PDB-6d01: Crystal structure of 1210 Fab in complex with circumsporozoite pr...

ID or keywords:

Entry

Database: PDB / ID: 6d01

Title

Crystal structure of 1210 Fab in complex with circumsporozoite protein NANP5

Components

1210 Antibody, Light chain
1210 Antibody, heavy chain
NANP5

Keywords

IMMUNE SYSTEM / Malaria / Antibody / Circumsporozoite protein

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: 3.2 Å

Authors

Scally, S.W. / Bosch, A. / Imkeller, K. / Wardemann, H. / Julien, J.P.

Citation

Journal: Science / Year: 2018
Title: Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope.
Authors: Imkeller, K. / Scally, S.W. / Bosch, A. / Marti, G.P. / Costa, G. / Triller, G. / Murugan, R. / Renna, V. / Jumaa, H. / Kremsner, P.G. / Sim, B.K.L. / Hoffman, S.L. / Mordmuller, B. / ...

History

Deposition	Apr 9, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Jul 4, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3	Oct 23, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6d01.cif.gz	691.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6d01.ent.gz	581.3 KB	Display	PDB format
PDBx/mmJSON format	6d01.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6d01_validation.pdf.gz	527.9 KB	Display	wwPDB validaton report
Full document	6d01_full_validation.pdf.gz	539.9 KB	Display
Data in XML	6d01_validation.xml.gz	60 KB	Display
Data in CIF	6d01_validation.cif.gz	79.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d0/6d01 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/6d01	HTTPS FTP

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Related structure data

Related structure data	6d0xC 6d11C C: citing same article (ref.)
Similar structure data	2or9-d 2a1w-d 3arg-d 6axl-d 6srx-d 3sdd-d 5dyo-d 6foe-d 5i1l-d 3rug-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

A: 1210 Antibody, heavy chain

B: 1210 Antibody, Light chain

C: 1210 Antibody, heavy chain

D: 1210 Antibody, Light chain

E: 1210 Antibody, heavy chain

F: 1210 Antibody, Light chain

G: 1210 Antibody, heavy chain

H: 1210 Antibody, Light chain

I: NANP5

J: NANP5

hetero molecules

199 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 1210 Antibody, heavy chain

B: 1210 Antibody, Light chain

C: 1210 Antibody, heavy chain

D: 1210 Antibody, Light chain

I: NANP5

hetero molecules

defined by author
Evidence: gel filtration
100 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: 1210 Antibody, heavy chain

F: 1210 Antibody, Light chain

G: 1210 Antibody, heavy chain

H: 1210 Antibody, Light chain

J: NANP5

hetero molecules

defined by author
Evidence: gel filtration
99 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	205.963, 150.856, 134.651
Angle α, β, γ (deg.)	90.00, 94.81, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Antibody	1210 Antibody, heavy chain Mass: 24313.230 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	1210 Antibody, Light chain Mass: 23498.098 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide	NANP5 Mass: 2000.006 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: P02893*PLUS
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
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: 5.37 Å³/Da / Density % sol: 77.11 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 0.2M sodium citrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 14, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 3.2→40 Å / Num. obs: 67565 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC_1/2: 0.99 / R_merge(I) obs: 0.147 / R_pim(I) all: 0.088 / Net I/σ(I): 8.9
Reflection shell	Resolution: 3.2→3.3 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.633 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5890 / CC_1/2: 0.57 / R_pim(I) all: 0.375 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→39.866 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.68

	R_factor	Num. reflection	% reflection
R_free	0.2267	2001	2.96 %
R_work	0.2039	-	-
obs	0.2046	67547	99.88 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.2→39.866 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13369	0	240	0	13609

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13891
X-RAY DIFFRACTION	f_angle_d	0.526	18832
X-RAY DIFFRACTION	f_dihedral_angle_d	12.837	8188
X-RAY DIFFRACTION	f_chiral_restr	0.044	2088
X-RAY DIFFRACTION	f_plane_restr	0.005	2411

