PDB-3qwo: Crystal structure of a motavizumab epitope-scaffold bound to mota...

ID or keywords:

Entry

Database: PDB / ID: 3qwo

Title

Crystal structure of a motavizumab epitope-scaffold bound to motavizumab Fab

Components

motavizumab epitope scaffold
motavizumab heavy chain
motavizumab light chain

Keywords

IMMUNE SYSTEM / Immune complex

Function / homology

Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha

Function and homology information

Biological species

Mus musculus (house mouse)

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

McLellan, J.S. / Kwong, P.D.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Design and characterization of epitope-scaffold immunogens that present the motavizumab epitope from respiratory syncytial virus.
Authors: McLellan, J.S. / Correia, B.E. / Chen, M. / Yang, Y. / Graham, B.S. / Schief, W.R. / Kwong, P.D.

History

Deposition	Feb 28, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 10, 2011	Group: Database references
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3qwo.cif.gz	547.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3qwo.ent.gz	458.6 KB	Display	PDB format
PDBx/mmJSON format	3qwo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3qwo_validation.pdf.gz	486.5 KB	Display	wwPDB validaton report
Full document	3qwo_full_validation.pdf.gz	496.7 KB	Display
Data in XML	3qwo_validation.xml.gz	40.6 KB	Display
Data in CIF	3qwo_validation.cif.gz	58.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qw/3qwo ftp://data.pdbj.org/pub/pdb/validation_reports/qw/3qwo	HTTPS FTP

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Related structure data

Related structure data	1lp1S 3ixtS S: Starting model for refinement
Similar structure data	6s3d-3 3kr3-d 6was-2 4dtg-d 6s3d-2 4n9g-4 6s3d-1 5od6-d 5kn5-2 6i9i-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 - 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: motavizumab light chain

H: motavizumab heavy chain

B: motavizumab light chain

A: motavizumab heavy chain

C: motavizumab epitope scaffold

P: motavizumab epitope scaffold

hetero molecules

108 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: motavizumab light chain

H: motavizumab heavy chain

P: motavizumab epitope scaffold

hetero molecules

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

2

B: motavizumab light chain

A: motavizumab heavy chain

C: motavizumab epitope scaffold

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.762, 74.425, 86.398
Angle α, β, γ (deg.)	90.00, 101.75, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules CP

#3: Protein	motavizumab epitope scaffold Mass: 6254.640 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: homo sapiens (human)

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Antibody , 2 types, 4 molecules LBHA

#1: Antibody	motavizumab light chain Mass: 23150.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: humanized-mouse antibody / Production host: homo sapiens (human)
#2: Antibody	motavizumab heavy chain Mass: 24284.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: humanized-mouse antibody / Production host: homo sapiens (human)

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Non-polymers , 3 types, 515 molecules

#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.22 Å³/Da / Density % sol: 44.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20.5% (w/v) PEG 4000, 0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl pH 8.5, 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2010
Radiation	Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. all: 73584 / Num. obs: 73143 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / % possible all: 92

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Processing

Software

Name	Version	Classification
SERGUI		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.4_486)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 3IXT, 1LP1

3ixt

1lp1

Resolution: 1.9→36.836 Å / SU ML: 0.26 / σ(F): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2306	3589	5.13 %	random
R_work	0.1875	-	-	-
all	0.1897	73697	-	-
obs	0.1897	69917	94.87 %	-

Solvent computation

Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.051 Å² / k_sol: 0.401 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.6225 Å²	0 Å²	3.4157 Å²
2-	-	4.0244 Å²	-0 Å²
3-	-	-	-0.4018 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→36.836 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7362	0	27	509	7898

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7559
X-RAY DIFFRACTION	f_angle_d	1.034	10270
X-RAY DIFFRACTION	f_dihedral_angle_d	11.586	2711
X-RAY DIFFRACTION	f_chiral_restr	0.067	1170
X-RAY DIFFRACTION	f_plane_restr	0.005	1310

