PDB-6wfy: Crystal structure of Fab224 in complex with NPNA4 peptide from ci...

ID or keywords:

Entry

Database: PDB / ID: 6wfy

Title

Crystal structure of Fab224 in complex with NPNA4 peptide from circumsporozoite protein

Components

Fab224 heavy chain
Fab224 light chain
NPNA4 peptide

Keywords

IMMUNE SYSTEM /

Malaria /

Sporozoite /

Circumsporozoite protein /

Antibody

Function / homology

Function and homology information

entry into host cell by a symbiont-containing vacuole / side of membrane /

cell surface /

plasma membrane /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.226 Å

Authors

Pholcharee, T. / Oyen, D. / Wilson, I.A.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2021
Title: Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum.
Authors: Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / Gonzalez-Paez, G. / Han, Z. / Williams, K.L. / Volkmuth, W. / Emerling, D. / Locke, E. / Richter King, C. / Zavala, F. / Wilson, I.A.

History

Deposition	Apr 4, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 3, 2021	Group: Database references / Category: citation / citation_author
Revision 1.2	Apr 3, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6wfy.cif.gz	195 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wf/6wfy ftp://data.pdbj.org/pub/pdb/validation_reports/wf/6wfy	HTTPS FTP

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Related structure data

Related structure data	6w00C 6w05C 6wfwC 6wfxC 6wfzC 6wg0C 6wg1C 6wg2C C: citing same article (ref.)
Similar structure data	35c8-d 3ifo-2 6ev2-1 1gig-d 1e4w-d 6ugu-2 2a6k-1 4uil-d 3hr5-3 1e4x-1 4m7j-d 1lo0-1 4fqh-2 6bb4-3 4qth-1 1cfq-d 2v7h-2 4xh2-4 4kk6-2 1e4x-2 Search similar-shape structures by Omokage search (details) 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

H: Fab224 heavy chain

L: Fab224 light chain

P: NPNA4 peptide

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	42.921, 67.335, 84.768
Angle α, β, γ (deg.)	90.00, 96.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Fab224 heavy chain Mass: 24529.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Fab224 light chain Mass: 23006.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide	NPNA4 peptide Mass: 1627.654 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: P02893*PLUS
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.52 Å³/Da / Density % sol: 51.16 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG6000, 0.1 M HEPES, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2019
Radiation	Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03324 Å / Relative weight: 1
Reflection	Resolution: 1.226→50 Å / Num. obs: 114397 / % possible obs: 81.7 % / Redundancy: 2.9 % / CC_1/2: 0.893 / R_pim(I) all: 0.034 / R_sym value: 0.054 / Net I/σ(I): 19.1
Reflection shell	Resolution: 1.23→1.25 Å / Redundancy: 1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 855 / CC_1/2: 0.674 / R_pim(I) all: 0.353 / R_sym value: 0.357 / % possible all: 12.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 1.226→42.676 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.76

	R_factor	Num. reflection	% reflection
R_free	0.1834	5705	4.99 %
R_work	0.169	-	-
obs	0.1697	114353	81.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.226→42.676 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3352	0	0	491	3843

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3541
X-RAY DIFFRACTION	f_angle_d	0.846	4864
X-RAY DIFFRACTION	f_dihedral_angle_d	14.535	1917
X-RAY DIFFRACTION	f_chiral_restr	0.087	547
X-RAY DIFFRACTION	f_plane_restr	0.006	636