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 (%)
3.2-3.28	0.3723	152	0.3237	4642	X-RAY DIFFRACTION	100
3.28-3.3687	0.3279	143	0.3044	4689	X-RAY DIFFRACTION	100
3.3687-3.4677	0.2962	128	0.2703	4619	X-RAY DIFFRACTION	100
3.4677-3.5796	0.2845	145	0.2574	4690	X-RAY DIFFRACTION	100
3.5796-3.7074	0.2689	139	0.2526	4653	X-RAY DIFFRACTION	100
3.7074-3.8558	0.2587	153	0.2354	4681	X-RAY DIFFRACTION	100
3.8558-4.0311	0.2587	143	0.2166	4664	X-RAY DIFFRACTION	100
4.0311-4.2434	0.208	140	0.1962	4671	X-RAY DIFFRACTION	100
4.2434-4.5089	0.1889	144	0.1662	4681	X-RAY DIFFRACTION	100
4.5089-4.8565	0.172	135	0.1527	4686	X-RAY DIFFRACTION	100
4.8565-5.3442	0.1901	149	0.1628	4686	X-RAY DIFFRACTION	100
5.3442-6.1151	0.2012	144	0.1818	4716	X-RAY DIFFRACTION	100
6.1151-7.6953	0.2216	143	0.2017	4694	X-RAY DIFFRACTION	100
7.6953-39.8691	0.1966	143	0.1819	4774	X-RAY DIFFRACTION	99

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	2.8687	2.0365	0.1068	5.2732	-2.2612	3.3928	0.1252	-0.5312	-0.837	0.613	-0.5026	-2.019	-0.0447	0.8613	0.3266	0.5078	-0.1815	-0.1867	0.858	0.2242	1.0673	265.0176	69.6439	150.8917
2	3.2548	1.3825	-0.046	4.8121	-2.162	3.5173	-0.0535	0.0595	0.2072	-0.5182	-0.366	-1.0368	1.1071	0.9877	0.4737	0.8749	0.4112	0.3274	0.9734	0.3144	1.3511	296.488	98.4328	107.6147
3	3.4672	-1.0152	-0.6589	5.402	-1.2659	5.581	0.0387	0.2194	0.7104	-0.1633	-0.3746	-1.067	0.3952	0.7281	0.1873	0.9692	0.1324	-0.124	0.8184	0.2724	0.8109	272.7625	187.4797	54.0201
4	5.0094	1.4046	1.5047	2.3455	0.2802	7.0735	-0.0229	0.2943	-0.1452	-0.1456	-0.2622	-1.002	-0.109	1.3814	0.3025	0.6232	0.0774	-0.0443	0.8003	0.2533	0.8377	292.9871	148.163	91.0439
5	5.9253	3.532	-4.4865	6.5133	-3.2868	5.2474	-0.0774	-0.0874	-0.4339	-0.1937	0.0448	-0.3019	0.2084	0.152	0.0491	0.4003	-0.0919	-0.1105	0.463	0.0112	0.5181	251.1814	67.9402	142.1865
6	6.6544	-0.6935	-1.5262	1.9105	0.104	3.664	0.197	-0.8249	-0.028	-0.1126	-0.3129	-1.4929	-0.1434	1.0662	0.1948	0.4287	-0.0345	0.0264	0.8419	0.2335	1.1045	291.1676	109.4197	118.5331
7	3.7307	-2.5262	2.8522	2.9025	-2.7277	5.4322	-0.2301	-0.0174	0.3545	0.4345	0.1054	-0.389	0.0813	0.0924	0.098	1.2644	0.0503	-0.1602	0.584	0.0574	0.5907	257.4804	189.1521	60.0246
8	4.0493	-0.2513	-0.4749	2.9088	0.0538	3.886	-0.1433	-0.1461	0.3947	0.4787	-0.1351	-0.4183	-0.2404	0.072	0.3135	0.5146	0.0051	-0.2574	0.4247	-0.0147	0.5622	281.9036	138.8425	129.8024
9	2.1852	-0.0488	-0.1801	5.0036	-1.792	2.8821	-0.1299	0.0879	-0.0126	-0.2065	-0.0082	-0.1998	-0.1658	-0.334	0.1703	0.3408	0.0611	-0.1048	0.4913	-0.1153	0.4083	267.7544	136.4557	113.2892
10	3.5652	1.559	-1.0398	8.6356	-3.1068	4.929	0.0908	-0.5065	0.0328	1.2283	-0.3772	-0.2433	-0.3375	0.066	0.259	0.5416	-0.2024	-0.0929	0.5772	-0.0737	0.4358	266.469	106.226	145.7836
11	2.2708	0.0952	0.4148	6.4472	-0.4473	4.0435	-0.1485	-0.04	-0.2566	-0.3148	-0.1474	0.4789	0.2483	-0.5335	0.2815	0.2894	-0.0824	0.0508	0.5084	-0.0525	0.4223	261.6513	98.0866	126.0869
12	0.8052	0.4712	-0.5126	4.0562	0.4761	2.9783	-0.2407	0.3415	-0.373	-1.5087	-0.5306	-1.0472	0.5659	0.4506	0.6932	1.3387	0.3375	0.515	0.8576	0.1447	0.9022	287.1026	118.9779	78.2192
13	1.969	1.091	-0.5811	4.939	-1.979	3.6187	0.042	0.2678	-0.225	-0.8968	-0.1302	-0.3245	0.423	0.0174	0.1154	0.6376	0.1538	0.0051	0.4913	-0.1351	0.4219	269.9627	120.768	91.6434
14	1.95	-0.6561	1.1411	3.6493	-3.3803	3.5025	-0.2459	0.5812	-0.0496	-1.1845	-0.2549	-0.3157	0.0732	0.1808	0.4673	1.4577	0.2884	0.1114	0.834	0.0207	0.5258	274.0566	151.0533	59.2958
15	1.998	-0.3984	-0.2769	7.2662	-2.2799	1.2031	-0.2027	0.0144	0.0944	-0.3495	-0.0651	0.2328	-0.4566	-0.25	0.2614	0.9554	0.1821	-0.1337	0.6602	-0.0172	0.3429	265.4052	159.0336	77.868
16	3.8271	5.4269	1.6538	7.8076	1.713	3.9666	-0.2018	-0.3845	0.6427	0.8752	0.4053	0.3952	0.1899	-0.3907	-0.2547	0.5145	0.0261	-0.1146	0.623	0.0199	0.4789	266.6873	124.5626	136.1298
17	6.398	-5.9966	-0.6725	2.0108	-4.9134	6.8109	-0.1511	0.2755	-0.4563	-2.0786	0.5781	0.054	0.9681	-0.6814	-0.4443	1.5298	0.1484	0.1693	0.7924	0.1019	0.5559	272.8929	132.6919	68.9785
18	3.2747	-0.609	-0.4846	3.7201	-1.2819	5.1501	-0.1086	0.3285	0.3939	-0.1644	-0.3667	-0.6082	-1.4567	1.0202	0.4576	0.9376	-0.2693	-0.2589	0.8437	0.3078	1.1186	296.0929	159.416	102.6898

