PDB-7rlz: Antibody 2F2 in complex with P. vivax CSP peptide GDRAAGQPAGNGAGGQAA

ID or keywords:

Entry

Database: PDB / ID: 7rlz

Title

Antibody 2F2 in complex with P. vivax CSP peptide GDRAAGQPAGNGAGGQAA

Components

2F2 Fab heavy chain
2F2 Fab light chain
peptide from Circumsporozoite protein variant VK210

Keywords

ANTIMICROBIAL PROTEIN / antibody / malaria / Plasmodium vivax / circumsporozoite protein

Function / homology

Function and homology information

side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Plasmodium vivax (malaria parasite P. vivax)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.27 Å

Authors

Kucharska, I. / Julien, J.P.

Funding support

Canada, 4items

Organization	Grant number	Country
Other government	Ontario Early Researcher Awards program	Canada
Other government	Canada Foundation for Innovation	Canada
Other government	Ontario Research Fund	Canada
Other government	Canada Research Chairs	Canada

Citation

Journal: Elife / Year: 2022
Title: Structural basis of Plasmodium vivax inhibition by antibodies binding to the circumsporozoite protein repeats.
Authors: Kucharska, I. / Hossain, L. / Ivanochko, D. / Yang, Q. / Rubinstein, J.L. / Pomes, R. / Julien, J.P.

History

Deposition	Jul 26, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 26, 2022	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7rlz.cif.gz	420.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7rlz_validation.pdf.gz	460 KB	Display	wwPDB validaton report
Full document	7rlz_full_validation.pdf.gz	462.4 KB	Display
Data in XML	7rlz_validation.xml.gz	31.2 KB	Display
Data in CIF	7rlz_validation.cif.gz	43.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rl/7rlz ftp://data.pdbj.org/pub/pdb/validation_reports/rl/7rlz	HTTPS FTP

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Related structure data

Related structure data	7rlvC 7rlwC 7rlxC 7rlyC 7rm0C 7rm1C 7rm3C C: citing same article (ref.)
Similar structure data	7rm3-2 1yed-2 2vl5-1 5mp3-2 4imk-1 1q9l-2 5mp3-1 3o45-2 6b5n-d 6wx2-2 6idg-d 6dca-3 7rd9-d 4mhj-6 6vl8-4 6mqm-2 5ewi-d 5mv4-1 7rlx-d 7rly-3 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

Related structure data

C: citing same article (ref.)

Similar structure data

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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)

Deposited unit

P: peptide from Circumsporozoite protein variant VK210

B: 2F2 Fab light chain

A: 2F2 Fab heavy chain

C: 2F2 Fab light chain

D: 2F2 Fab heavy chain

R: peptide from Circumsporozoite protein variant VK210

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

1

P: peptide from Circumsporozoite protein variant VK210

B: 2F2 Fab light chain

A: 2F2 Fab heavy chain

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

2

C: 2F2 Fab light chain

D: 2F2 Fab heavy chain

R: peptide from Circumsporozoite protein variant VK210

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

Unit cell

Length a, b, c (Å)	93.360, 60.490, 159.060
Angle α, β, γ (deg.)	90.000, 101.219, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-316- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and resid 3 through 214)
d_2	ens_1	chain "D"
d_1	ens_2	(chain "B" and (resid 1 through 9 or resid 11 through 26 or resid 27A through 213))
d_2	ens_2	(chain "C" and (resid 1 through 9 or resid 11 through 26 or resid 27A through 213))
d_1	ens_3	chain "P"
d_2	ens_3	chain "R"

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	GLN	LYS	C	1 - 220
d_2	1	ens_1	GLN	LYS	E	1 - 220
d_1	1	ens_2	ASP	LEU	B	1 - 9
d_1	2	ens_2	LEU	SER	B	11 - 26
d_1	3	ens_2	SER	GLU	B	28 - 218
d_2	1	ens_2	ASP	LEU	D	1 - 9
d_2	2	ens_2	LEU	SER	D	11 - 26
d_2	3	ens_2	SER	GLU	D	28 - 218
d_1	1	ens_3	ASP	ASN	A	1 - 10
d_2	1	ens_3	ASP	ASN	F	1 - 10

NCS ensembles :

