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

ID or keywords:

Entry

Database: PDB / ID: 6azz

Title

Crystal structure of Pfs25 in complex with the transmission blocking antibody 1190

Components

(1190 antibody, ...) x 2
Pfs25

Keywords

IMMUNE SYSTEM / Transmission blocking vaccine /

malaria /

antibody /

EGF-like domain

Function / homology

Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Orthogonal Prism /

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta /

ACETATE ION

Function and homology information

Biological species

Homo sapiens (human)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Scally, S.W. / McLeod, B. / 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 13, 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

-
Download

PDBx/mmCIF format	6azz.cif.gz	463.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6azz.ent.gz	380.1 KB	Display	PDB format
PDBx/mmJSON format	6azz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/6azz ftp://data.pdbj.org/pub/pdb/validation_reports/az/6azz	HTTPS FTP

-
Related structure data

Related structure data	6b08C 6b0aC 6b0eC 6b0gC 6b0hC 1z27S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7dpm-3 6b0h-2 6u6u-d 3ma9-d 6z2l-d 7dpm-1 2dd8-d 6zlr-2 6b0a-d 6zlr-1 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 - HomologyF&H Search

-
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)

Deposited unit

F: 1190 antibody, heavy chain

E: 1190 antibody, light chain

C: 1190 antibody, heavy chain

B: 1190 antibody, light chain

A: Pfs25

D: Pfs25

hetero molecules

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

1

F: 1190 antibody, heavy chain

E: 1190 antibody, light chain

D: Pfs25

hetero molecules

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

2

C: 1190 antibody, heavy chain

B: 1190 antibody, light chain

A: Pfs25

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.572, 203.136, 65.486
Angle α, β, γ (deg.)	90.00, 109.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Protein , 1 types, 2 molecules AD

#3: Protein	Pfs25 Mass: 20104.156 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)

-
Antibody , 2 types, 4 molecules FCEB

#1: Antibody	1190 antibody, heavy chain Mass: 23986.904 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: Antibody	1190 antibody, light chain Mass: 23035.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Non-polymers , 3 types, 427 molecules

#4: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.72 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.085 M Tris pH 8.5, 0.17 M sodium acetate, 25.5 % (w/v) PEG 4000

-
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: 2.4→40 Å / Num. obs: 51230 / % possible obs: 99.9 % / Redundancy: 3.9 % / R_pim(I) all: 0.068 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.4→2.5 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5894 / R_pim(I) all: 0.33 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XPREP		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1Z27, 1276 Fab

1z27

Resolution: 2.4→39.179 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.04

	R_factor	Num. reflection	% reflection
R_free	0.2169	2024	3.95 %
R_work	0.191	-	-
obs	0.1921	51179	99.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→39.179 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8735	0	54	416	9205

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9006
X-RAY DIFFRACTION	f_angle_d	0.544	12292
X-RAY DIFFRACTION	f_dihedral_angle_d	13.137	5409
X-RAY DIFFRACTION	f_chiral_restr	0.044	1412
X-RAY DIFFRACTION	f_plane_restr	0.005	1565

