PDB-3o41: Crystal Structure of 101F Fab Bound to 15-mer Peptide Epitope

ID or keywords:

Entry

Database: PDB / ID: 3o41

Title

Crystal Structure of 101F Fab Bound to 15-mer Peptide Epitope

Components

Fusion glycoprotein F1
Mouse monoclonal antibody 101F Fab heavy chain
Mouse monoclonal antibody 101F Fab light chain

Keywords

IMMUNE SYSTEM/VIRAL PROTEIN / Immunoglobulin / IMMUNE SYSTEM-VIRAL PROTEIN complex

Function / homology

Function and homology information

symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Human respiratory syncytial virus A

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

McLellan, J.S. / Chen, M. / Chang, J.S. / Yang, Y. / Kim, A. / Graham, B.S. / Kwong, P.D.

Citation

Journal: J.Virol. / Year: 2010
Title: Structure of a Major Antigenic Site on the Respiratory Syncytial Virus Fusion Glycoprotein in Complex with Neutralizing Antibody 101F.
Authors: McLellan, J.S. / Chen, M. / Chang, J.S. / Yang, Y. / Kim, A. / Graham, B.S. / Kwong, P.D.

History

Deposition	Jul 26, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 13, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Jan 24, 2018	Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.4	Sep 6, 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
Revision 1.5	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3o41.cif.gz	364.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3o41.ent.gz	296.1 KB	Display	PDB format
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Validation report

Summary document	3o41_validation.pdf.gz	476 KB	Display	wwPDB validaton report
Full document	3o41_full_validation.pdf.gz	484.1 KB	Display
Data in XML	3o41_validation.xml.gz	41.4 KB	Display
Data in CIF	3o41_validation.cif.gz	60 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o4/3o41 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o41	HTTPS FTP

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Related structure data

Related structure data	3o45C 1dqdS 1iqwS 2j88S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3t77-d 3o45-1 5f89-1 2or9-2 3ikc-2 4hs6-2 1clz-2 5mp3-1 2dtm-d 3hns-d 3o45-2 3mly-2 6fy0-2 2r23-d 5ik3-2 4xmk-2 6dca-3 2omb-2 3ggw-2 3ls4-d 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

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#170 - Feb 2014 Broadly Neutralizing Antibodies similarity (3) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (2)

Deposited unit

L: Mouse monoclonal antibody 101F Fab light chain

H: Mouse monoclonal antibody 101F Fab heavy chain

A: Mouse monoclonal antibody 101F Fab heavy chain

B: Mouse monoclonal antibody 101F Fab light chain

P: Fusion glycoprotein F1

C: Fusion glycoprotein F1

hetero molecules

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

1

L: Mouse monoclonal antibody 101F Fab light chain

H: Mouse monoclonal antibody 101F Fab heavy chain

P: Fusion glycoprotein F1

hetero molecules

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

2

A: Mouse monoclonal antibody 101F Fab heavy chain

B: Mouse monoclonal antibody 101F Fab light chain

C: Fusion glycoprotein F1

hetero molecules

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

Unit cell

Length a, b, c (Å)	79.899, 92.985, 141.221
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Mouse monoclonal antibody 101F Fab light chain Mass: 24064.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody	Mouse monoclonal antibody 101F Fab heavy chain Mass: 23704.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide	Fusion glycoprotein F1 / Protein F Mass: 1650.880 Da / Num. of mol.: 2 / Fragment: Residues 422-436 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Human respiratory syncytial virus A / References: UniProt: P03420
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H₂O
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: 2.65 Å³/Da / Density % sol: 53.65 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8266 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2009
Radiation	Monochromator: Si 220. Rosenbaum-Rock double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8266 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. all: 73963 / Num. obs: 73963 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 1.95→2.02 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.479 / Mean I/σ(I) obs: 2 / % possible all: 77.4

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Processing

Software

Name	Version	Classification
SERGUI		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.5_2)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DQD,1IQW,2J88

1dqd

1iqw

2j88

Resolution: 1.95→33.079 Å / SU ML: 0.22 / σ(F): 0.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.217	3560	5.09 %	random
R_work	0.1775	-	-	-
obs	0.1795	69877	90.37 %	-
all	-	69877	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.951 Å² / k_sol: 0.35 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.5213 Å²	-0 Å²	0 Å²
2-	-	-2.2788 Å²	0 Å²
3-	-	-	5.8001 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→33.079 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6850	0	70	732	7652

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7089
X-RAY DIFFRACTION	f_angle_d	0.941	9663
X-RAY DIFFRACTION	f_dihedral_angle_d	15.66	2463
X-RAY DIFFRACTION	f_chiral_restr	0.062	1082
X-RAY DIFFRACTION	f_plane_restr	0.003	1219

