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- PDB-7ui1: Pfs230 D1D2 domain in complex with 230AL-37 -

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Open data

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Basic information

Entry

Database: PDB / ID: 7ui1

Title

Pfs230 D1D2 domain in complex with 230AL-37

Components

230AL-37
Gametocyte surface protein P230

Keywords

CELL INVASION / antibody / Plasmodium falciparum / Pfs230 / transmission blocking

Function / homology

6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230

Function and homology information

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Tang, W.K. / Tolia, N.H.

Funding support

United States, 1items

Citation

Journal: Immunity / Year: 2023
Title: A human antibody epitope map of Pfs230D1 derived from analysis of individuals vaccinated with a malaria transmission-blocking vaccine.
Authors: Tang, W.K. / Coelho, C.H. / Miura, K. / Nguemwo Tentokam, B.C. / Salinas, N.D. / Narum, D.L. / Healy, S.A. / Sagara, I. / Long, C.A. / Duffy, P.E. / Tolia, N.H.

History

Deposition	Mar 28, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 1, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	7ui1.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb7ui1.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	7ui1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ui1_validation.pdf.gz	497.3 KB	Display	wwPDB validaton report
Full document	7ui1_full_validation.pdf.gz	527.3 KB	Display
Data in XML	7ui1_validation.xml.gz	70.9 KB	Display
Data in CIF	7ui1_validation.cif.gz	95.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ui/7ui1 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7ui1	HTTPS FTP

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Related structure data

Related structure data	7u9eC 7u9wC 7ua2C 7ua8C 7ubsC 7uc8C 7ucqC 7ufwC 7jumS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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)

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Assembly

Deposited unit

A: Gametocyte surface protein P230

H: 230AL-37

B: Gametocyte surface protein P230

I: 230AL-37

C: Gametocyte surface protein P230

J: 230AL-37

D: Gametocyte surface protein P230

K: 230AL-37

hetero molecules

274 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

A: Gametocyte surface protein P230

hetero molecules

defined by author
Evidence: gel filtration
40.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

H: 230AL-37

hetero molecules

defined by author
27.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

B: Gametocyte surface protein P230

I: 230AL-37

defined by author
68.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

C: Gametocyte surface protein P230

J: 230AL-37

hetero molecules

defined by author
68.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

D: Gametocyte surface protein P230

K: 230AL-37

hetero molecules

defined by author
68.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.580, 155.140, 375.220
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y+1/2,-z+1/2 #4: -x,-y+1/2,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	chain "A"
d_2	ens_1	chain "B"
d_3	ens_1	chain "C"
d_4	ens_1	chain "D"
d_1	ens_2	chain "H"
d_2	ens_2	chain "I"
d_3	ens_2	chain "J"
d_4	ens_2	chain "K"

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	ASP	GLY	A	1 - 308
d_2	1	ens_1	ASP	GLY	C	1 - 308
d_3	1	ens_1	ASP	GLY	E	1 - 308
d_4	1	ens_1	ASP	GLY	G	1 - 308
d_1	1	ens_2	GLN	LYS	B	1 - 227
d_2	1	ens_2	GLN	LYS	D	1 - 227
d_3	1	ens_2	GLN	LYS	F	1 - 227
d_4	1	ens_2	GLN	LYS	H	1 - 227

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.999603612699, 0.0230629594252, 0.0161467452205), (-0.0228687890103, -0.99966514551, 0.0121084821927), (0.0164205958438, 0.0117344260344, 0.999796312895)	3.37862202545, -158.901129554, 1.79766392546
2	given	(0.946641733384, -0.216576903133, -0.23867105741), (0.187741716872, 0.972499404618, -0.137833072093), (0.261958921134, 0.0856700241977, 0.961269041732)	25.2684313968, -71.4023138581, 9.96737462006
3	given	(-0.974637700808, 0.221592397848, -0.0312755715954), (-0.219830116586, -0.97417169827, -0.0516161034072), (-0.041905512817, -0.0434316877994, 0.998177146848)	-2.69726578108, -231.486434405, -2.90837866877
4	given	(-0.999894932678, 0.0144956223343, -2.32029131386E-5), (-0.0144862746509, -0.999190045034, 0.0375419998246), (0.000521010531309, 0.037538391511, 0.999295050378)	3.76099786983, -160.325462186, 2.85455417329
5	given	(0.967368930765, -0.172094973989, -0.185958790376), (0.150141453193, 0.980550817304, -0.126402684772), (0.204095310636, 0.0943579069927, 0.974392985178)	24.4862259956, -71.9104791701, 8.96174022712
6	given	(-0.976294459853, 0.182291528194, -0.11670015599), (-0.174146290983, -0.981733071, -0.0766371100806), (-0.128538698439, -0.054497486668, 0.990205951785)	0.583815854186, -229.959004478, -3.72821154891