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 (%)
1.2261-1.2401	0.3238	29	0.2807	490	X-RAY DIFFRACTION	11
1.2401-1.2547	0.2327	22	0.2574	687	X-RAY DIFFRACTION	15
1.2547-1.27	0.3504	54	0.2844	940	X-RAY DIFFRACTION	21
1.27-1.286	0.2242	65	0.2416	1221	X-RAY DIFFRACTION	28
1.286-1.303	0.2593	84	0.2459	1567	X-RAY DIFFRACTION	36
1.303-1.3208	0.2506	108	0.2312	2073	X-RAY DIFFRACTION	47
1.3208-1.3397	0.2457	112	0.2352	2488	X-RAY DIFFRACTION	56
1.3397-1.3597	0.2501	142	0.228	3096	X-RAY DIFFRACTION	70
1.3597-1.3809	0.2083	210	0.2213	3620	X-RAY DIFFRACTION	81
1.3809-1.4036	0.2463	229	0.2172	3937	X-RAY DIFFRACTION	90
1.4036-1.4278	0.2464	207	0.2146	4277	X-RAY DIFFRACTION	96
1.4278-1.4537	0.224	224	0.1927	4316	X-RAY DIFFRACTION	98
1.4537-1.4817	0.188	208	0.1963	4430	X-RAY DIFFRACTION	99
1.4817-1.5119	0.1999	207	0.1854	4375	X-RAY DIFFRACTION	99
1.5119-1.5448	0.2005	224	0.1784	4443	X-RAY DIFFRACTION	100
1.5448-1.5807	0.1825	240	0.1678	4402	X-RAY DIFFRACTION	100
1.5807-1.6203	0.2064	231	0.1687	4410	X-RAY DIFFRACTION	100
1.6203-1.6641	0.1863	246	0.1638	4450	X-RAY DIFFRACTION	100
1.6641-1.7131	0.1882	225	0.1668	4450	X-RAY DIFFRACTION	100
1.7131-1.7684	0.17	235	0.1655	4407	X-RAY DIFFRACTION	100
1.7684-1.8316	0.1716	249	0.165	4402	X-RAY DIFFRACTION	100
1.8316-1.9049	0.1705	240	0.169	4437	X-RAY DIFFRACTION	100
1.9049-1.9916	0.175	235	0.1605	4454	X-RAY DIFFRACTION	100
1.9916-2.0966	0.1898	239	0.1585	4437	X-RAY DIFFRACTION	100
2.0966-2.2279	0.1563	238	0.1588	4436	X-RAY DIFFRACTION	100
2.2279-2.3999	0.2037	262	0.1679	4442	X-RAY DIFFRACTION	100
2.3999-2.6414	0.1943	232	0.1737	4447	X-RAY DIFFRACTION	100
2.6414-3.0236	0.2022	217	0.1733	4479	X-RAY DIFFRACTION	100
3.0236-3.809	0.167	239	0.1581	4495	X-RAY DIFFRACTION	100
3.809-42.676	0.1473	252	0.1446	4540	X-RAY DIFFRACTION	100

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	2.5541	0.5244	0.6797	0.3071	-0.4301	2.0847	-0.1061	0.2863	-0.0625	-0.3389	0.1727	-0.147	0.0332	0.1542	-0.0559	0.0548	0.0245	0.011	0.1167	0.0005	0.1085	39.9369	-20.5217	24.2086
2	1.0792	-0.3279	0.4572	0.8387	0.0842	0.889	0.0168	0.0187	-0.0582	-0.0187	-0.0077	-0.0431	-0.005	0.0261	-0.0084	0.0549	-0.0039	-0.0029	0.0608	0.0003	0.1238	40.587	-18.5557	36.2412
3	0.4267	0.1578	0.4333	0.4632	0.4496	1.3022	0.0201	0.0272	0.0083	-0.0218	-0.0102	0.0258	-0.0058	-0.0443	-0.0161	0.0517	0.0054	-0.0075	0.0703	0.0081	0.1377	29.4102	-16.0679	24.73
4	1.3913	-0.8391	1.1311	1.8635	-1.216	1.9046	-0.0481	0.1149	0.1908	-0.0349	0.0272	-0.0572	-0.1288	0.0301	0.0096	0.1264	-0	-0.0208	0.1278	0.0101	0.2107	20.7957	-14.8813	0.912
5	0.864	-0.1257	0.1333	1.4096	-0.1652	0.5208	0.0098	-0.0078	0.0102	-0.0121	-0.022	0.0583	-0.0209	-0.0378	0.0001	0.0521	0.001	-0.0068	0.0765	-0.0019	0.1266	22.3571	-4.3085	38.1367
6	0.3299	0.3168	0.4424	3.5751	0.5247	0.7735	-0.0746	-0.0258	0.0594	0.1523	0.0764	-0.2212	-0.083	0.003	0.0046	0.1357	0.0209	-0.0436	0.1451	-0.0224	0.2195	8.9814	-15.0661	8.3549
7	1.6322	-1.0873	0.0068	0.8052	0.3275	1.3025	-0.2354	-0.3322	0.4897	0.1479	0.1532	-0.2891	-0.1072	0.0845	0.0347	0.178	0.0564	-0.076	0.1997	-0.0816	0.3023	11.3319	-14.2319	14.3189
8	1.6603	0.0939	-0.0753	3.4961	-0.1178	1.7497	-0.0291	-0.0688	-0.0663	0.2424	-0.0353	0.2929	-0.1159	-0.1973	0.051	0.1317	0.0115	0.0024	0.19	-0.0205	0.211	3.376	-21.3488	8.5908
9	7.1256	-0.409	-2.015	3.968	-1.641	3.9974	-0.074	-0.4942	-0.3164	0.3466	0.0564	0.1432	0.023	-0.1808	0.018	0.0892	-0.0036	-0.007	0.1184	0.0168	0.1675	34.5239	-13.5466	51.5584

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 81 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 82 through 134 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 135 through 214 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 1 through 106A)
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 107 through 150 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 151 through 173 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 174 through 210 )
9	X-RAY DIFFRACTION	9	chain 'P' and (resid 1 through 12 )

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