PDB-7rm1: Antibody 2F2 in complex with P. vivax CSP peptide EDGAGNQPGANGAGN...

ID or keywords:

Entry

Database: PDB / ID: 7rm1

Title

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

Components

2E10.E9 Fab heavy chain
2E10.E9 Fab light chain
peptide from Circumsporozoite protein variant VK247

Keywords

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

Function / homology

Circumsporozoite protein variant VK247

Function and homology information

Biological species

Mus musculus (house mouse)

Plasmodium vivax (malaria parasite P. vivax)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.19 Å

Authors

Kucharska, I. / Ivanochko, D. / 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
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7rm1.cif.gz	375.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7rm1.ent.gz	293.9 KB	Display	PDB format
PDBx/mmJSON format	7rm1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7rm1_validation.pdf.gz	442.8 KB	Display	wwPDB validaton report
Full document	7rm1_full_validation.pdf.gz	447.1 KB	Display
Data in XML	7rm1_validation.xml.gz	30.7 KB	Display
Data in CIF	7rm1_validation.cif.gz	42.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rm/7rm1 ftp://data.pdbj.org/pub/pdb/validation_reports/rm/7rm1	HTTPS FTP

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Related structure data

Related structure data	7rlvC 7rlwC 7rlxC 7rlyC 7rlzC 7rm0C 7rm3C 1uywS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3c4x-d 3qc9-1 21040 3pnm-d 3c51-d 5hbt-d 3c50-d 3pno-d 3ab4-3 6w7s-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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)

Deposited unit

A: 2E10.E9 Fab heavy chain

B: 2E10.E9 Fab light chain

C: 2E10.E9 Fab heavy chain

D: 2E10.E9 Fab light chain

P: peptide from Circumsporozoite protein variant VK247

98.7 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	142.420, 142.420, 91.290
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁
Space group name Hall	P3₁
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	ALA	ALA	(chain 'A' and (resid 1 through 126 or resid 128 or resid 130 through 213 or resid 215))	A	A	1 - 125	3 - 133
1	2	1	SER	SER	GLU	GLU	(chain 'A' and (resid 1 through 126 or resid 128 or resid 130 through 213 or resid 215))	A	A	130 - 212	138 - 220
2	1	1	GLN	GLN	ALA	ALA	(chain 'C' and (resid 1 through 126 or resid 128 or resid 130 through 213 or resid 215))	C	C	1 - 125	3 - 133
2	2	1	SER	SER	GLU	GLU	(chain 'C' and (resid 1 through 126 or resid 128 or resid 130 through 213 or resid 215))	C	C	130 - 212	138 - 220
1	1	2	ASP	ASP	ARG	ARG	(chain 'B' and resid 1 through 212)	B	B	1 - 211	1 - 217
2	1	2	ASP	ASP	ARG	ARG	(chain 'D' and resid 1 through 212)	D	D	1 - 211	1 - 217

NCS ensembles :

ID
1
2

#1: Antibody	2E10.E9 Fab heavy chain Mass: 23939.869 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)
#2: Antibody	2E10.E9 Fab light chain Mass: 24215.910 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: Protein/peptide	peptide from Circumsporozoite protein variant VK247 Mass: 2377.316 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium vivax (malaria parasite P. vivax) References: UniProt: B7SA68
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.42 Å³/Da / Density % sol: 77.29 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.08 M sodium acetate pH 4.6, 20% glycerol (v/v) and 1.6 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033167 Å / Relative weight: 1
Reflection	Resolution: 3.19→29.55 Å / Num. obs: 34411 / % possible obs: 99.8 % / Redundancy: 20.1 % / B_iso Wilson estimate: 98.87 Å² / CC_1/2: 0.998 / Net I/σ(I): 13.2
Reflection shell	Resolution: 3.19→3.3 Å / Redundancy: 20.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3469 / CC_1/2: 0.756 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1uyw

1uyw

Resolution: 3.19→29.54 Å / SU ML: 0.4275 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.4029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2097	1732	5.03 %
R_work	0.1798	32679	-
obs	0.1813	34411	99.83 %