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'C' and resid 114 through 215)
2	X-RAY DIFFRACTION	2	(chain 'E' and resid 114 through 215)
3	X-RAY DIFFRACTION	3	(chain 'G' and resid 114 through 214)
4	X-RAY DIFFRACTION	4	(chain 'B' and resid 108 through 213)
5	X-RAY DIFFRACTION	5	(chain 'D' and resid 108 through 213)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 108 through 213)
7	X-RAY DIFFRACTION	7	(chain 'H' and resid 108 through 214)
8	X-RAY DIFFRACTION	8	(chain 'A' and resid 1 through 113)
9	X-RAY DIFFRACTION	9	(chain 'B' and resid 1 through 107)
10	X-RAY DIFFRACTION	10	(chain 'C' and resid 1 through 113)
11	X-RAY DIFFRACTION	11	(chain 'D' and resid 1 through 107)
12	X-RAY DIFFRACTION	12	(chain 'E' and resid 1 through 113)
13	X-RAY DIFFRACTION	13	(chain 'F' and resid 1 through 107)
14	X-RAY DIFFRACTION	14	(chain 'G' and resid 1 through 113)
15	X-RAY DIFFRACTION	15	(chain 'H' and resid 1 through 107)
16	X-RAY DIFFRACTION	16	(chain 'I' and resid 2 through 20)
17	X-RAY DIFFRACTION	17	(chain 'J' and resid 2 through 20)
18	X-RAY DIFFRACTION	18	(chain 'A' and resid 114 through 213)

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