PDB-8f9w: Crystal structure of Ky15.8 Fab in complex with circumsporozoite ...

ID or keywords:

Entry

Database: PDB / ID: 8f9w

Title

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

Components

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

Keywords

IMMUNE SYSTEM / Malaria / Antibody

Function / homology

Function and homology information

side of membrane / cell surface / 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: 2.4 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	8f9w.cif.gz	824.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8f9w.ent.gz	571.9 KB	Display	PDB format
PDBx/mmJSON format	8f9w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8f9w_validation.pdf.gz	502.5 KB	Display	wwPDB validaton report
Full document	8f9w_full_validation.pdf.gz	511 KB	Display
Data in XML	8f9w_validation.xml.gz	59.6 KB	Display
Data in CIF	8f9w_validation.cif.gz	82.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/8f9w ftp://data.pdbj.org/pub/pdb/validation_reports/f9/8f9w	HTTPS FTP

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Related structure data

Related structure data	8f95C 8f9eC 8f9fC 8f9sC 8f9tC 8f9uC 8f9vC 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

O: Circumsporozoite protein NPDP peptide

A: Ky15.8 Antibody, heavy chain

B: Ky15.8 Antibody, light chain

P: Circumsporozoite protein NPDP peptide

C: Ky15.8 Antibody, heavy chain

D: Ky15.8 Antibody, light chain

Q: Circumsporozoite protein NPDP peptide

E: Ky15.8 Antibody, heavy chain

F: Ky15.8 Antibody, light chain

R: Circumsporozoite protein NPDP peptide

G: Ky15.8 Antibody, heavy chain

H: Ky15.8 Antibody, light chain

hetero molecules

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

1

O: Circumsporozoite protein NPDP peptide

A: Ky15.8 Antibody, heavy chain

B: Ky15.8 Antibody, light chain

hetero molecules

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

2

P: Circumsporozoite protein NPDP peptide

C: Ky15.8 Antibody, heavy chain

D: Ky15.8 Antibody, light chain

hetero molecules

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

3

Q: Circumsporozoite protein NPDP peptide

E: Ky15.8 Antibody, heavy chain

F: Ky15.8 Antibody, light chain

hetero molecules

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

4

R: Circumsporozoite protein NPDP peptide

G: Ky15.8 Antibody, heavy chain

H: Ky15.8 Antibody, light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.672, 130.851, 101.540
Angle α, β, γ (deg.)	90.000, 109.336, 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: Protein/peptide	Circumsporozoite protein NPDP peptide / CS Mass: 1659.668 Da / Num. of mol.: 4 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote) References: UniProt: P08307
#2: 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)
#3: 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)
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.5 Å³/Da / Density % sol: 50.76 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5, 25% PEG3350

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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: 2.4→40 Å / Num. obs: 75328 / % possible obs: 99.3 % / Redundancy: 6.9 % / B_iso Wilson estimate: 50.17 Å² / CC_1/2: 0.997 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.4→2.44 Å / Num. unique obs: 3622 / CC_1/2: 0.695

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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: 2.4→39.27 Å / SU ML: 0.3438 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2411	1978	2.63 %
R_work	0.2018	73288	-
obs	0.2028	75266	99.41 %

Solvent computation

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

Displacement parameters

B_iso mean: 58.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→39.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13554	0	32	202	13788

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	14018
X-RAY DIFFRACTION	f_angle_d	0.5327	19101
X-RAY DIFFRACTION	f_chiral_restr	0.0427	2136
X-RAY DIFFRACTION	f_plane_restr	0.0043	2438
X-RAY DIFFRACTION	f_dihedral_angle_d	11.3117	5022

