PDB-5ezi: Crystal Structure of Fab of parasite invasion inhibitory antibody...

ID or keywords:

Entry

Database: PDB / ID: 5ezi

Title

Crystal Structure of Fab of parasite invasion inhibitory antibody c1 - hexagonal form

Components

Fab c12 Light chain
Fab c12 heavy chain

Keywords

IMMUNE SYSTEM / MALARIA INHIBITORY ANTIBODY / FAB / cyrpa

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.61 Å

Authors

Favuzza, P. / Pluschke, G. / Rudolph, M.G.

Citation

Journal: Elife / Year: 2017
Title: Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody.
Authors: Favuzza, P. / Guffart, E. / Tamborrini, M. / Scherer, B. / Dreyer, A.M. / Rufer, A.C. / Erny, J. / Hoernschemeyer, J. / Thoma, R. / Schmid, G. / Gsell, B. / Lamelas, A. / Benz, J. / Joseph, ...

History

Deposition	Nov 26, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jan 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Feb 15, 2017	Group: Structure summary
Revision 1.2	Mar 1, 2017	Group: Structure summary
Revision 1.3	Apr 26, 2017	Group: Other / Structure summary
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ezi.cif.gz	204.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ezi.ent.gz	161.8 KB	Display	PDB format
PDBx/mmJSON format	5ezi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ezi_validation.pdf.gz	799.2 KB	Display	wwPDB validaton report
Full document	5ezi_full_validation.pdf.gz	799.7 KB	Display
Data in XML	5ezi_validation.xml.gz	22.3 KB	Display
Data in CIF	5ezi_validation.cif.gz	33.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ez/5ezi ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ezi	HTTPS FTP

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Related structure data

Related structure data	5ezjC 5ezlC 5eznC 5ezoC C: citing same article (ref.)
Similar structure data	5lfj-d 3nfg-3 4d5k-d 1hia-d 6vvg-d 3eno-2 5e0c-d 3atj-d 2dwp-d 4wio-d 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

H: Fab c12 heavy chain

L: Fab c12 Light chain

hetero molecules

49 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	82.700, 82.700, 361.880
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	H-684- HOH

#1: Antibody

Fab c12 heavy chain

Mass: 23676.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#2: Antibody

Fab c12 Light chain

Mass: 23684.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#3: Polysaccharide

beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...

Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-4-3-1-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1_g2-h1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#4: Chemical

ChemComp-CL / CHLORIDE ION

Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 444 / 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: 3.77 Å³/Da / Density % sol: 67.39 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M sodium citrate pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 1970
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.61→50.9 Å / Num. obs: 96028 / % possible obs: 100 % / Redundancy: 13.8 % / Net I/σ(I): 8.54
Reflection shell	Resolution: 1.61→1.67 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 0.84 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XSCALE		data scaling
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 1.61→56.154 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2209	4802	5.01 %
R_work	0.1949	-	-
obs	0.1961	95862	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.61→56.154 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3329	0	111	444	3884

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3588
X-RAY DIFFRACTION	f_angle_d	0.887	4924
X-RAY DIFFRACTION	f_dihedral_angle_d	15.286	2176
X-RAY DIFFRACTION	f_chiral_restr	0.054	578
X-RAY DIFFRACTION	f_plane_restr	0.005	610