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Components

#1: Protein	Gametocyte surface protein P230 Mass: 40738.957 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Komagataella pastoris (fungus) / References: UniProt: P68874
#2: Antibody	230AL-37 Mass: 27582.699 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
Has ligand of interest	N

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.41 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 14, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.3→19.89 Å / Num. obs: 44493 / % possible obs: 98.7 % / Redundancy: 7.2 % / B_iso Wilson estimate: 65.24 Å² / CC_1/2: 0.98 / Net I/σ(I): 5.54
Reflection shell	Resolution: 3.3→3.39 Å / Num. unique obs: 3161 / CC_1/2: 0.45

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7JUM

7jum

Resolution: 3.3→19.89 Å / SU ML: 0.4484 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2995	1716	4.97 %
R_work	0.2639	32811	-
obs	0.2657	34527	77.23 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 94.34 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→19.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17060	0	25	0	17085

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0034	17444
X-RAY DIFFRACTION	f_angle_d	0.5883	23594
X-RAY DIFFRACTION	f_chiral_restr	0.0473	2604
X-RAY DIFFRACTION	f_plane_restr	0.0056	2988
X-RAY DIFFRACTION	f_dihedral_angle_d	27.014	2316

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	1.22466359432
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.976399830654
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	1.04925273096
ens_2	d_2	B	X-RAY DIFFRACTION	Torsion NCS	0.671525493137
ens_2	d_3	B	X-RAY DIFFRACTION	Torsion NCS	0.820673939944
ens_2	d_4	B	X-RAY DIFFRACTION	Torsion NCS	0.787584624185

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 (%)
3.3-3.4	0.3691	37	0.3467	630	X-RAY DIFFRACTION	18.58
3.4-3.51	0.3784	71	0.3245	1319	X-RAY DIFFRACTION	38.03
3.51-3.63	0.3288	78	0.3188	1717	X-RAY DIFFRACTION	49.25
3.63-3.78	0.361	114	0.3131	2177	X-RAY DIFFRACTION	61.59
3.78-3.95	0.308	136	0.3122	2548	X-RAY DIFFRACTION	73.92
3.95-4.15	0.2918	157	0.2973	3061	X-RAY DIFFRACTION	86.2
4.15-4.41	0.3056	181	0.2638	3446	X-RAY DIFFRACTION	98.35
4.41-4.75	0.2814	185	0.2327	3512	X-RAY DIFFRACTION	99.95
4.75-5.22	0.2679	183	0.23	3484	X-RAY DIFFRACTION	98.18
5.22-5.95	0.2815	189	0.2532	3570	X-RAY DIFFRACTION	99.6
5.95-7.43	0.3094	189	0.2791	3621	X-RAY DIFFRACTION	99.69
7.43-19.89	0.2986	196	0.2383	3726	X-RAY DIFFRACTION	98.22

