PDB-6bqb: MGG4 Fab in complex with peptide

ID or keywords:

Entry

Database: PDB / ID: 6bqb

Title

MGG4 Fab in complex with peptide

Components

MGG4 Fab heavy chain
MGG4 Fab light chain
N-terminal junction peptide

Keywords

IMMUNE SYSTEM / human Fab fragment peptide binding Plasmodium falciparum circumsporozoite protein

Function / homology

Function and homology information

host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole /

heparan sulfate proteoglycan binding / 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: 1.769 Å

Authors

Oyen, D. / Tan, J. / Lanzavecchia, A. / Wilson, I.A.

Funding support

United States, 1items

Citation

Journal: Nat. Med. / Year: 2018
Title: A public antibody lineage that potently inhibits malaria infection through dual binding to the circumsporozoite protein.
Authors: Tan, J. / Sack, B.K. / Oyen, D. / Zenklusen, I. / Piccoli, L. / Barbieri, S. / Foglierini, M. / Fregni, C.S. / Marcandalli, J. / Jongo, S. / Abdulla, S. / Perez, L. / Corradin, G. / Varani, ...

History

Deposition	Nov 27, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 4, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 25, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6bqb.cif.gz	272.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6bqb.ent.gz	235.6 KB	Display	PDB format
PDBx/mmJSON format	6bqb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Similar structure data	6h0e-1 4xh2-4 2g5b-1 6qnk-2 6h06-3 6xli-3 2fx8-1 3bkj-d 7k8o-d 3f58-d 2f58-d 3rvu-d 1lo0-1 1e4x-1 5myo-1 2fx9-1 5zia-1 1e4w-d 6xuk-d 5vkk-1 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

L: MGG4 Fab light chain

H: MGG4 Fab heavy chain

P: N-terminal junction peptide

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	55.782, 68.062, 148.610
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	MGG4 Fab light chain Mass: 24224.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody	MGG4 Fab heavy chain Mass: 23982.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Protein/peptide	N-terminal junction peptide Mass: 1459.520 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: Q7K740*PLUS
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.84 Å³/Da / Density % sol: 56.69 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.04M KH2PO4 20% Glycerol 16% PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97648 Å / Relative weight: 1
Reflection	Resolution: 1.77→43.14 Å / Num. obs: 56018 / % possible obs: 98.8 % / Redundancy: 7.2 % / CC_1/2: 0.947 / R_pim(I) all: 0.038 / Net I/σ(I): 21
Reflection shell	Resolution: 1.77→1.8 Å / Mean I/σ(I) obs: 1.6 / CC_1/2: 0.652 / R_pim(I) all: 0.48

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.769→43.143 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1956	2710	4.84 %
R_work	0.1664	-	-
obs	0.1678	55940	99.74 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.769→43.143 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3397	0	18	559	3974

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3667
X-RAY DIFFRACTION	f_angle_d	1.02	5023
X-RAY DIFFRACTION	f_dihedral_angle_d	20.897	1333
X-RAY DIFFRACTION	f_chiral_restr	0.099	559
X-RAY DIFFRACTION	f_plane_restr	0.006	660