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 (%)
1.61-1.6283	0.4685	179	0.466	2943	X-RAY DIFFRACTION	100
1.6283-1.6475	0.4154	171	0.441	2967	X-RAY DIFFRACTION	100
1.6475-1.6675	0.4553	153	0.4322	2957	X-RAY DIFFRACTION	100
1.6675-1.6887	0.4526	153	0.4184	3001	X-RAY DIFFRACTION	100
1.6887-1.7109	0.4174	159	0.4035	2968	X-RAY DIFFRACTION	100
1.7109-1.7343	0.4474	143	0.387	2982	X-RAY DIFFRACTION	100
1.7343-1.7591	0.3958	172	0.3697	2968	X-RAY DIFFRACTION	100
1.7591-1.7854	0.397	142	0.3511	2984	X-RAY DIFFRACTION	100
1.7854-1.8133	0.3691	159	0.3302	2982	X-RAY DIFFRACTION	99
1.8133-1.843	0.359	146	0.3091	2983	X-RAY DIFFRACTION	100
1.843-1.8748	0.3229	155	0.2846	2998	X-RAY DIFFRACTION	100
1.8748-1.9089	0.25	172	0.2705	2967	X-RAY DIFFRACTION	100
1.9089-1.9456	0.2889	141	0.2685	3008	X-RAY DIFFRACTION	100
1.9456-1.9853	0.2674	152	0.2463	3033	X-RAY DIFFRACTION	100
1.9853-2.0285	0.2467	166	0.227	2978	X-RAY DIFFRACTION	100
2.0285-2.0756	0.2799	160	0.2158	3007	X-RAY DIFFRACTION	100
2.0756-2.1276	0.2193	151	0.2057	3020	X-RAY DIFFRACTION	100
2.1276-2.1851	0.2327	158	0.2001	3015	X-RAY DIFFRACTION	100
2.1851-2.2494	0.2277	164	0.2041	3006	X-RAY DIFFRACTION	100
2.2494-2.322	0.2381	143	0.197	3033	X-RAY DIFFRACTION	100
2.322-2.405	0.2316	154	0.2017	3046	X-RAY DIFFRACTION	100
2.405-2.5013	0.2269	178	0.2058	3030	X-RAY DIFFRACTION	100
2.5013-2.6151	0.2557	165	0.2119	3043	X-RAY DIFFRACTION	100
2.6151-2.753	0.2723	175	0.2095	3068	X-RAY DIFFRACTION	100
2.753-2.9255	0.2326	188	0.2044	3031	X-RAY DIFFRACTION	100
2.9255-3.1513	0.2148	142	0.1943	3105	X-RAY DIFFRACTION	100
3.1513-3.4684	0.2017	158	0.1672	3141	X-RAY DIFFRACTION	100
3.4684-3.9702	0.1522	172	0.136	3128	X-RAY DIFFRACTION	100
3.9702-5.0015	0.138	156	0.1171	3204	X-RAY DIFFRACTION	100
5.0015-56.1883	0.1681	175	0.1609	3464	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	3.5915	2.5096	-1.7284	3.1413	-0.0695	3.7574	0.2944	-0.6048	0.6559	-0.2371	-0.3196	0.2449	-0.3582	-0.1929	-0.0141	0.4163	0.0768	-0.0036	0.2238	-0.0562	0.3076	50.2211	-6.4154	2.6602
2	5.0083	-1.3158	1.35	0.4966	-0.963	0.9886	-0.1981	0.0824	0.2189	-0.3639	0.0868	-0.0773	0.0147	0.0655	-0.1187	0.4548	-0.0103	-0.062	0.1341	-0.0383	0.2432	48.16	-3.0669	-10.0427
3	3.8409	-0.1484	-0.5378	4.8426	-0.2637	4.8123	-0.1879	0.0588	-0.2992	-0.4264	0.0234	0.3432	0.2734	-0.336	0.1746	0.3712	0.0367	-0.0064	0.1978	-0.0503	0.2736	50.783	-15.7337	-6.6955
4	6.1937	1.7868	-4.1096	2.2838	-2.1041	6.609	-0.1881	0.0477	-0.0011	-0.5877	0.0132	0.2394	-0.0474	-0.4218	0.1599	0.3978	0.0755	-0.0596	0.2144	-0.0764	0.2736	47.4131	-8.868	-3.5475
5	5.2613	-0.1327	-1.3606	3.406	0.8902	3.1251	0.0965	0.1112	0.1165	-0.3202	-0.0408	-0.2052	-0.0917	-0.0448	-0.0732	0.4075	0.0415	0.0087	0.2156	-0.0133	0.2517	58.4667	-13.6494	-1.7267
6	6.6658	0.2114	5.269	2.0371	1.0134	5.3233	-0.0803	-0.4736	0.2127	0.2546	0.0033	0.1926	-1.1072	-0.6686	0.1818	0.3949	-0.1219	0.1249	0.2316	-0.0309	0.3196	42.4909	-5.2576	23.4073
7	1.5575	0.4973	-1.3969	2.407	0.9438	2.0197	0.1625	-0.4808	0.1382	0.2401	0.0319	-0.2416	-0.1308	0.6435	-0.1777	0.4692	-0.2179	0.0815	0.4254	-0.1066	0.3526	56.3971	-9.1836	36.7271
8	2.6842	-1.7275	1.7917	1.7152	-0.6694	3.8474	0.1252	0.025	-0.0016	0.0226	-0.0772	0.0238	-0.256	0.3075	-0.0555	0.3963	-0.1861	0.0876	0.2937	-0.0425	0.2721	54.1797	-9.0287	24.3305
9	3.9413	1.0178	4.2303	1.4655	1.7595	7.0988	0.5802	0.3928	0.6084	0.23	-0.1472	-0.2021	-0.6269	0.9048	-0.2845	0.6045	-0.3839	0.0753	0.3052	-0.1658	0.367	58.5296	-0.5555	30.2286