ID
ens_1
ens_2
ens_3

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.996768280681, -0.0376489744572, 0.0709616047611), (-0.0423089824435, 0.996964868058, -0.0653529024749), (-0.0682857571719, -0.0681440135275, -0.995335847233)	30.6231152507, -25.9351463732, 79.2257584016
2	given	(-0.998145285493, -0.00389124653283, 0.0607523435656), (-0.00826885976432, 0.99737233591, -0.0719725608838), (-0.060312643836, -0.0723414249403, -0.995554671141)	30.8488407469, -26.919788444, 79.1071247661
3	given	(-0.992971514117, -0.0540163854721, 0.105308130039), (-0.0659059011358, 0.991417524765, -0.112905729635), (-0.0983055662071, -0.119052600515, -0.988009359249)	29.1581638169, -24.1043740335, 79.5846125859

#1: Protein/peptide	peptide from Circumsporozoite protein variant VK210 / CS Mass: 1526.550 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Plasmodium vivax (malaria parasite P. vivax) References: UniProt: P08677
#2: Antibody	2F2 Fab light chain Mass: 24284.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody	2F2 Fab heavy chain Mass: 24046.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.25 Å³/Da / Density % sol: 45.31 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-sodium tartrate and 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033167 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033167 Å / Relative weight: 1
Reflection	Resolution: 2.25→29.69 Å / Num. obs: 41601 / % possible obs: 99.9 % / Redundancy: 11.6 % / B_iso Wilson estimate: 50.02 Å² / CC_1/2: 0.927 / Net I/σ(I): 9.4
Reflection shell	Resolution: 2.25→2.32 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3874 / CC_1/2: 0.435

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.27→29.69 Å / SU ML: 0.3138 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2387	2026	5 %
R_work	0.1914	38476	-
obs	0.1938	40502	99.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 53.74 Å²

Refinement step

Cycle: LAST / Resolution: 2.27→29.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6832	0	0	100	6932

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0032	7009
X-RAY DIFFRACTION	f_angle_d	0.7073	9532
X-RAY DIFFRACTION	f_chiral_restr	0.0464	1067
X-RAY DIFFRACTION	f_plane_restr	0.0045	1214
X-RAY DIFFRACTION	f_dihedral_angle_d	11.1327	2510

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	C	X-RAY DIFFRACTION	Torsion NCS	0.876363208918
ens_2	d_2	B	X-RAY DIFFRACTION	Torsion NCS	0.631436664896
ens_3	d_2	A	X-RAY DIFFRACTION	Torsion NCS	1.03148168901

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 (%)
2.27-2.33	0.345	146	0.282	2759	X-RAY DIFFRACTION	100
2.33-2.39	0.3764	142	0.2797	2702	X-RAY DIFFRACTION	100
2.39-2.46	0.3521	142	0.2681	2709	X-RAY DIFFRACTION	100
2.46-2.54	0.3064	146	0.2571	2768	X-RAY DIFFRACTION	100
2.54-2.63	0.2973	144	0.2409	2730	X-RAY DIFFRACTION	100
2.63-2.74	0.2875	143	0.2285	2712	X-RAY DIFFRACTION	100
2.74-2.86	0.2865	143	0.2281	2728	X-RAY DIFFRACTION	100
2.86-3.01	0.2666	145	0.237	2744	X-RAY DIFFRACTION	100
3.01-3.2	0.257	145	0.2146	2748	X-RAY DIFFRACTION	100
3.2-3.45	0.2898	144	0.1978	2759	X-RAY DIFFRACTION	100
3.45-3.79	0.2502	145	0.1895	2743	X-RAY DIFFRACTION	100
3.79-4.34	0.1889	144	0.1628	2780	X-RAY DIFFRACTION	99.86
4.34-5.46	0.1795	147	0.1438	2762	X-RAY DIFFRACTION	99.56
5.46-29.69	0.2061	150	0.1696	2832	X-RAY DIFFRACTION	99.2