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 (%)
2.4-2.46	0.2781	158	0.2872	3498	X-RAY DIFFRACTION	100
2.46-2.5265	0.2864	133	0.2735	3511	X-RAY DIFFRACTION	100
2.5265-2.6008	0.3187	146	0.2597	3474	X-RAY DIFFRACTION	100
2.6008-2.6848	0.2649	144	0.2514	3541	X-RAY DIFFRACTION	100
2.6848-2.7807	0.2887	145	0.2352	3497	X-RAY DIFFRACTION	100
2.7807-2.892	0.2852	133	0.2292	3505	X-RAY DIFFRACTION	100
2.892-3.0236	0.243	151	0.2295	3518	X-RAY DIFFRACTION	100
3.0236-3.1829	0.2506	143	0.2104	3504	X-RAY DIFFRACTION	100
3.1829-3.3822	0.2331	147	0.1944	3506	X-RAY DIFFRACTION	100
3.3822-3.6432	0.2125	140	0.1809	3524	X-RAY DIFFRACTION	100
3.6432-4.0095	0.2001	149	0.1665	3485	X-RAY DIFFRACTION	100
4.0095-4.5889	0.1624	146	0.1436	3523	X-RAY DIFFRACTION	100
4.5889-5.7786	0.1573	145	0.1481	3528	X-RAY DIFFRACTION	100
5.7786-39.1845	0.1909	144	0.1738	3541	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	1.8169	-0.7658	0.4879	3.9783	-0.3341	1.6513	0.1466	-0.084	-0.2407	-0.2323	-0.0976	0.2075	0.1076	-0.2094	-0.0089	0.1869	-0.0286	-0.0683	0.2961	0.0003	0.2024	-37.6034	-41.8527	43.8277
2	2.984	-0.8342	1.0824	4.874	0.5224	4.1293	-0.1339	-0.0508	0.1938	-0.1205	-0.0825	-0.3907	-0.1816	0.3551	0.2471	0.2846	-0.0628	-0.0175	0.1972	0.0017	0.4012	-15.7498	-67.8968	53.224
3	7.3046	-1.9954	3.4576	5.6807	-0.3717	3.8627	0.0136	-0.2954	-0.1075	0.3103	0.0059	-0.3592	0.1297	0.2298	0.0012	0.3398	-0.0424	0.0434	0.3053	0.0021	0.3861	-15.0917	-72.9325	57.7459
4	3.5302	-0.0963	0.816	3.0865	0.3762	1.1826	0.1622	-0.1701	-0.0771	-0.2216	0.0069	-0.3753	-0.0961	0.0313	-0.1188	0.189	-0.0256	0.0416	0.2525	-0.0006	0.1764	-17.7136	-31.2187	46.3533
5	3.5244	2.6089	0.5043	6.2258	0.1155	2.6161	-0.6484	0.419	-0.1494	-0.9354	0.3315	-0.4265	-0.1436	0.3928	0.2739	0.512	-0.1419	0.0294	0.3803	0.021	0.5275	-7.8372	-64.1162	42.7714
6	2.018	1.3089	-0.3345	4.057	0.1183	2.2356	0.0369	0.2532	0.1727	-0.0026	-0.0321	0.4502	-0.0528	-0.2362	0.0395	0.1602	0.0387	0.0316	0.3247	-0.0123	0.1856	-34.6356	-13.3615	76.1932
7	1.3016	0.1511	-0.7155	3.9565	0.1148	1.3298	0.1138	-0.042	0.1843	0.3748	-0.0975	0.1883	0.0169	-0.1676	-0.0191	0.2279	0.0017	0.0471	0.3067	-0.0146	0.204	-32.2285	-12.4894	81.9747
8	1.4567	0.5695	0.3726	3.8204	-0.5507	3.383	-0.0206	0.0252	-0.0237	0.1155	-0.0059	-0.1508	0.0847	0.1609	0.1049	0.2682	0.0416	0.08	0.239	-0.0611	0.5344	-12.9744	12.4986	70.1766
9	4.8277	0.449	-1.3727	4.9777	-1.2793	3.8688	-0.1377	0.4345	0.2089	-0.5683	0.1006	-0.4356	-0.2036	0.0481	0.0283	0.4172	-0.0087	0.0727	0.2631	-0.0716	0.5178	-10.2085	18.5982	64.562
10	3.8474	-0.1907	-0.4964	3.2275	0.5876	1.9635	-0.0407	-0.0469	0.1469	0.3631	0.1511	-0.407	0.1878	0.055	-0.1381	0.2173	0.031	-0.0483	0.2347	-0.0244	0.1993	-13.396	-26.0189	77.4356
11	3.7089	0.2584	-1.3241	3.4303	0.6079	2.1822	-0.1397	0.0217	0.2989	0.274	0.3439	-0.5638	0.5185	-0.0606	0.2007	0.2097	0.0943	-0.0334	0.269	-0.0011	0.2887	-13.0788	-19.2246	78.2179
12	3.7002	-1.6494	-0.7612	4.9177	0.2997	3.1311	-0.5081	-0.2125	0.1142	0.8799	0.3254	-0.4554	-0.0491	0.3664	0.1777	0.4548	0.0826	-0.1163	0.3155	-0.0352	0.5987	-3.3808	9.3592	80.318
13	2.7152	0.9161	-1.0811	4.3076	1.3912	1.0591	-0.1769	0.5261	-1.8912	-0.1105	-0.1586	-0.4941	0.437	0.0657	0.2882	0.7466	-0.0584	0.2875	0.4879	-0.1512	1.0581	-24.5823	-56.3851	75.9392
14	7.9932	-3.7815	2.3516	2.0106	-1.6692	1.8068	-0.1818	-0.3962	-1.5697	0.1413	0.0292	-0.6453	-0.3651	0.6855	0.2448	0.7099	-0.038	0.1437	0.5674	0.1357	1.1481	-10.722	-49.7373	82.4318