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	0.3633	137	0.3445	5240	X-RAY DIFFRACTION	99.5
2.46-2.53	0.3128	142	0.2942	5201	X-RAY DIFFRACTION	99.68
2.53-2.6	0.3005	144	0.2941	5212	X-RAY DIFFRACTION	99.7
2.6-2.68	0.3632	147	0.2763	5227	X-RAY DIFFRACTION	99.61
2.68-2.78	0.3269	137	0.2777	5236	X-RAY DIFFRACTION	99.65
2.78-2.89	0.3119	153	0.2604	5223	X-RAY DIFFRACTION	99.7
2.89-3.02	0.2772	139	0.2486	5198	X-RAY DIFFRACTION	98.58
3.02-3.18	0.3028	136	0.2399	5200	X-RAY DIFFRACTION	98.76
3.18-3.38	0.2718	139	0.2263	5246	X-RAY DIFFRACTION	99.89
3.38-3.64	0.2768	143	0.211	5263	X-RAY DIFFRACTION	99.85
3.64-4.01	0.2378	137	0.1853	5255	X-RAY DIFFRACTION	99.63
4.01-4.59	0.1948	139	0.1551	5198	X-RAY DIFFRACTION	98.5
4.59-5.78	0.1815	143	0.146	5263	X-RAY DIFFRACTION	99.59
5.78-39.27	0.1729	142	0.17	5326	X-RAY DIFFRACTION	99.09