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	0.803418717364	-0.539446097923	-1.3300540289	0.89190700304	1.16169441161	2.91092988273	-0.37254896135	-0.0356225750505	-0.255140924896	0.611410628995	0.154812001452	-1.2878065243	-0.321921589463	0.111686712435	0.365532192268	0.642244390909	0.0322441656246	-0.0977727649251	0.518428179382	0.069757716398	0.707550810785	20.3499146895	-41.0044057976	84.3314529916
2	0.145734021533	0.115870356282	-0.248981367737	1.44206988382	0.312060329289	0.524697333018	-0.341448886358	-0.199626522967	-1.08186408151	-0.129886625285	0.139261897035	-0.651574259512	0.684631535959	-0.132336141424	-0.0089621201724	0.659710556553	0.00532105457539	0.0845310724012	0.687844384368	0.00688425086273	0.681816409785	19.0571134468	-31.7461375843	37.0481732034
3	2.2797007814	-1.8211174571	-0.620617339261	6.19762823006	0.444854569651	0.154028325356	0.765775456083	-0.195312224208	0.22920645614	-0.930733470905	0.470596652757	-1.04847481244	1.34018756966	0.140929894422	0.276560560264	0.954933708883	-0.0911760136247	-0.143076270356	0.509218965742	0.192320355716	0.0859198993892	14.72734134	-1.97372148291	41.8499644221
4	4.04618389804	0.000585683212033	-0.122214592736	1.44039993386	0.601036335214	3.28971684323	0.0499460640561	-0.301489851718	0.0618653355324	0.236157177654	-0.0715522098049	-0.0667462252128	-0.00470660945669	0.141929748495	-0.0420121185916	0.594699673072	-0.0216978183519	-0.0399181194259	0.426983993998	0.0370852857824	0.344962166308	31.5031601865	-0.313445461924	29.4782541767
5	2.72521310483	-0.637031429724	2.09154330615	1.37828871112	-0.47820018095	6.63683535368	0.166675352298	0.445929186809	0.0566377706096	-0.304869493146	-0.14929446806	-0.101061188605	0.15018443384	0.513714245554	-0.017092406427	0.520107851758	0.02852326101	-0.0311984521777	0.329572656614	-0.0177019033012	0.359103349459	28.676225816	-3.24042735758	-8.31306375385
6	3.32752365124	0.363067403388	0.726918863629	2.88342848985	-0.241348115224	4.14686549372	0.221633411882	-0.478136247778	-0.32190437705	0.0076662121451	-0.0517150562666	0.491794518574	0.563178671926	-0.47564018135	0.0269972700522	0.453334632135	-0.00842467157774	-0.000782405456014	0.389870439921	0.0289519539871	0.354411835149	7.93317176817	-3.48445012569	24.796852251
7	4.47315410229	0.186271005707	0.259595328009	1.88654794619	-1.47288188417	4.24307115186	0.0810497945243	-0.482479597562	0.251484920512	0.251717161584	-0.0401908072406	0.250794380966	-0.0702520610428	-0.292928930067	0.058653904884	0.550112544374	-0.0260993663658	0.0411964135766	0.440956248942	-0.0830849410607	0.358525555416	11.3317172898	0.70171267044	28.3623538721
8	3.430914551	-1.99117346765	-1.12045625795	4.76472073451	0.983257051354	1.37533447971	0.0546681658189	0.0820589333065	0.0740879659347	-0.100703893208	-0.0245970755842	-0.0497493875253	-0.030703999061	-0.000349199125713	0.025289627485	0.462830579111	-0.0134847576507	-0.105793753416	0.324963967737	-0.0116651741483	0.315223517174	16.7827721915	-9.56868302958	-1.74807485399
9	1.96461912497	-1.11863375243	-0.575948057894	3.73238948462	-0.791503774178	3.11360697113	0.6511297316	1.09228759672	-0.14357596134	-0.758709922272	-0.355831734479	0.174411934009	0.104463997015	-1.11189729666	0.445561001612	0.522680599536	-0.00149813374069	-0.117571892583	0.477835802458	-0.0531427088909	0.593334211587	11.212378621	-14.9753475963	-6.2592582575
10	2.82512954827	0.299270178614	-2.3780156121	0.328695597281	-1.47115961741	8.61706763316	-0.121659356116	0.373778975857	-0.192832583235	-0.277219213211	0.0645209047391	-0.0843180989094	0.261710163927	-0.109100513579	-0.00145000514318	0.487254833838	-0.0331264223838	-0.0844515531948	0.38016574595	0.0208289006974	0.384907667877	-0.301040194804	-30.9237200413	48.1616753567
11	1.2464086201	0.139462258999	0.246657466469	0.635904307669	0.565113513587	2.77673038656	0.0878158856651	-0.142262856704	0.0244472381913	0.115306889966	-0.0893192995186	-0.102565264309	-0.0556441992561	0.223112027935	-0.024892272387	0.379321904124	-0.00961175094075	-0.0638545630626	0.274832206244	0.0149949505374	0.302604379024	5.22229437089	-29.5892623067	67.3654343232
12	2.44650766889	0.787068311655	0.871492054077	2.27852634073	1.28503013026	4.43687638255	0.0879651209435	-0.283709561309	0.117491054092	0.309379315769	-0.087530419585	0.0138767744583	0.106701387506	-0.000367726140703	-0.042823167135	0.474915104776	-0.00400887680015	-0.0336344941247	0.319815842438	0.00771774936879	0.423699268491	1.26358435447	-28.6106070257	87.32105848
13	2.3630016257	0.253977502524	0.519807343225	4.87820930956	1.43609172474	5.97982842024	0.0471316803895	0.48811025581	-0.254744488861	-0.322164813149	-0.101738773274	-0.301423866574	0.245162479344	0.373640423614	0.0780800865602	0.327101651306	-0.0144522437187	0.0284872702429	0.441230723954	0.0382390371926	0.397970703278	23.0233255387	-29.3677313767	51.960126171
14	3.1802803614	2.11002273741	0.487506987431	1.90594201414	1.10982824707	7.40645709826	-0.245167205716	0.74387030679	0.983380369533	-0.375937267445	0.751903359452	-0.585253816717	-1.33887142545	0.689300473978	0.0905448962308	0.59510420421	-0.0425426869787	-0.00523855433076	0.601628742895	0.211946236142	0.582180406121	25.9256221885	-21.2534634886	48.4295115844
15	2.51962960987	0.820220664947	-1.05919538713	1.45608439027	2.34750662458	8.41270854855	0.0289294967392	0.0102400448658	0.562498843711	-0.118915409186	0.305178452539	-0.22328446651	-0.489701160147	0.680779411336	-0.119784626762	0.50455415637	-0.040727644063	-0.000339960540071	0.674739410115	0.0765957415072	0.65440587885	27.687228208	-24.8352644304	55.2238462573
16	0.829600732242	0.218760882911	0.411089598876	0.844278458174	-0.0409411909862	2.8980279046	-0.108507905584	0.0324102442503	-0.074403440579	-0.0786717079897	-0.0423672089363	-0.241341010673	-0.102249546934	0.267922392084	0.24242025786	0.378209796501	0.027250007632	-0.0365525920517	0.267908393838	-0.0100154162092	0.415493660797	14.9289122248	-33.7842733679	67.2680019053
17	2.75871748003	1.07320416862	0.427324906316	3.09685971193	-1.21507279238	2.05894230252	-0.054486692977	-0.0987749139782	-0.0528008411724	0.127983121493	0.020547224289	-0.0636624944893	0.0912526531436	0.157929463002	0.0929877412483	0.429426129345	-0.00358749424859	-0.0555176777061	0.292621282597	-0.0446887103995	0.414314959126	14.3316930975	-36.9545928383	78.1318282887