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	2.96944279946	1.11238897041	0.814454646447	0.517002687056	0.811714973123	4.46608304868	0.214959575179	0.41615875455	-0.370804299166	-0.918609487637	-0.440123913754	0.75247924918	0.533838872965	-0.872398738561	0.250733353494	1.30865492042	-0.0477103476547	-0.366051870726	0.773645831911	-0.218390292916	0.650330753159	-16.7491297895	-59.0764448806	44.419236751
2	3.09738145905	0.27585053921	-0.531942733725	1.63507437629	1.49611269064	1.71863812185	-0.0357072538825	1.88896734084	-0.474642615921	-1.52698002706	-0.370854363207	1.01424258723	-0.270497758603	-1.82017663832	0.464886514403	2.4825621988	-0.258642554855	-0.466994412732	2.20676009483	-0.332797875047	1.19369087604	-25.5884255546	-62.3827499407	13.2777166318
3	7.85711544925	-2.6910135459	-2.11229998733	2.85080705396	0.988354090455	4.21211899408	0.566051364406	0.63691238772	0.693540817435	0.433939794039	-0.473202820215	0.0339671981111	0.649721429594	-3.01445667509	-0.0123597540426	2.12560851108	0.202972057593	-0.41033840399	2.35569999041	-0.303594558833	1.15021131838	-27.8746810465	-50.4985049367	13.6404383123
4	1.85925560996	0.357601134037	0.835343425899	0.44480150214	0.103829907258	2.13056605349	-0.129251809006	0.31487354242	0.162576578481	-0.117806270649	0.0263226947089	-0.235707382488	-0.0889537771357	0.47070773884	-0.249140229017	0.218392569097	-0.422699217558	0.0805172497322	1.18414951871	-0.418966140783	0.884438086052	10.8642124472	-44.2310554468	76.450455238
5	1.04358878005	0.0578463545947	0.404930879857	0.560874031413	0.172072528244	0.961711530225	0.124686705142	-0.104207268611	0.00763520406987	-0.00144896203203	0.0703604036067	-0.19874293607	-0.125293509963	0.187628571413	0.237728580662	0.119980615537	-0.501423502028	0.0153232543012	0.239407033683	-0.250066521855	0.414703146661	0.790971781738	-47.3112204159	78.2310383661
6	5.15944283009	0.387122887596	2.47861328938	4.67687913567	2.83296091397	2.69732520726	-0.0547620056646	-0.415980267426	0.0222069608406	0.155295187207	0.14905707665	-0.0346603740085	0.0705836139748	0.00138085434206	-0.220333838498	0.280832546726	-0.278445867056	-0.025488332591	0.667453963248	-0.0182557146781	0.434588094107	4.86330407348	-44.8675348171	85.9897496023
7	3.55942182514	0.61982379114	1.93711959711	3.31421309444	1.11347414978	2.08566148129	-0.279360539824	-0.274201183825	0.0464410019988	-0.327921584894	0.499369251251	-0.742147319058	-0.328116183184	0.129270754674	-0.155258758113	0.384519052763	-0.197123684443	0.111047106803	0.505135525432	-0.160900563005	0.471015931316	5.85781680805	-56.354067948	76.7223694413
8	3.15979587366	0.958965321237	1.88516555326	2.51641541164	-0.123358325963	3.12520668316	0.102736187829	0.260191648126	-0.266924531696	-0.645275558305	0.226627494312	-0.592109346411	0.476696456432	0.581354283506	-0.257348661632	0.257454627635	-0.119032197558	0.0858905599567	0.303796529411	-0.122208905487	0.574928081924	7.05338739795	-69.1436775336	69.1857632745
9	6.92985780008	-5.75768402488	-1.83783639396	8.06347045012	1.10248785659	1.35190099866	-0.831005735732	-0.706659248693	-0.489789668732	-0.0866319087907	0.940663219631	0.146512736691	0.0984956624065	-0.0602971956261	-0.0973139843434	0.279124190005	-0.170092476983	0.0730149837506	0.41317664768	-0.0620723536455	0.240171595701	2.37882959294	-64.8418436498	76.4129320564
10	6.22720176965	-1.88254860659	-0.896629875012	2.46104985771	0.756253870633	3.4674985095	-0.269461514295	0.127615093992	0.228192396374	-0.625006807023	0.00329838051798	-0.68502302696	0.341090498421	0.676170563076	0.197846594179	1.10115418893	-0.0406710024319	0.430810077778	0.6371794466	-0.00251778548427	0.801344102806	19.9141316279	-96.0056662585	47.6539023987
11	3.6688592753	0.330678677041	-1.14025502729	0.0544893609542	-0.230273923358	4.67780115853	-0.175033564587	0.852526026005	0.492083084817	-1.21670160857	-0.0752984784694	-0.573504190868	-0.525107194173	0.498672992853	0.217536786992	1.47782390594	-0.095986648766	0.548193237134	0.878362337256	0.0467436228661	0.916153402909	19.8693550191	-98.4642065792	42.1138776112
12	7.887119542	3.23503308055	0.202938054489	3.14901929601	-2.19362369536	2.85301615746	0.257760696231	2.01301021065	-0.773355122334	-0.915774576522	-0.0940673158226	-0.737484670072	-0.501138642823	1.37255164024	-0.179203871455	2.01833946882	0.0656177837345	0.520585319353	1.93268652078	-0.0385208874148	1.19430561248	28.2534937596	-103.97520946	13.8711440089
13	0.156879476313	-0.14974156355	0.359236972664	0.290695339921	-0.420837486659	0.859777765549	0.288292259266	0.527200219956	-0.152504821706	0.111584393647	-0.35219579288	0.307364487389	0.751195778287	0.638314058488	0.0826958363446	2.7888665709	0.347263471653	0.962251436357	2.0037764217	0.129616293199	1.87679705425	31.6266825705	-104.041849204	12.8150236996
14	2.25757111881	0.309982655273	-1.41749199804	1.93738431546	1.17710057275	3.15642222852	0.242864221833	-0.22410185234	-0.314023444217	0.123536688906	-0.00248970723285	0.245214458444	-0.0470953727176	0.168634063127	-0.062987640836	0.221517209773	0.145531580244	-0.0513732089712	0.118848521557	-0.012249777425	0.440741411453	-2.86100734713	-110.462344454	77.9517442992
15	2.00626383234	-0.0571615923823	-0.690802225427	2.54396086534	0.313553313463	5.25608717343	-0.372933180688	-0.393773

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