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	0.21728555179	0.309389281819	-0.818766309875	0.855445006161	-0.889707364942	3.23425246701	0.497516688513	-0.240406310734	-0.392192519404	-0.0576095061745	-0.368910205709	-0.539943300178	-1.19453794084	1.34927443099	-0.0598125890399	0.448577856021	-0.164491752978	0.0265572643331	0.615922340238	-0.00715399096499	0.741028859043	1.414	44.62	44.014
2	0.732704628939	0.820232417781	0.328846035596	4.23213035878	1.15554780262	1.28178843025	0.137633883506	0.032070230351	0.21672795492	-0.254298078591	0.0118156368485	0.126944761874	-0.217410359679	0.0766127666206	-0.142180736932	0.352900362869	0.0334291979373	0.0283469805646	0.351574921812	0.0119236543388	0.471120189972	-7.829	31.784	35.551
3	2.82786565204	0.588410787335	-0.596625174346	2.35082902556	-0.536374259553	1.50925198494	0.0214183261867	0.0937899760483	-0.0564867031353	-0.0852144803892	0.0421772608693	0.2917671474	-0.10939905379	-0.205495465038	-0.0839456345402	0.317317908902	0.0109645984153	-0.0142102014286	0.330712221317	-0.00878695590403	0.394726060776	-23.643	0.084	37.212
4	2.19390429038	0.0802393888455	-0.657931595545	3.53244683623	-1.42542442538	3.48266555335	0.149404351488	-0.191379060392	-0.0771771965142	0.418386033661	-0.0949874682816	-0.0874898873208	-0.0182582977726	0.324868842302	-0.0466721330048	0.419456183144	-0.0283558841745	-0.0160315023495	0.428158360689	-0.0866281210303	0.451846241159	-5.097	26.272	56.943
5	2.17187066438	-1.67646803155	-1.62383265079	6.86387019565	3.89108926639	6.1213302796	0.0374449397468	-0.0437252914592	-0.166526549166	0.124533657248	-0.0611019352869	-0.110248441212	0.144454425532	0.107238972763	0.0122873888105	0.224091833695	-0.0275141068579	-0.0220763849294	0.287211129224	0.0631220761327	0.415551915399	-10.552	-6.383	43.527
6	4.81726896326	-4.43017078234	3.25233454507	8.96395757743	1.57220752891	6.45351880867	-0.142445621697	0.253039805138	0.672285627179	1.04266885201	0.34308857516	-0.955183688778	-1.93341021586	1.19662830917	-0.165893814025	1.55701002565	-0.392307223704	0.331164487336	0.658188976447	-0.0857906270945	0.862426336997	-20.807	59.91	-1.59
7	0.990255179823	1.79129083125	-0.438446230685	5.04127359015	0.206817393098	3.44552928483	0.484416683591	-0.152506604494	0.394959326198	0.342476932852	-0.0439566165828	0.318551951224	-0.870049776077	-0.348394419911	-0.262572889705	0.500427652493	0.0965488163194	0.185700302427	0.429303348552	0.0401410704059	0.538589441137	-29.563	47.356	-11.068
8	3.16786550725	0.859938366538	-0.0727890591614	5.27681922435	-1.2031655213	2.36959529106	0.0390429204624	-0.0774542294385	-0.0841774394219	0.0617741998614	-0.0480836365879	0.640804406745	0.0867458425312	-0.108262182598	0.0284133018266	0.349350074836	-0.0392512341724	0.026910840796	0.396941922342	0.0127901256063	0.434344350976	-44.551	15.536	-11.938
9	1.08547140489	0.701024293581	-0.775414624354	3.56491070386	-1.02553495936	3.83102110235	0.919125746751	-0.771249407767	-0.0188380799062	1.79010700614	-0.817794447248	0.0754066084672	-0.935308341172	0.400410222616	-0.0620161594503	1.24733116791	-0.341649998528	0.058851360552	0.665354127179	0.0337286587835	0.512217377255	-27.216	40.696	9.756
10	2.34771972392	-0.0556541031324	-1.19139876569	5.51781964473	2.21500891486	4.28239418401	0.0557869187881	-0.0619721364859	-0.13756513411	0.409599381112	-0.0956377871495	-0.467725187847	0.221205313303	0.332292557661	0.00712570598459	0.368940961805	-0.0244169347613	-0.0392406543553	0.375441361726	0.127037592621	0.487979395856	-31.755	8.671	-5.638
11	3.23571734	-3.00880109374	-0.965442270607	6.64279850978	-3.5766323788	5.52463272939	0.562988376813	0.0842340301182	0.190509369571	-0.703634661377	0.48791839316	-1.7409329633	1.94530994216	1.41862548234	-0.797787371925	1.0055198963	0.325435958973	0.000465239591699	0.748416247849	-0.218230731301	0.778941833182	-37.933	24.598	50.449
12	2.18352449837	-1.4057580191	-0.211267968757	4.10329231292	-0.144830695995	2.1258324512	0.169930033122	0.0777598067516	-0.395252634113	-0.0641612237037	-0.057554671893	0.0696584030987	0.565873616259	0.133890838191	-0.0883224686616	0.364942277173	-0.0123386894654	-0.0349513471112	0.325597231206	-0.00295823344868	0.381730457406	-46.917	37.408	59.23
13	3.03456843096	-1.41405585869	0.635905511204	3.1072524767	-1.13636553051	1.93461850832	-0.0554853536453	-0.0296052408397	0.1632299258	-0.0268706092151	0.128422345911	0.302519964447	-0.0353937430378	-0.22208273582	-0.081739582407	0.312103033691	-0.0173984676543	0.0242414138295	0.294771537154	-0.000562662954394	0.441551944391	-62.373	68.972	58.796
14	2.25287415727	-0.450214339783	0.804993313101	3.7379739801	-1.30627583173	1.80075828411	0.221762363723	0.537558387087	0.0315972310723	-1.06812305485	-0.265103790411	-0.117422443022	0.483994625523	0.540300467759	0.0424210199264	0.807502531928	0.162514690622	0.0445293318605	0.548691564239	-0.060137033502	0.371817359359	-44.268	43.373	37.874
15	1.92541477401	0.771498789973	0.296359982289	4.82857743479	2.03428771421	4.75684561244	0.0531398178951	0.0691844864201	0.241371874378	-0.125705588305	-0.0333236679678	-0.088031586869	-0.158191352292	0.088006125778	-0.0435486753644	0.261770710369	0.0232861420086	0.0199715819318	0.338466208439	0.073865009347	0.43062669887	-49.167	75.609	52.684
16	4.30374444619	-5.53155865097	-3.36142601164	9.63067479851	0.275040692969	9.69505778499	0.0535407772261	0.889479264272	0.796106443259	0.150862359661	0.452530090271	-0.476732088359	0.926249850979	-1.38972380826	-0.390217312765	0.54685269661	-0.0649654398987	-0.0180896823311	0.940410003617	0.198866325948	0.816673250689	-17.731	-26.318	-5.208
17	1.25909118877	0.317510065823	-0.518396800202	5.58732392495	-1.70291396753	1.60243438706	-0.116299968239	0.372361938643	-0.112199034996	-0.342825623212	0.242358659939	0.375131151943	0.200421131716	-0.209202491849	-0.134416319839	0.403522786655	-0.0309209435008	-0.0372945247838	0.558350169343	0.0145953301827	0.472456618036	-8.218	-13.619	-13.244
18	0.619158311931	-0.0804113297656	-0.254814127954	4.34124994145	1.02786577543	1.97779335211	0.0157136918695	-0.0485131036879	0.058307634103	-0.275707461332	0.26631894368	-0.891818388776	-0.228933437265	0.224166335683	-0.328918758004	0.415935826297	0.0018330641506	-0.0112384831473	0.562710348206	0.0269254440841	0.659467849326	7.62	18.254	-9.657
19	1.95296292036	0.901333509347	0.51731936773	5.70088929891	0.359119997766	2.44387955322	-0.0159328074999	-0.013037640543	0.233543638291	0.833680109901	0.157756383223	0.583015786725	-0.243539456817	-0.431954489661	-0.115157658118	0.57745284784	0.0744831886485	0.176775227289	0.5028193165	0.144616696346	0.617963538044	-12.674	-8.334	7.943
20	1.01808509879	-0.810304899702	1.23589085384	6.20021929052	-2.17005557255	6.56001502158	0.0231144751039	0.108596021083	0.145765704052	0.0334015511622	-0.0168529194761	0.0929067470823	-0.36611067772	0.103957978856	0.0207055284425	0.32310525899	0.014015585295	0.00912717646898	0.447052301391	0.0708022730009	0.441315642069	-5.795	24.525	-4.485