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'D' and (resid 204 through 214 )	D	E	204 - 214	210 - 220
2	2	chain 'R' and (resid 2 through 11 )	R	F	2 - 11	1 - 10
3	3	chain 'P' and (resid 2 through 11 )	P	A	2 - 11	1 - 10
4	4	chain 'B' and (resid 1 through 101 )	B	B	1 - 101	1 - 106
5	5	chain 'B' and (resid 102 through 213 )	B	B	102 - 213	107 - 218
6	6	chain 'A' and (resid 3 through 39 )	A	C	3 - 39	1 - 37
7	7	chain 'A' and (resid 40 through 111 )	A	C	40 - 111	38 - 117
8	8	chain 'A' and (resid 112 through 203 )	A	C	112 - 203	118 - 209
9	9	chain 'A' and (resid 204 through 215 )	A	C	204 - 215	210 - 221
10	10	chain 'C' and (resid 1 through 83 )	C	D	1 - 83	1 - 88
11	11	chain 'C' and (resid 84 through 128 )	C	D	84 - 128	89 - 133
12	12	chain 'C' and (resid 129 through 213 )	C	D	129 - 213	134 - 218
13	13	chain 'D' and (resid 3 through 59 )	D	E	3 - 59	1 - 58
14	14	chain 'D' and (resid 60 through 72 )	D	E	60 - 72	59 - 71
15	15	chain 'D' and (resid 73 through 87 )	D	E	73 - 87	72 - 89
16	16	chain 'D' and (resid 88 through 145 )	D	E	88 - 145	90 - 151
17	17	chain 'D' and (resid 146 through 203 )	D	E	146 - 203	152 - 209

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