10	0.6768	0.6305	0.8335	1.7871	-0.8808	7.7727	0.1699	-0.0442	0.1846	0.1183	-0.1262	0.1173	-1.2558	0.7623	0.1495	0.7111	-0.2553	0.0962	0.383	-0.11	0.4085	54.1451	0.7567	34.1872
11	3.7391	-0.1262	2.7017	2.7003	0.1414	5.7723	-0.0297	-0.1869	-0.3457	0.302	0.0193	0.2424	0.5521	0.0976	-0.0961	0.4816	0.0435	0.1221	0.2257	0.03	0.3667	63.6189	-33.763	6.2645
12	3.7098	0.3944	1.3	4.5175	0.4898	4.769	-0.0083	0.2807	-0.2063	-0.2371	0.0891	0.1138	0.3098	0.2181	0.0769	0.4578	0.0794	0.058	0.1817	-0.0194	0.2947	63.2163	-28.3137	-5.0459
13	4.1561	-1.7843	0.279	2.9096	-1.4758	2.372	-0.1057	-0.0473	0.0256	-0.0226	0.0273	-0.2094	0.0507	0.2661	0.1376	0.3966	0.0318	0.087	0.1967	-0.0114	0.242	70.4155	-25.4589	0.4996
14	4.8623	-2.2199	1.429	3.1258	-1.6994	2.4661	-0.0824	-0.0818	-0.1339	-0.0292	0.0176	0.0642	0.0285	0.1244	0.036	0.4444	0.014	0.0891	0.1924	-0.0245	0.2738	63.4577	-25.8243	2.023
15	0.4031	0.8121	1.1078	1.2603	1.9714	2.7082	-0.0645	-0.2434	0.0042	-0.1019	-0.2658	-0.2052	0.5076	0.414	0.3034	0.5005	0.1155	0.1183	0.5483	0.0633	0.3202	66.3344	-28.12	23.182
16	5.8274	-3.6345	-1.7636	3.2649	0.1068	2.8579	0.1585	-0.0195	0.2423	-0.0495	-0.1638	-0.0638	0.0115	0.0696	-0.1216	0.3555	-0.1624	0.0784	0.272	-0.0595	0.2459	52.6196	-14.7457	34.8367
17	7.0239	-1.1667	-4.3173	0.512	0.2488	4.5731	0.0348	-0.2977	-0.6812	0.1699	-0.1817	0.3069	0.6432	-0.0241	0.2533	0.5021	-0.1765	0.0224	0.3354	-0.0578	0.342	46.4914	-24.8214	39.7961
18	3.9467	-1.934	-0.6496	2.9382	0.4995	4.486	0.4457	0.4198	0.415	-0.4385	-0.3037	-0.1954	-0.0782	0.3301	-0.0516	0.4916	-0.0857	0.0688	0.1975	-0.0161	0.2328	57.1395	-21.1255	25.9537
19	4.349	-2.2979	-1.7463	2.8161	0.8228	3.7957	-0.0797	-0.3118	0.0257	0.1893	0.0724	0.1708	0.0426	-0.18	-0.0039	0.3803	-0.2005	0.0665	0.3054	-0.0775	0.3035	44.9758	-17.29	40.2328
20	6.2968	-4.503	-3.6478	6.2773	2.4361	5.0623	-0.2138	-0.6774	0.0825	0.4364	0.1132	-0.0328	0.3316	0.5442	-0.0486	0.3957	-0.1627	0.0394	0.4689	0.0038	0.2552	54.4282	-20.7251	45.3191

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 15 through 31 )
2	X-RAY DIFFRACTION	2	chain 'H' and ((resid 32 through 47 ) or (resid 501 through 510))
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 48 through 87 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 88 through 105 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 106 through 131 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 132 through 144 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 145 through 165 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 166 through 204 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 205 through 222 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 223 through 236 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 25 through 49 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 50 through 62 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 63 through 99 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 100 through 125 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 126 through 137 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 138 through 167 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 168 through 179 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 180 through 198 )
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 199 through 222 )
20	X-RAY DIFFRACTION	20	chain 'L' and (resid 223 through 238 )

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Yorodumi