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN O AND RESID 1:9 )	O	1 - 9
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 1:122 )	A	1 - 122
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 123:214 )	A	123 - 214
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 1:106 )	B	1 - 106
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 107:213 )	B	107 - 213
6	X-RAY DIFFRACTION	6	( CHAIN P AND RESID 1:9 )	P	1 - 9
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 1:122 )	C	1 - 122
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 123:214 )	C	123 - 214
9	X-RAY DIFFRACTION	9	( CHAIN D AND RESID 1:106 )	D	1 - 106
10	X-RAY DIFFRACTION	10	( CHAIN D AND RESID 107:212 )	D	107 - 212
11	X-RAY DIFFRACTION	11	( CHAIN Q AND RESID 1:9 )	Q	1 - 9
12	X-RAY DIFFRACTION	12	( CHAIN E AND RESID 1:122 )	E	1 - 122
13	X-RAY DIFFRACTION	13	( CHAIN E AND RESID 123:214 )	E	123 - 214
14	X-RAY DIFFRACTION	14	( CHAIN F AND RESID 1:106 )	F	1 - 106
15	X-RAY DIFFRACTION	15	( CHAIN F AND RESID 107:212 )	F	107 - 212
16	X-RAY DIFFRACTION	16	( CHAIN R AND RESID 2:9 )	R	2 - 9
17	X-RAY DIFFRACTION	17	( CHAIN G AND RESID 1:122 )	G	1 - 122
18	X-RAY DIFFRACTION	18	( CHAIN G AND RESID 123:216 )	G	123 - 216
19	X-RAY DIFFRACTION	19	( CHAIN H AND RESID 1:106 )	H	1 - 106
20	X-RAY DIFFRACTION	20	( CHAIN H AND RESID 107:213 )	H	107 - 213

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