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 (%)
1.9-1.9293	0.332	102	0.2624	1932	X-RAY DIFFRACTION	73
1.9293-1.9558	0.2559	122	0.2286	2187	X-RAY DIFFRACTION	82
1.9558-1.9837	0.2307	122	0.2177	2274	X-RAY DIFFRACTION	86
1.9837-2.0133	0.2501	130	0.2206	2472	X-RAY DIFFRACTION	90
2.0133-2.0448	0.2754	131	0.2116	2422	X-RAY DIFFRACTION	91
2.0448-2.0783	0.2698	137	0.2019	2460	X-RAY DIFFRACTION	92
2.0783-2.1141	0.2456	146	0.1991	2489	X-RAY DIFFRACTION	93
2.1141-2.1526	0.2283	158	0.1856	2490	X-RAY DIFFRACTION	94
2.1526-2.194	0.2522	134	0.1799	2526	X-RAY DIFFRACTION	95
2.194-2.2387	0.204	130	0.1852	2540	X-RAY DIFFRACTION	95
2.2387-2.2874	0.2415	130	0.1813	2595	X-RAY DIFFRACTION	96
2.2874-2.3406	0.2649	147	0.1925	2560	X-RAY DIFFRACTION	96
2.3406-2.3991	0.2518	143	0.1991	2603	X-RAY DIFFRACTION	97
2.3991-2.464	0.2433	148	0.1919	2600	X-RAY DIFFRACTION	97
2.464-2.5365	0.2646	140	0.1943	2662	X-RAY DIFFRACTION	98
2.5365-2.6183	0.2239	148	0.1983	2610	X-RAY DIFFRACTION	98
2.6183-2.7119	0.2714	138	0.1946	2640	X-RAY DIFFRACTION	98
2.7119-2.8204	0.2324	129	0.1947	2681	X-RAY DIFFRACTION	99
2.8204-2.9487	0.266	147	0.1961	2654	X-RAY DIFFRACTION	99
2.9487-3.1041	0.248	124	0.1981	2707	X-RAY DIFFRACTION	99
3.1041-3.2985	0.2595	140	0.1904	2678	X-RAY DIFFRACTION	100
3.2985-3.553	0.2248	145	0.1835	2699	X-RAY DIFFRACTION	100
3.553-3.9102	0.211	139	0.1758	2703	X-RAY DIFFRACTION	100
3.9102-4.4751	0.175	153	0.1518	2699	X-RAY DIFFRACTION	100
4.4751-5.635	0.2114	158	0.1645	2718	X-RAY DIFFRACTION	100
5.635-36.8433	0.2256	148	0.2101	2727	X-RAY DIFFRACTION	98

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	1.4565	-1.3467	-0.3025	2.1237	0.1704	0.5809	-0.0938	0.0548	-0.0934	-0.0098	0.142	-0.363	0.2279	0.0174	-0.0458	0.2417	-0.0004	0.0312	0.1778	-0.059	0.2689	-4.7182	-21.8439	23.8324
2	2.678	-0.1923	-0.1903	0.9164	0.4828	0.8672	-0.2539	-1.2742	-0.3788	0.0273	-0.0118	-0.2574	-0.0133	0.1433	0.2153	0.1183	0.0555	-0.0726	0.6887	-0.0414	0.6333	16.5395	-11.351	52.3211
3	2.0569	-1.0441	-0.106	1.1132	0.8532	1.6472	-0.0298	0.0308	-0.0726	0.0868	0.2269	-0.0479	0.3282	0.2064	-0.1614	0.2402	0.0448	-0.0385	0.1877	-0.0223	0.1579	5.0541	-20.7995	-18.4438
4	0.6554	-0.4769	0.1788	0.725	0.2373	0.9933	-0.0388	0.134	-0.146	0.0299	-0.0481	0.066	0.0166	0.4026	0.0339	0.1734	-0.0002	-0.0323	0.4962	-0.1313	0.3375	24.8725	-10.6275	10.6421
5	1.3884	0.5487	-0.2804	0.4396	0.3909	2.0859	0.0175	0.101	0.0666	0.0669	0.1112	-0.0153	-0.1738	-0.1701	-0.1262	0.1797	0.0148	0.0182	0.1564	0.0413	0.1409	-18.4848	-5.9223	31.4524
6	1.6331	-0.3966	-1.1771	1.8711	-0.3669	2.4407	0.3963	-0.2326	0.5995	-0.0943	-0.0221	-0.8213	-0.2344	0.5933	-0.3574	0.1132	-0.0795	0.0831	0.1627	-0.1581	0.4875	9.4399	0.8142	44.568
7	1.0463	0.1977	0.367	0.3516	0.627	2.1452	0.1	-0.0482	0.1507	0.0483	0.0139	0.0101	0.0306	-0.1894	-0.1157	0.16	0.0047	0.0192	0.1685	0.0295	0.1391	-10.0022	-5.9206	-10.8137
8	0.79	-0.424	1.1715	2.9462	-0.6059	2.8004	0.1065	0.436	0.3805	0.013	-0.2582	-0.6548	-0.4241	0.774	0.1975	0.2346	-0.1304	-0.0101	0.4198	0.0428	0.471	17.6212	1.8687	3.5202
9	0.4533	0.0733	-0.4057	0.4224	0.03	1.4169	-0.1223	0.9242	0.0658	-0.0737	0.0988	0.0768	0.0453	-0.6718	-0.0151	0.1786	-0.0544	-0.0041	0.7496	0.0587	0.2217	-29.23	-10.9037	7.2717
10	0.4895	-0.3527	0.1642	1.163	0.2807	2.1168	0.0615	0.3092	-0.0709	-0.0833	-0.0999	0.1899	-0.0658	-0.6418	0.004	0.1685	0.0268	-0.0277	0.3946	0.0243	0.2165	-19.8428	-11.4522	-35.2561

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain L and resid 1:109
2	X-RAY DIFFRACTION	2	chain L and resid 110:212
3	X-RAY DIFFRACTION	3	chain B and resid 1:109
4	X-RAY DIFFRACTION	4	chain B and resid 110:212
5	X-RAY DIFFRACTION	5	chain H and resid 1:114
6	X-RAY DIFFRACTION	6	chain H and resid 115:213
7	X-RAY DIFFRACTION	7	chain A and resid 1:114
8	X-RAY DIFFRACTION	8	chain A and resid 115:213
9	X-RAY DIFFRACTION	9	chain P
10	X-RAY DIFFRACTION	10	chain C

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