PDB-6b0g: Crystal structure of Pfs25 in complex with the transmission block...

ID or keywords:

Entry

Database: PDB / ID: 6b0g

Title

Crystal structure of Pfs25 in complex with the transmission blocking antibody 1245

Components

1245 Antibody, Heavy Chain
1245 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: 1.9 Å

Authors

McLeod, B. / Scally, S.W. / 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 8, 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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Download

PDBx/mmCIF format	6b0g.cif.gz	258.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6b0g.ent.gz	205.7 KB	Display	PDB format
PDBx/mmJSON format	6b0g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6b0g_validation.pdf.gz	447.6 KB	Display	wwPDB validaton report
Full document	6b0g_full_validation.pdf.gz	450 KB	Display
Data in XML	6b0g_validation.xml.gz	28.7 KB	Display
Data in CIF	6b0g_validation.cif.gz	43 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/6b0g ftp://data.pdbj.org/pub/pdb/validation_reports/b0/6b0g	HTTPS FTP

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Related structure data

Related structure data	6azzC 6b08C 6b0aC 6b0eC 6b0hC 1z27S 5d1xS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4zpt-2 4rrp-5 6b0e-d 4zpv-2 6c6y-2 6tl4-d 6c6y-1 5vag-d 6phc-1 6ayz-1 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

C: 1245 Antibody, Light Chain

D: 1245 Antibody, Heavy Chain

E: 25 kDa ookinete surface antigen

hetero molecules

69.1 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)	51.772, 83.692, 76.212
Angle α, β, γ (deg.)	90.00, 93.65, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	1245 Antibody, Light Chain Mass: 24081.752 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	1245 Antibody, Heavy Chain Mass: 24450.361 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.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.4 Å³/Da / Density % sol: 48.76 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M citric acid pH 5.0, 1 M lithium chloride, 20 % (w/v) PEG 6000

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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: 1.9→40 Å / Num. obs: 51093 / % possible obs: 99.8 % / Redundancy: 3.8 % / R_pim(I) all: 0.065 / Net I/σ(I): 11.8
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7230 / R_pim(I) all: 0.351 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XPREP		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5D1X, 1Z27

5d1x

1z27

Resolution: 1.9→38.989 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.07

	R_factor	Num. reflection	% reflection
R_free	0.1997	2003	3.92 %
R_work	0.1638	-	-
obs	0.1653	51072	99.85 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→38.989 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4534	0	30	546	5110

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4676
X-RAY DIFFRACTION	f_angle_d	1.098	6341
X-RAY DIFFRACTION	f_dihedral_angle_d	11.66	2866
X-RAY DIFFRACTION	f_chiral_restr	0.069	710
X-RAY DIFFRACTION	f_plane_restr	0.006	807