15	3.1623	-0.1538	0.0511	3.2971	-0.5132	0.1017	-0.19	0.2131	-1.0656	0.2421	-0.1436	0.46	0.3993	-0.1699	0.2153	0.5366	-0.1133	0.1738	0.419	-0.1283	0.498	-36.9713	-43.6708	80.5032
16	3.9841	2.6565	1.6556	7.3893	1.8351	2.837	0.1183	-0.7865	1.2538	0.5162	0.0812	-0.5616	0.0518	0.1401	-0.3361	0.4975	0.1003	0.0254	0.5132	-0.2317	0.763	-39.0565	-0.5421	51.398
17	4.1238	3.8374	0.4271	4.3236	-0.9408	2.3215	0.2482	-0.8632	1.6555	0.1673	-0.0192	-0.4475	-0.1517	-0.2269	-0.1983	0.6382	0.1045	0.0585	0.4089	-0.2046	1.5433	-24.3599	5.1828	47.0145
18	1.4169	0.6509	-0.0794	2.0137	-1.4411	1.6183	0.0902	0.4434	1.5767	-0.1888	-0.0049	-0.1964	0.1726	0.3882	-0.0245	0.5595	0.0511	0.0126	0.4456	-0.0516	1.2069	-16.4151	-2.9688	43.7922
19	5.6987	-0.5412	0.2069	6.4366	-0.3246	5.2496	0.1974	-0.069	1.0447	-0.8384	-0.2833	-0.9809	-0.2988	-0.2729	-0.0456	0.3537	0.0333	0.0353	0.2463	-0.0152	0.3294	-30.989	-13.637	40.6405
20	0.669	-1.8816	1.9608	5.3669	-5.6251	5.9575	-0.3147	-0.3392	0.3024	0.5338	0.0256	-0.1669	-0.7742	-0.309	0.0219	0.3901	0.0914	-0.0286	0.4278	-0.0992	0.157	-34.8896	-16.9851	50.2859
21	2.41	-1.1147	0.2229	4.2658	-0.7366	2.2101	0.5818	0.1124	0.5908	-0.5299	-0.4307	0.2575	-0.1739	-0.3868	0.0078	0.321	0.095	-0.0119	0.3704	-0.0753	0.3908	-46.7114	-10.1807	43.65
22	6.376	-5.8313	3.005	5.6854	-3.4631	3.2106	0.1147	-0.6798	1.946	-0.5745	-0.0766	0.145	-0.7805	0.2324	-0.3178	0.4697	0.1874	0.1525	0.5343	-0.1023	1.0167	-47.7605	4.2028	44.5181
23	0.9908	0.5769	-1.419	0.3784	-1.31	7.3421	0.6326	0.5905	0.1164	-0.2848	-0.5739	0.676	-1.6279	-0.3505	0.2218	0.8003	0.3121	0.2035	0.5854	0.2062	1.3759	-49.842	16.5594	45.4906

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'F' and (resid 1 through 119 )
2	X-RAY DIFFRACTION	2	chain 'F' and (resid 120 through 175 )
3	X-RAY DIFFRACTION	3	chain 'F' and (resid 176 through 214 )
4	X-RAY DIFFRACTION	4	chain 'E' and (resid 1 through 114 )
5	X-RAY DIFFRACTION	5	chain 'E' and (resid 115 through 210 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 1 through 40 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 41 through 119 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 120 through 177 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 178 through 215 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 75 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 76 through 114 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 115 through 210 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 2 through 62 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 63 through 82 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 83 through 157 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 2 through 25 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 26 through 48 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 49 through 82 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 83 through 96 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 97 through 108 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 109 through 144 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 145 through 158 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 159 through 172 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AD

-
Antibody , 2 types, 4 molecules FCEB

-
Non-polymers , 3 types, 427 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AD

-Antibody , 2 types, 4 molecules FCEB

-Non-polymers , 3 types, 427 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AD

-
Antibody , 2 types, 4 molecules FCEB

-
Non-polymers , 3 types, 427 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi