061	0.6687	1.6211	1.0265	2.2729	-0.2765	0.3102	-0.7332	-0.2695	0.5499	0.9947	0.4857	-0.9191	-0.2938	0.6458	-0.1438	-0.0369	0.9407	0.0037	1.0692	25.3011	9.8811	35.0954
4	2.2551	-0.6115	-1.2688	4.0002	-1.3275	6.1084	-0.2721	-0.4165	-0.5317	0.166	-0.1369	-0.1666	1.1913	0.2113	0.3122	0.91	0.0242	0.0775	0.4692	0.0989	0.753	48.4093	4.8137	42.923
5	1.4567	0.7163	-0.016	3.2833	-0.5516	1.0671	-0.091	-0.0877	-0.0498	0.0986	0.1243	0.183	-0.0229	-0.1224	-0.035	0.3991	0.0556	0.0054	0.3876	-0.0191	0.3994	47.8423	35.0329	32.0356
6	0.247	0.0811	-0.8919	1.7198	-0.4005	3.309	0.0467	0.2069	0.0935	-0.0005	0.0332	0.0308	-0.1722	-0.2262	-0.0627	0.2878	0.0112	-0.0221	0.4358	0.0156	0.4379	58.3337	56.7408	5.6134
7	1.7096	-0.1497	-1.2339	2.514	0.1931	3.6936	-0.1779	0.0834	-0.0816	-0.2412	-0.0192	0.0279	0.4869	-0.198	0.1964	0.4995	0.0343	-0.0595	0.2905	-0.0063	0.4118	52.6127	20.6658	16.1893
8	2.0705	2.6333	0.6689	5.147	-0.1166	2.5468	-0.0736	-0.0611	-0.2699	-0.4481	0.0387	-0.7945	0.0831	0.5414	0.0222	0.4068	0.0346	0.0948	0.5355	-0.0378	0.5143	71.4506	48.5805	1.839
9	4.6001	0.7457	-2.4684	4.9622	0.6866	6.3192	-0.1785	0.546	-0.0224	-0.0889	-0.2263	0.6601	0.3644	-1.2258	0.3727	0.4652	-0.0029	-0.001	0.614	-0.2082	0.6298	6.7204	47.9588	21.4294
10	1.4278	-1.2362	0.9555	1.8878	-0.1679	1.1765	-0.5821	0.3736	-0.1192	-0.0608	-0.446	0.1186	0.8304	-0.6669	0.9513	0.9972	-0.1459	0.2643	0.77	-0.3406	0.8967	8.4308	31.5639	13.3493
11	5.5427	-2.7133	-0.6912	4.3221	-0.4391	3.7508	0.3872	-0.8588	-0.3089	-0.0729	-0.2246	0.2213	0.8007	0.0078	-0.1467	1.1708	-0.1493	0.2171	0.8142	-0.118	0.9798	1.1318	37.4263	36.615
12	4.0171	1.4569	-0.2146	2.0897	0.1411	0.8649	0.0676	0.0727	-0.0573	0.07	-0.2062	0.064	0.0756	0.0454	0.1178	0.4748	0.1091	0.0056	0.3749	-0.0314	0.3953	28.7481	55.4696	27.8571
13	1.2769	0.4969	-0.4417	0.4412	0.5511	2.8973	-0.0834	-0.7378	0.4194	0.5206	0.4288	-0.5465	0.0083	0.4451	-0.2785	0.7024	0.1974	-0.189	0.6828	-0.2456	0.6318	57.919	67.0253	45.2403
14	2.5471	0.1554	0.0676	1.9303	0.8817	2.889	-0.0497	-0.1794	0.1117	0.3673	-0.1319	0.107	0.1407	-0.0303	0.16	0.5481	0.1274	0.0537	0.4157	-0.0266	0.4216	19.8218	65.6098	44.9335
15	3.2401	0.2023	-0.8854	1.5372	0.1961	2.805	-0.2181	-0.2577	0.6848	-0.1983	0.3578	-0.3055	-0.2278	0.0994	-0.1753	0.7377	0.0032	-0.0834	0.6027	-0.2909	0.7686	52.812	81.5629	48.4733
16	3.3038	2.2059	0.7131	6.6705	1.6151	2.3035	0.0913	0.0107	0.3529	-0.0572	-0.4355	2.0968	0.0942	-0.7244	0.2413	0.5005	0.1043	0.0274	0.8062	-0.303	1.2127	-2.6776	57.4957	27.6458

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'I' and (resid 1 through 38 )
2	X-RAY DIFFRACTION	2	chain 'I' and (resid 39 through 86 )
3	X-RAY DIFFRACTION	3	chain 'I' and (resid 87 through 131 )
4	X-RAY DIFFRACTION	4	chain 'I' and (resid 132 through 171 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1 through 113 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 114 through 216 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 107 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 108 through 213 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 1 through 38 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 39 through 86 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 87 through 131 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 113)
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 114 through 216)
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 107 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 108 through 213 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 132 through 159 )

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