PDB-8f9v: Crystal structure of Ky15.8 Fab in complex with circumsporozoite ...

ID or keywords:

Entry

Database: PDB / ID: 8f9v

Title

Crystal structure of Ky15.8 Fab in complex with circumsporozoite protein KQPA peptide

Components

Circumsporozoite protein KQPA peptide
Ky15.8 Antibody, heavy chain
Ky15.8 Antibody, light chain

Keywords

IMMUNE SYSTEM / Malaria / Antibody

Function / homology

Function and homology information

entry into host cell by a symbiont-containing vacuole / external side of plasma membrane / cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Thai, E. / Prieto, K. / Julien, J.P.

Funding support

United States, 1items

Citation

Journal: Cell Rep / Year: 2023
Title: Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein.
Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / ...

History

Deposition	Nov 24, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Mar 20, 2024	Group: Source and taxonomy / Category: pdbx_entity_src_syn Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8f9v.cif.gz	840.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8f9v_validation.pdf.gz	510.5 KB	Display	wwPDB validaton report
Full document	8f9v_full_validation.pdf.gz	518.2 KB	Display
Data in XML	8f9v_validation.xml.gz	67.8 KB	Display
Data in CIF	8f9v_validation.cif.gz	95.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/8f9v ftp://data.pdbj.org/pub/pdb/validation_reports/f9/8f9v	HTTPS FTP

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Related structure data

Related structure data	8f95C 8f9eC 8f9fC 8f9sC 8f9tC 8f9uC 8f9wC 8fa6C 8fa7C 8fa8C 8fa9C 8fanC 8fasC 8fatC 8fb5C 8fb6C 8fb7C 8fb8C 8fbaC 8fdcC 8fddC 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)

Deposited unit

A: Ky15.8 Antibody, heavy chain

B: Ky15.8 Antibody, light chain

C: Ky15.8 Antibody, heavy chain

D: Ky15.8 Antibody, light chain

E: Ky15.8 Antibody, heavy chain

F: Ky15.8 Antibody, light chain

G: Ky15.8 Antibody, heavy chain

H: Ky15.8 Antibody, light chain

M: Circumsporozoite protein KQPA peptide

N: Circumsporozoite protein KQPA peptide

O: Circumsporozoite protein KQPA peptide

P: Circumsporozoite protein KQPA peptide

hetero molecules

199 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ky15.8 Antibody, heavy chain

B: Ky15.8 Antibody, light chain

M: Circumsporozoite protein KQPA peptide

hetero molecules

defined by author
Evidence: surface plasmon resonance
49.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Ky15.8 Antibody, heavy chain

D: Ky15.8 Antibody, light chain

N: Circumsporozoite protein KQPA peptide

hetero molecules

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

3

E: Ky15.8 Antibody, heavy chain

F: Ky15.8 Antibody, light chain

O: Circumsporozoite protein KQPA peptide

hetero molecules

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

4

G: Ky15.8 Antibody, heavy chain

H: Ky15.8 Antibody, light chain

P: Circumsporozoite protein KQPA peptide

hetero molecules

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)	80.046, 133.488, 101.861
Angle α, β, γ (deg.)	90.000, 110.150, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Antibody	Ky15.8 Antibody, heavy chain Mass: 24311.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody	Ky15.8 Antibody, light chain Mass: 23387.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide	Circumsporozoite protein KQPA peptide / CS / PfCSP Mass: 1549.577 Da / Num. of mol.: 4 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote) References: UniProt: P19597
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 744 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.57 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20% isopropanol, 20% PEG4000, 0.1 M tri-sodium citrate pH 5.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2021
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→40 Å / Num. obs: 90017 / % possible obs: 94.5 % / Redundancy: 2.7 % / B_iso Wilson estimate: 30.36 Å² / CC_1/2: 0.676 / Net I/σ(I): 4.8
Reflection shell	Resolution: 2.25→2.28 Å / Num. unique obs: 3503 / CC_1/2: 0.716

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4080	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→39.31 Å / SU ML: 0.2765 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.0683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2789	1963	2.23 %
R_work	0.2587	85988	-
obs	0.2592	87951	92.48 %