Solvent computation

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

Displacement parameters

B_iso mean: 111.07 Å²

Refinement step

Cycle: LAST / Resolution: 3.19→29.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6818	0	0	0	6818

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0106	6981
X-RAY DIFFRACTION	f_angle_d	1.394	9489
X-RAY DIFFRACTION	f_chiral_restr	0.0739	1056
X-RAY DIFFRACTION	f_plane_restr	0.0103	1213
X-RAY DIFFRACTION	f_dihedral_angle_d	13.7576	947

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 (%)
3.19-3.28	0.3476	180	0.3348	2676	X-RAY DIFFRACTION	99.58
3.28-3.39	0.3496	96	0.2946	2832	X-RAY DIFFRACTION	99.86
3.39-3.51	0.2898	178	0.2539	2663	X-RAY DIFFRACTION	99.89
3.51-3.65	0.2873	143	0.2427	2723	X-RAY DIFFRACTION	99.83
3.65-3.82	0.2603	112	0.2193	2725	X-RAY DIFFRACTION	99.65
3.82-4.02	0.2165	178	0.2028	2684	X-RAY DIFFRACTION	99.83
4.02-4.27	0.2137	84	0.1697	2779	X-RAY DIFFRACTION	100
4.27-4.6	0.1634	172	0.1426	2737	X-RAY DIFFRACTION	99.97
4.6-5.06	0.1695	176	0.1322	2681	X-RAY DIFFRACTION	100
5.06-5.78	0.1637	86	0.1474	2783	X-RAY DIFFRACTION	99.9
5.79-7.27	0.2396	172	0.1844	2695	X-RAY DIFFRACTION	99.93
7.28-29.54	0.165	155	0.1577	2701	X-RAY DIFFRACTION	99.65