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 (%)
1.7692-1.8014	0.2802	150	0.2806	2634	X-RAY DIFFRACTION	95
1.8014-1.836	0.3071	137	0.2603	2754	X-RAY DIFFRACTION	100
1.836-1.8735	0.2304	142	0.2308	2762	X-RAY DIFFRACTION	100
1.8735-1.9142	0.2297	134	0.2065	2783	X-RAY DIFFRACTION	100
1.9142-1.9588	0.2	140	0.1913	2787	X-RAY DIFFRACTION	100
1.9588-2.0077	0.185	144	0.1737	2767	X-RAY DIFFRACTION	100
2.0077-2.062	0.2014	129	0.174	2791	X-RAY DIFFRACTION	100
2.062-2.1227	0.2035	146	0.1777	2760	X-RAY DIFFRACTION	100
2.1227-2.1912	0.2128	137	0.1718	2786	X-RAY DIFFRACTION	100
2.1912-2.2695	0.1983	134	0.1697	2803	X-RAY DIFFRACTION	100
2.2695-2.3604	0.1927	131	0.1657	2789	X-RAY DIFFRACTION	100
2.3604-2.4678	0.1891	145	0.1588	2785	X-RAY DIFFRACTION	100
2.4678-2.5979	0.211	163	0.1622	2794	X-RAY DIFFRACTION	100
2.5979-2.7606	0.1824	129	0.1566	2825	X-RAY DIFFRACTION	100
2.7606-2.9737	0.2368	117	0.1623	2861	X-RAY DIFFRACTION	100
2.9737-3.2729	0.2252	149	0.1616	2828	X-RAY DIFFRACTION	100
3.2729-3.7463	0.1769	151	0.1497	2843	X-RAY DIFFRACTION	100
3.7463-4.719	0.1576	158	0.1308	2866	X-RAY DIFFRACTION	100
4.719-43.1562	0.1812	174	0.1764	3012	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	1.4865	0.8395	-0.1742	5.8332	-0.9224	0.8151	-0.0558	0.0348	-0.1709	-0.1938	-0.0252	-0.4169	0.1503	0.3055	0.0769	0.1623	0.0666	0.0459	0.251	-0.0123	0.1771	73.0515	36.6481	2.0066
2	2.1986	2.7859	0.5513	5.9162	2.7772	7.4764	0.1594	-0.1889	0.2848	0.1184	-0.2535	0.5057	-0.3525	-0.3124	0.1215	0.0998	0.0265	0.0217	0.1587	0.0105	0.1746	62.067	43.9261	7.0345
3	0.6748	0.5462	0.1631	1.4239	0.2486	0.8142	-0.0068	-0.0068	0.0228	0.0298	0.01	0.0157	-0.0008	0.1053	0.0081	0.0815	0.0242	0.0117	0.1629	0.0108	0.144	69.2446	49.2414	8.4325
4	1.578	0.1257	0.8104	1.2753	1.146	2.2875	0.0755	-0.229	0.0052	0.3432	-0.062	-0.1389	0.3851	0.3514	0.0338	0.2636	-0.0207	0.0073	0.2404	0.0116	0.1727	79.9189	63.9853	21.6778
5	3.5842	0.6043	1.7301	2.8066	0.4232	3.1376	0.1361	-0.2651	-0.1008	0.3134	-0.0354	-0.1056	0.1996	0.1956	-0.0762	0.1712	-0.0056	0.0427	0.2028	-0.0068	0.1604	76.8215	61.7761	20.8555
6	0.2436	0.2643	0.5795	1.0031	0.8814	3.4045	0.193	-0.6001	0.0761	0.3661	-0.1252	-0.1148	-0.3891	1.0113	-0.1432	0.3989	-0.1628	-0.022	0.5508	-0.0389	0.2395	83.9411	68.6368	30.1711
7	1.7832	0.0537	-0.1005	1.9602	0.8053	0.3518	-0.1209	-0.2537	0.1389	0.2425	0.0542	-0.0374	-0.5413	-0.2117	0.128	0.2215	0.0081	0.0575	0.1665	0.0165	0.1833	54.9936	39.3951	27.1435
8	1.4258	0.4565	0.5551	1.8908	-0.0707	4.6623	0.0887	0.0092	0.0064	0.0281	0.028	0.1042	0.0692	-0.1972	-0.1167	0.1422	0.0318	0.0266	0.1194	0.0211	0.1698	55.2638	34.6681	17.8917
9	4.9386	2.1682	1.8733	2.2963	0.4277	3.1748	0.0581	0.0378	-0.3164	0.0454	0.062	-0.0783	0.3412	0.0251	-0.122	0.2131	0.0182	0.0283	0.1311	0.0133	0.2013	58.4506	26.2703	20.4098
10	6.2181	3.8702	3.3155	3.7692	1.2025	6.1367	0.0678	-0.0934	-0.0164	0.1268	-0.0859	0.0611	0.0245	0.0527	0.0052	0.1276	0.0632	0.0649	0.0876	-0.0172	0.1336	59.2451	35.411	25.2945
11	1.2664	0.3171	1.4268	0.1923	0.1008	6.6602	0.0281	-0.0355	-0.0678	-0.0339	0.0049	0.0825	0.0204	-0.394	-0.0146	0.1316	0.0083	0.0268	0.1676	0.0061	0.203	55.0997	35.3691	9.2853
12	0.7433	-0.9594	0.3747	2.389	0.5894	1.6368	0.179	-0.1181	0.2505	0.339	-0.1672	-0.2365	-0.4216	0.294	0.0352	0.3495	-0.0591	0.0701	0.236	-0.0357	0.2372	67.9208	66.216	31.9339
13	0.939	1.7449	-0.2792	3.4976	-1.1606	1.3541	0.1527	-0.0081	0.3576	0.3029	-0.1	0.4408	-0.1635	-0.0802	-0.04	0.2484	0.0122	0.0899	0.1584	-0.0286	0.2648	63.7856	67.0338	26.9938
14	2.3935	4.4335	-1.078	8.4232	-2.6768	2.385	0.7382	-0.4848	0.9331	0.6622	-0.3621	0.3341	-0.8233	0.1266	-0.3062	0.4993	-0.0681	0.221	0.2891	-0.1215	0.5182	60.1819	72.4377	33.8834
15	4.5145	0.4106	0.6168	2.7876	0.2682	9.5944	0.1442	1.2276	-1.1396	-1.0525	-0.488	0.2816	0.7042	-0.6164	0.4559	0.5431	-0.0582	0.084	0.3597	-0.0322	0.3823	58.4112	21.1898	6.5549

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 32 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 33 through 48 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 49 through 128 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 129 through 150 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 151 through 174 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 175 through 213 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 2 through 17 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 18 through 45 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 46 through 75 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 76 through 93 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 94 through 109 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 110 through 134 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 135 through 203 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 204 through 214 )
15	X-RAY DIFFRACTION	15	chain 'P' and (resid 7 through 13 )

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