Solvent computation

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

Displacement parameters

B_iso mean: 36.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→39.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13627	0	104	744	14475

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0036	14160
X-RAY DIFFRACTION	f_angle_d	0.7187	19240
X-RAY DIFFRACTION	f_chiral_restr	0.0482	2140
X-RAY DIFFRACTION	f_plane_restr	0.0048	2451
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3556	5096

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 (%)
2.25-2.31	0.3281	146	0.3313	6305	X-RAY DIFFRACTION	95.4
2.31-2.37	0.3671	145	0.3338	6335	X-RAY DIFFRACTION	95.48
2.37-2.44	0.3702	132	0.3187	6264	X-RAY DIFFRACTION	94.9
2.44-2.52	0.3408	147	0.3015	6231	X-RAY DIFFRACTION	94.06
2.52-2.61	0.3951	142	0.3072	6215	X-RAY DIFFRACTION	93.98
2.61-2.71	0.3895	146	0.2989	6125	X-RAY DIFFRACTION	92.21
2.71-2.83	0.2961	140	0.2865	6192	X-RAY DIFFRACTION	93.75
2.83-2.98	0.2842	142	0.2771	6154	X-RAY DIFFRACTION	92.74
2.98-3.17	0.285	137	0.2623	6072	X-RAY DIFFRACTION	91.59
3.17-3.42	0.2581	132	0.2506	5975	X-RAY DIFFRACTION	89.98
3.42-3.76	0.2394	141	0.2378	5980	X-RAY DIFFRACTION	89.96
3.76-4.3	0.2458	130	0.212	6066	X-RAY DIFFRACTION	91.12
4.3-5.42	0.2137	140	0.2066	6122	X-RAY DIFFRACTION	91.63
5.42-39.31	0.239	143	0.249	5952	X-RAY DIFFRACTION	88.19

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	0.304433707944	0.325131939702	0.0840227454419	2.1934626982	0.482301681332	0.84564983155	-0.0709347449878	-0.0857123492301	0.127065416872	-0.063078910719	0.065220250995	-0.225717736695	0.25479846167	0.0709741732074	0.0334716762084	0.259258256249	0.0144238636061	0.0261633720977	0.307220899148	-0.0595407443281	0.192110921043	-8.591	8.912	-11.063
2	2.56383796464	0.722251767837	0.663793627138	2.40992725858	-0.134179940836	0.610662237766	0.0445900196848	-0.0718853306286	0.454720667042	-0.153098799673	-0.11388853287	-0.13213307309	0.212646308032	0.0686732952412	0.0862428222052	0.300318235392	0.0148350899173	0.0537278476875	0.297158469783	0.0178638626507	0.183441566971	5.526	42.35	-10.992
3	0.316356723439	0.498979751814	0.589718662861	1.82967520151	0.511431387259	1.83802012942	-0.164602525079	0.0974219977783	-0.488533367384	0.248885549122	0.210945159812	-0.00302507807912	-0.103530472286	-0.114198412103	-0.0437393328728	0.269473330676	-0.0360903023276	0.0901825612879	0.303264165938	-0.0751278327612	0.726921387108	-12.032	15.531	9.903
4	1.71038887706	-0.390446075035	0.987122006773	2.23976116559	-1.43717097495	1.16349301159	0.0304958220639	-0.120854873886	0.129275950615	0.26686811916	-0.0341422075804	0.0552637027064	-0.146466388411	-0.0459336853566	0.0311456824537	0.416693736409	0.0579581366264	0.0259415201677	0.367143572755	-0.0389819472633	0.132679769316	-7.7	47.524	-4.824
5	1.30197421226	0.080990685358	-0.312316835477	1.24781931686	-0.678810206644	1.03222743478	0.0663944110642	0.0543611738294	-0.32138628979	-0.0576782358717	0.177726166958	0.583420278913	0.0697133881515	0.125519545379	-0.262594317352	0.304261311792	0.0538092054061	0.00758729992467	0.250153948049	-0.0106161648965	0.685637256688	-26.074	8.927	36.806
6	1.23293077062	0.789973777352	0.925002571346	2.1005042728	0.0592762596564	0.954424041371	-0.0417439260003	0.284662793688	-0.978302377781	-0.0198436939367	0.109580067596	-0.44408063749	-0.0696901858018	0.00822436425575	-0.105166609099	0.274921436094	-0.030661629335	0.100029214995	0.245032335943	-0.0792732699564	0.768662455398	-12.065	42.229	36.842
7	1.75564028365	0.567998743868	0.325439701538	2.04792555558	0.514269610141	0.292503006049	0.131590724108	-0.238110495797	0.110274299758	0.153820365323	-0.154765036669	0.0150079490496	0.12661858719	0.248249685676	0.015248806931	0.358155109908	0.0372306890021	0.0297252354104	0.364295132515	0.0147071644108	0.124975461264	-29.576	15.582	57.68
8	0.742986321272	0.111706692795	0.708795826515	1.18849683349	-1.10587343686	2.50663752183	0.0886673299227	-0.0174970906992	-0.0951890565702	0.158927740626	0.0836054529313	0.270130983892	-0.187869532922	-0.0255726593159	-0.123032198835	0.350812363303	-0.0177074830502	0.169498778473	0.2075925142	-0.0445122666792	0.863915835955	-25.309	47.408	43.178
9	1.16485608926	0.706076885131	0.527177935395	1.59970352707	0.287990934465	0.53389099899	0.030475508328	0.188979522015	-0.295155786648	-0.135398732354	-0.0516641948488	0.0149685427634	-0.206320294725	-0.093618864319	-0.00204075389576	0.327721405319	0.0508297258304	0.0553830287307	0.325583780968	-0.0178934113192	0.226702582112	-32.463	67.624	-11.798
10	0.52136520965	0.641019962951	-0.601500771588	0.868490504464	-0.523300485233	0.461314114606	0.126115868313	-0.0777989596955	-0.174118029425	-0.266387762486	0.0179431235891	0.697216824675	0.142213478933	-0.0713256081299	-0.193058946921	0.282488383447	-0.0371652935329	0.00689131955444	0.26513275809	0.0424688661133	0.950735626596	-45.942	34.187	-12.071
11	1.52710973162	0.382358722105	-1.66636904387	2.72292466338	-1.09954195136	2.32001350632	0.0255284318272	-0.173758657749	0.314339762307	-0.0553909993749	0.0206122184477	-0.0006038929002	0.0236383221954	0.35614172502	-0.0523348701806	0.181149290652	-0.0160647434561	-0.0581821057669	0.355419828323	-0.0760981282696	0.285163043782	-29.832	61.361	9.293
12	1.63168585719	-0.701645062127	-1.18418238493	2.44822537548	0.413492654387	1.23538644612	0.0252341810694	0.0275869785974	0.0104009009662	-0.0690072012278	-0.0290256404521	-0.093168176353	0.0260720566714	-0.0284085574122	-0.055109155008	0.263919542051	0.0105992420923	-0.0464141149651	0.333332375132	-0.00789510830468	0.133286951035	-32.595	28.936	-5.54
13	1.63016345715	-0.137997009665	-0.522999570875	1.8851081877	0.269014253784	1.37369519524	0.241130306831	-0.0406495300061	0.662768334156	-0.284348856673	-0.0146754770079	-0.0913296103089	-0.222122960217	-0.050828039919	-0.22616240263	0.24966257832	0.023668558606	0.0895641056665	0.226462326585	0.0569496496685	0.465207638915	-49.967	67.603	35.949
14	1.71068517278	0.103232134237	0.0558372885851	0.533386182692	0.190502210476	0.189931748926	-0.0819361430338	0.201354860419	0.380135421626	-0.164497553937	0.265523769106	0.105677186458	0.165225979598	-0.333444930061	-0.0968437412499	0.441240545289	0.0409830805393	0.0144896991624	0.469876902643	0.0442668145822	0.112771375397	-63.504	34.046	35.953
15	2.21948694935	1.59211385797	-0.872459145998	2.83189967764	-1.45681356319	1.87974043152	-0.0164495326717	-0.0650182150042	-0.343771211818	0.272419307921	-0.0646714432234	-0.148431174468	0.0613400330258	0.0748915103459	0.1103300305	0.342091827925	0.0377764325193	0.069138118525	0.233327678607	0.0196165772069	0.278601079084	-47.462	61.302	56.957
16	0.600245581386	0.105280442925	-0.533420795824	1.79498641064	0.985745228186	3.4844387136	0.182959341088	-0.0201783347224	0.0418327712838	0.0826516526182	0.0884794728369	0.232922086108	0.057224586041	-0.000913120885433	-0.213430575663	0.296375974469	0.0260447140132	0.0635955479232	0.228527440174	0.00211152487582	0.597716100612	-50.232	28.897	42.168
17	5.14897455548	-2.57036370456	-1.79876741951	6.97374778494	-0.12214495079	4.16859387939	0.143043475864	-0.139317905058	-0.153542895757	0.048242865821	0.350989911904	0.331967607873	-0.0762943258592	-0.65616696048	-0.164649061925	0.594700605858	0.00841294683171	-0.0630323421046	0.217963411206	-0.292711562398	-0.233443573974	-18.053	-2.956	-1.954
18	4.89791333737	-3.64081182836	-2.0488160241	6.46015060342	-1.09200497494	2.67990552447	0.244878278612	0.338038471021	-0.349192241984	-0.382069521371	-0.0883509589079	0.159815668381	0.298318645093	-0.248363323225	-0.183028007264	0.163865431075	0.282858420186	0.0574818260755	0.261418550275	0.415254170383	0.747320459112	-35.598	-2.948	45.855
19	6.05510043688	-3.6865459691	1.44899807009	6.86984344087	2.08696645625	3.22338489016	0.231811042207	0.237395644538	-0.0988204895444	0.00800343612495	0.199331689824	-0.883708282185	0.106659018115	0.56980866262	-0.303294390965	0.483191952822	-0.178220471309	0.183663112466	0.261799725066	-0.0769099202998	0.922041313867	-24.026	79.996	-2.283
20	5.68621298624	-2.52874282725	0.709652077421	4.69592416703	0.898579416227	2.75365052457	0.0459089761983	0.172243138785	0.177597328731	-0.0513336614575	0.0745417546948	-0.348933123756	-0.0538323063452	0.448770771184	-0.0215691028938	0.461066204175	0.167182531968	0.0830499725761	0.393606648317	0.23946260576	-0.0551674767884	-41.551	80.002	45.513