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	1.5896582198	0.179945496427	0.596495694341	0.371101489624	0.0892757929907	0.374121761635	0.0209064391641	0.129123104819	-0.0184783293454	0.000919383874047	-0.00990977782093	-0.0379066247364	-0.136032807806	0.272105026345	1.11701317229E-8	0.681303742399	-0.104820207427	9.6186536788E-5	0.665423538036	-0.0363718387677	0.689662706266	25.8631502754	14.6423968797	2.85936610631
2	0.060681206631	0.0387565245854	0.154057289811	-0.210181156725	0.143007478581	-0.0167288045512	0.212278987555	0.223923237233	0.225364145999	-0.19844406659	-0.165936651734	-0.061353177002	0.112656854223	-0.185916424421	-1.43384193192E-7	1.04237585111	0.01748038142	0.188329327985	0.712214976417	0.0351250098478	0.894149587802	-9.83304323693	22.2615314193	-2.85564443822
3	0.416321552912	0.13200748065	0.0294848684906	0.169831018664	0.1609205659	-0.100810959498	0.00876955179627	0.0981049841152	0.406272756408	0.00819219285897	0.0480842092928	0.117691847692	-0.0205213843348	0.228861285647	-2.59074294909E-8	1.05975250404	-0.00814575474635	0.124498418841	0.666312734811	-0.00440264827363	0.905154586712	-0.25124178782	24.0814744999	-3.08915777478
4	1.30893106226	0.177267519818	-0.563423798448	0.217311625075	-0.186283620199	0.764627810589	0.202264976301	-0.463012610612	-0.421003252854	0.216814580278	-0.193704989971	-0.0854399507418	-0.437967131312	-0.0768495175297	3.59195629603E-8	0.704023782421	-0.1649605404	-0.0769330519197	0.856288265861	0.108148148233	0.732277822387	17.5560362762	2.76931352372	21.8462364939
5	0.0223900687614	0.218713599997	-0.282312113209	0.420123205079	-0.808914408376	0.228525209671	0.0234199493009	-0.219222431505	-0.0255030698297	-0.139162739133	-0.0977870318193	-0.1536392316	0.0224997921811	-0.109227779706	-1.75343652832E-8	0.748672162352	-0.024614779343	-0.0382907328088	0.817325523704	-0.00778055422188	0.873217492441	10.8608997216	4.27887997992	15.5490522608
6	0.628348206458	-0.0866260452597	-0.095431589916	0.146160740603	0.187121341014	0.4979971463	0.192363461872	0.0262250497016	0.0878806158401	-0.102864375644	-0.030571858406	0.069010357086	0.389987860133	0.0834554679061	-8.21833741243E-9	0.897315145516	0.0329843795644	-0.0210689807309	0.733498531946	0.0478673164033	0.711980080294	-12.4522297068	12.125633699	-6.2014921408
7	-0.0212495081963	0.2165657828	0.0039800572755	0.15665289438	0.0151918367795	-0.0114830467917	-0.433544151808	-0.186544268003	-0.156309066084	-0.515910239258	0.0112139491011	-0.304729097052	0.372078234968	-0.31349325078	-6.92693711686E-7	0.996817900309	-0.0268820915169	-0.0182109292179	0.716433927073	0.107195122586	0.770058192919	63.512059572	12.3193530342	-4.42537702726
8	0.425478917538	0.282180606859	-0.00361167302096	0.0221663994184	-0.345313836136	0.227666350393	-0.0782814069333	-0.188544493938	-0.198861431892	-0.162005058563	-0.0513548253872	0.0286016430483	-0.166982651721	-0.0024832013791	-1.30145674027E-7	0.766468697374	-0.11672386301	-0.00103135945589	0.568023740364	0.0992195901779	0.774069750745	56.5161439622	13.6908308869	4.25082837241
9	0.139098787357	0.296005706182	0.218769631698	0.0313695109246	0.0379116871353	-0.0538220292542	-0.543404480514	0.0419921797651	-0.068681307436	0.193629507825	-0.0714238150567	-0.0847801413671	-0.127317692319	-0.346696093709	-1.1855922299E-6	0.805208141371	-0.159710949207	0.0146601118441	0.912318451016	0.0990031694987	0.760971320271	45.9713622699	14.0280903498	1.54380015757
10	0.709216047206	0.07520014144	0.103408126021	0.302053935663	-0.0458579412765	0.215381819134	-0.241075887863	-0.256068425532	-0.11873180119	-0.338498107829	0.0620148601358	0.0175357295258	0.0654066228587	-0.365717183796	-2.33220158352E-8	0.849972920441	-0.186293958495	0.0233015298358	0.654190330638	0.0921582226283	0.742813366305	55.1494090834	13.2058629847	0.634419614629
11	0.192902361793	-0.110073122828	-0.330844187266	0.0885451610598	-0.214697920497	0.147468308238	-0.13382225953	-0.0677449785032	0.0155562477975	-0.223115426654	0.263856080994	-0.100753872608	0.68980420655	-0.131874683545	5.30522015642E-7	0.82457156863	0.0030730597557	0.0112169809227	0.601660509174	0.0583683106598	0.7311757206	69.8298067302	18.9662131066	-6.52961004347
12	0.0577150651884	0.127059975199	-0.272731329122	0.119464099328	-0.167239669041	0.101583567081	-0.442119330974	0.551861453197	-0.438632882618	0.145824743403	0.50507633585	-0.276175095409	0.0539353023873	0.55072369268	2.8838244175E-7	1.00064277163	0.241811513577	-0.126710725188	1.0467613145	-0.11260980564	0.948613618672	92.2265198269	28.841365724	-6.45333672714