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 (%)
1.9-1.9475	0.335	142	0.2711	3480	X-RAY DIFFRACTION	100
1.9475-2.0002	0.247	148	0.2331	3474	X-RAY DIFFRACTION	100
2.0002-2.059	0.2816	139	0.2079	3496	X-RAY DIFFRACTION	100
2.059-2.1255	0.2391	148	0.1909	3467	X-RAY DIFFRACTION	100
2.1255-2.2014	0.2353	145	0.1856	3496	X-RAY DIFFRACTION	100
2.2014-2.2896	0.2342	141	0.1783	3503	X-RAY DIFFRACTION	100
2.2896-2.3938	0.2198	142	0.1755	3498	X-RAY DIFFRACTION	100
2.3938-2.5199	0.2381	144	0.1716	3509	X-RAY DIFFRACTION	100
2.5199-2.6778	0.2213	134	0.1636	3494	X-RAY DIFFRACTION	100
2.6778-2.8845	0.2229	147	0.1665	3543	X-RAY DIFFRACTION	100
2.8845-3.1746	0.2064	138	0.1578	3492	X-RAY DIFFRACTION	100
3.1746-3.6337	0.1807	144	0.1365	3514	X-RAY DIFFRACTION	100
3.6337-4.577	0.1438	146	0.123	3516	X-RAY DIFFRACTION	100
4.577-38.9974	0.1462	145	0.1582	3587	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	1.6349	-0.3856	-0.8773	1.8708	-0.2031	2.2049	0.1878	-0.0707	0.3699	0.0868	0.0004	0.0242	-0.2907	0.2139	-0.1855	0.2506	-0.0679	0.0175	0.1388	-0.0337	0.1678	259.6231	177.7692	115.8872
2	3.6223	1.948	-1.4956	3.0902	0.6081	4.0608	-0.059	0.1949	-0.2508	-0.1242	0.175	-0.1961	0.0319	0.5763	-0.0572	0.1384	-0.0439	-0.0036	0.1916	-0.0262	0.1523	263.2614	166.4731	110.8501
3	5.1747	-0.4548	-0.6455	6.463	1.1181	2.8233	0.095	-0.4558	-0.1282	0.2996	0.0278	-0.3238	-0.2033	0.5372	-0.1054	0.1996	-0.0912	0.0092	0.2142	0.0011	0.1276	263.4135	170.5258	121.2888
4	4.6162	0.6901	-2.2184	1.7009	-0.2422	2.9664	-0.1136	-0.1158	-0.3437	0.1857	-0.0368	-0.1618	0.0819	0.5634	0.1807	0.1971	-0.0366	0.0014	0.2063	-0.0381	0.1585	268.4784	170.4043	112.359
5	2.7026	0.7205	-2.0422	0.8241	-0.9422	1.7046	0.16	-0.3138	0.0542	0.1043	-0.1115	0.1038	-0.1172	0.1582	-0.0343	0.2035	-0.0527	-0.0039	0.1235	-0.0334	0.1495	264.9854	176.7094	107.3208
6	2.3513	0.197	0.761	1.67	-0.7839	3.9646	-0.0684	0.336	0.2698	-0.2691	0.1714	0.105	0.0564	-0.0679	-0.0907	0.124	-0.0243	-0.0103	0.1343	0.0579	0.1705	274.8741	183.4663	82.0837
7	2.6006	0.8361	1.1128	1.9185	-0.7762	6.3116	-0.1427	0.2506	0.2553	-0.3144	0.1144	-0.0245	-0.1893	0.112	0.0333	0.1238	0.0123	0.0362	0.1185	0.0315	0.1904	277.5081	185.1342	83.1924
8	1.2621	0.3101	-1.1328	1.281	-1.1413	4.3723	-0.017	0.0746	-0.0505	-0.0865	-0.0002	-0.0421	0.1502	0.1457	0.0223	0.1073	-0.0165	-0.0332	0.0912	0.0134	0.1192	252.133	158.8561	100.2782
9	1.3784	-1.2579	1.7798	2.7556	-0.391	3.3987	0.0214	0.2741	0.4298	-0.008	0.204	0.4765	-0.264	-0.3069	-0.2637	0.1492	0.0157	0.0092	0.0929	0.0536	0.2087	243.4446	164.8839	105.5632
10	3.1266	-2.9644	1.1507	8.6728	-5.7187	5.2236	0.0114	0.1872	0.101	-0.2275	0.0725	0.11	0.2782	-0.1855	-0.0731	0.1412	-0.021	-0.0553	0.1434	0.0246	0.1463	243.6468	157.1231	99.7492
11	1.0818	0.3101	-1.456	0.2973	-1.3256	6.2175	0.0791	0.0522	0.1456	0.0699	0.0666	0.1242	-0.2874	-0.0888	-0.1458	0.1482	-0.0243	0.0011	0.0618	-0.001	0.1398	250.3766	163.4818	105.5173
12	5.3642	0.448	-0.459	1.2518	-0.3572	2.3873	0.0202	0.3687	0.0769	-0.1514	0.0696	-0.128	0.0224	0.0352	-0.0897	0.1556	-0.0052	-0.0047	0.1111	-0.0368	0.1129	275.4255	170.1563	79.4985
13	6.4773	0.8882	0.5872	1.3537	0.1007	1.9851	-0.0997	0.2422	-0.1345	-0.0882	0.0544	-0.1226	0.0893	-0.0108	0.0406	0.1314	0.0051	-0.0152	0.0885	0.0034	0.1074	278.406	168.6114	82.3137
14	5.6405	6.1987	-0.1122	7.1795	-0.377	1.328	-0.6516	0.9067	-0.6887	-0.9041	0.5103	-0.6599	0.1359	0.0024	0.0376	0.3178	-0.0351	0.04	0.3306	-0.1031	0.2677	280.971	166.2531	73.4962
15	5.3149	-0.3327	0.463	1.8147	0.4367	5.5109	0.1968	0.0044	0.3522	0.1089	0.0043	0.2076	0.0315	-0.3294	-0.1575	0.1152	-0.0072	0.0265	0.1132	0.0201	0.1699	238.4954	156.0592	132.5236
16	4.1494	3.1963	1.6907	6.4273	3.0262	2.7996	0.0743	0.2073	0.6098	-0.341	0.1623	0.5975	-0.6753	-0.2922	-0.1011	0.374	0.0561	0.179	0.1928	0.0374	0.3645	234.973	168.8779	132.7828
17	1.0374	-1.232	0.2909	5.7537	1.7548	1.0738	0.2637	-0.5246	0.6215	0.1986	0.2661	0.6057	-0.9821	0.0379	-0.1798	0.738	0.011	0.4155	0.3046	-0.0956	0.7695	238.6782	180.6069	139.6805
18	1.4709	0.1252	-0.3181	3.5528	-0.1473	4.4732	0.18	-0.2247	0.1444	0.5521	0.1147	-0.285	-0.2961	0.5572	-0.2646	0.2713	-0.0773	0.0077	0.3277	-0.1105	0.2212	252.3098	163.7622	138.76
19	0.8127	-0.7182	0.1135	0.6953	-0.2888	0.8216	-0.1354	-0.5016	0.2198	0.1233	0.4525	-0.5028	0.298	1.2084	-0.231	0.1923	0.1174	-0.0729	0.5035	-0.1285	0.2361	258.4974	152.5864	130.1534
20	5.0532	1.4963	-3.7056	3.2151	-0.3852	3.7171	-0.444	0.0139	-0.8466	-0.0296	0.306	-0.1462	0.6955	0.2882	0.1809	0.2604	0.0474	-0.0163	0.1824	-0.0302	0.1644	247.0668	145.6263	127.3691
21	5.3295	3.2799	-0.9247	3.726	0.0929	1.1422	-0.3218	0.3386	0.0528	-0.4156	0.3568	0.3883	0.5088	-0.6969	-0.0158	0.2091	-0.1028	-0.0409	0.2966	0.054	0.1709	235.5391	150.182	122.1487

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 32 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 33 through 48 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 49 through 75 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 76 through 90 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 91 through 113 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 114 through 163 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 164 through 213 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 2 through 44 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 45 through 63 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 64 through 82 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 82A through 111 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 112 through 162 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 163 through 208 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 209 through 220 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 3 through 25 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 26 through 43 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 44 through 73 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 74 through 109 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 110 through 129 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 130 through 139 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 140 through 159 )

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