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:122 )	A	1 - 122
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 123:216 )	A	123 - 216
3	X-RAY DIFFRACTION	3	( CHAIN B AND RESID 1:106 )	B	1 - 106
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 107:213 )	B	107 - 213
5	X-RAY DIFFRACTION	5	( CHAIN C AND RESID 1:122 )	C	1 - 122
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID 123:216 )	C	123 - 216
7	X-RAY DIFFRACTION	7	( CHAIN D AND RESID 1:106 )	D	1 - 106
8	X-RAY DIFFRACTION	8	( CHAIN D AND RESID 107:213 )	D	107 - 213
9	X-RAY DIFFRACTION	9	( CHAIN E AND RESID 1:122 )	E	1 - 122
10	X-RAY DIFFRACTION	10	( CHAIN E AND RESID 123:216 )	E	123 - 216
11	X-RAY DIFFRACTION	11	( CHAIN F AND RESID 1:106 )	F	1 - 106
12	X-RAY DIFFRACTION	12	( CHAIN F AND RESID 107:213 )	F	107 - 213
13	X-RAY DIFFRACTION	13	( CHAIN G AND RESID 1:122 )	G	1 - 122
14	X-RAY DIFFRACTION	14	( CHAIN G AND RESID 123:216 )	G	123 - 216
15	X-RAY DIFFRACTION	15	( CHAIN H AND RESID 1:106 )	H	1 - 106
16	X-RAY DIFFRACTION	16	( CHAIN H AND RESID 107:213 )	H	107 - 213
17	X-RAY DIFFRACTION	17	( CHAIN M AND RESID 8:15 )	M	8 - 15
18	X-RAY DIFFRACTION	18	( CHAIN N AND RESID 8:15 )	N	8 - 15
19	X-RAY DIFFRACTION	19	( CHAIN O AND RESID 8:15 )	O	8 - 15
20	X-RAY DIFFRACTION	20	( CHAIN P AND RESID 8:15 )	P	8 - 15

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