13	0.182411737006	-0.0364576998733	-0.340652605252	-0.560880114848	-0.0969396691194	0.25427480416	-0.165006419995	0.000798998609342	-0.24979258114	-0.197859977898	-0.057266580007	-0.254516318409	0.0595574310939	0.0790121108725	-7.93246126428E-8	0.993329189511	0.154024650203	-0.116566419107	0.807531622245	0.0529296507093	0.880788966963	84.3752789885	22.6435170058	-4.96257241221
14	0.0284583935591	-0.0300947114076	-0.023275657668	-0.0234653903889	0.0837319336139	0.192214588743	0.306077632311	-0.115375271416	0.057068364472	-0.260969375005	-0.160903325453	-0.181813183892	0.213241093611	-0.0018257181704	-3.6447310673E-7	1.06562740285	0.208155790131	0.0140705472866	0.757401949814	-0.0847902122078	1.32989939155	87.3769671019	16.8602636793	-11.0521483451
15	0.658969682365	1.35691434181	-0.111956598629	0.516188757139	0.450287287541	0.525722157806	0.198018241833	-0.277218406751	0.370043682098	0.341004318905	-0.27740362791	0.154438211866	0.312459754224	0.118812737039	-6.10988030113E-8	0.676576700386	-0.179079927645	0.00766362357725	0.765285192585	-0.0101718273761	0.711223217121	58.7222126517	28.7611725741	19.0236017816
16	-0.0699208351157	0.143149507646	-0.38638738672	0.340773117197	0.183308108799	-0.326422201604	-0.110931032763	-0.315147338274	0.144602546823	-0.105884761536	-0.130818735843	0.217953163192	-0.0406430411082	0.224417005289	2.34788686157E-7	0.609776000507	-0.153184054452	0.0229138006936	0.73559191703	0.0282263357474	0.751929859693	64.8752064985	31.2834631065	12.6252306961
17	1.41232189015	1.01966729629	0.101701627006	-0.306201247203	0.0629988159815	0.433138563851	0.0618415548154	0.223775612197	-0.0186992380072	0.0104841762617	0.0282448775684	-0.103721518916	-0.23399337211	-0.265870168176	-7.03114757992E-10	0.800214289844	0.0454411316317	0.0218510172892	0.812998365897	0.0313400661238	0.718268373067	88.3587927699	38.15265919	-9.31833870601
18	-0.00228760989536	-0.0317245135559	0.000693575835076	0.00711525425964	0.00571493584047	0.00234287276685	-0.345204523766	0.0936998068489	0.246893966458	-0.0319813993563	0.163321695456	-0.134181868343	0.14813073897	0.0977234015538	2.08540760547E-5	1.1186160035	-0.162647615058	0.0836316226334	0.675736607909	0.0351510941613	1.28451514733	48.3049547887	9.54703831262	16.8071587763
19	0.00737671426224	0.00592885158501	-0.0254556331765	-0.0100509328989	0.00947414450739	0.0200074981172	-0.518553237233	-0.194279316975	-0.0834383935895	-0.195798724394	-0.438252481778	0.0637208938729	-0.0436714167411	-0.330899071444	4.36922108349E-5	1.01577119427	-0.265615117211	0.0725240242766	1.00063656354	0.126454626831	1.02942713125	43.8255554883	15.8997840693	18.9881800305
20	0.00629969624667	-0.00177875483896	-0.00947297506958	-0.00808035303073	-0.00356352862638	0.0100995366543	0.0757574915061	-0.176106474383	0.130164883294	-0.00264310605104	-0.103107669519	0.0756175307217	0.340081212057	0.662923658942	-6.20312846568E-5	0.865903935528	-0.230081040218	-0.0895051493134	1.1212211728	-0.17942739286	1.18853470705	36.6457525184	11.7620724834	18.624002477
21	0.00143820511552	0.00209543105668	-0.00875783517724	0.0231466269155	-0.0462926711006	0.0958473105323	-0.1226941074	-0.0374804171221	-0.128520999403	0.184913511482	-0.0619344545193	-0.0215440942124	0.0956697511626	-0.0649059034016	0.000261333752954	0.999500271672	0.198910448919	0.121708131739	0.772766056357	0.0853031488311	1.64449673111	37.1538027115	4.29542561815	21.8663276016

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 124 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 125 through 145 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 146 through 215 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 75 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 76 through 113 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 114 through 213 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 16 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 17 through 51 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 52 through 66 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 67 through 100A)
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 100B through 124 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 125 through 145 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 146 through 200 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 201 through 215 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 75 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 76 through 113 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 114 through 213 )
18	X-RAY DIFFRACTION	18	chain 'P' and (resid 3 through 7 )
19	X-RAY DIFFRACTION	19	chain 'P' and (resid 8 through 12 )
20	X-RAY DIFFRACTION	20	chain 'P' and (resid 13 through 17 )
21	X-RAY DIFFRACTION	21	chain 'P' and (resid 18 through 20 )

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