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 (%)
1.95-1.9766	0.2511	80	0.2321	1760	X-RAY DIFFRACTION	60
1.9766-2.0048	0.3088	125	0.2345	1925	X-RAY DIFFRACTION	67
2.0048-2.0347	0.2834	127	0.221	2108	X-RAY DIFFRACTION	73
2.0347-2.0665	0.2712	117	0.2111	2312	X-RAY DIFFRACTION	80
2.0665-2.1004	0.2359	124	0.1979	2419	X-RAY DIFFRACTION	83
2.1004-2.1366	0.2412	133	0.1936	2543	X-RAY DIFFRACTION	88
2.1366-2.1754	0.251	155	0.1961	2579	X-RAY DIFFRACTION	89
2.1754-2.2173	0.2415	171	0.1863	2579	X-RAY DIFFRACTION	89
2.2173-2.2625	0.2314	129	0.1779	2648	X-RAY DIFFRACTION	91
2.2625-2.3117	0.2625	133	0.1785	2677	X-RAY DIFFRACTION	91
2.3117-2.3655	0.2159	145	0.1844	2634	X-RAY DIFFRACTION	91
2.3655-2.4246	0.2828	142	0.1901	2737	X-RAY DIFFRACTION	93
2.4246-2.4901	0.2335	137	0.1999	2698	X-RAY DIFFRACTION	93
2.4901-2.5634	0.2226	124	0.1976	2811	X-RAY DIFFRACTION	95
2.5634-2.6461	0.2513	137	0.1981	2786	X-RAY DIFFRACTION	95
2.6461-2.7406	0.2346	153	0.1884	2802	X-RAY DIFFRACTION	96
2.7406-2.8503	0.2124	157	0.1883	2821	X-RAY DIFFRACTION	96
2.8503-2.9799	0.2427	165	0.1858	2807	X-RAY DIFFRACTION	97
2.9799-3.1369	0.2157	160	0.1878	2860	X-RAY DIFFRACTION	98
3.1369-3.3333	0.2253	140	0.1745	2915	X-RAY DIFFRACTION	98
3.3333-3.5904	0.2162	150	0.165	2919	X-RAY DIFFRACTION	99
3.5904-3.9512	0.1732	163	0.1491	2915	X-RAY DIFFRACTION	99
3.9512-4.5217	0.1563	155	0.1362	2957	X-RAY DIFFRACTION	99
4.5217-5.6921	0.1663	176	0.1331	2972	X-RAY DIFFRACTION	99
5.6921-33.0835	0.2201	162	0.1855	3133	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	0.684	0.2742	0.7964	0.1548	-0.1703	0.3642	0.0349	-0.0751	-0.2725	-0.0519	0.0106	0.15	0.0661	-0.0987	-0.0537	0.0782	-0.0226	0.0022	0.0827	0.0122	0.2674	-27.0169	-9.6672	-5.8879
2	0.9947	0.0966	-0.0229	1.1691	-0.009	1.1068	-0.052	0.1561	-0.1036	-0.2951	0.0548	-0.0933	0.0324	-0.0325	0.0043	0.1786	-0.0672	0.0156	0.1952	-0.0683	0.1328	-53.379	0.6943	-30.8542
3	0.814	-0.5146	0.1004	0.8323	-0.2561	0.3863	0.0516	-0.0187	-0.3082	-0.0039	0.0147	0.0175	0.024	0.001	-0.0515	0.1197	-0.002	0.0045	0.1096	0.0011	0.217	-65.3784	-11.6867	9.1388
4	1.7709	-0.0324	-0.1926	1.4687	-0.4147	0.624	0.0056	-0.661	-0.1363	0.4094	-0.0903	-0.1798	-0.1519	0.0427	0.075	0.2531	-0.0239	-0.0467	0.3994	0.0613	0.143	-39.0066	-0.7907	33.5662
5	1.01	-0.427	0.2444	1.5267	-0.6021	0.5458	-0.033	0.0794	-0.0392	-0.0758	0.0292	-0.0477	0.0083	0.0378	0.0024	0.0969	-0.0097	0.0178	0.104	0.0015	0.1102	-20.6267	11.9384	-8.3236
6	1.1555	0.3722	-0.3314	0.725	-0.5219	0.8633	-0.011	0.193	-0.0001	0.0081	0.0334	0.0694	-0.0288	-0.1976	-0.006	0.1691	-0.0359	0.0219	0.2228	-0.0395	0.1535	-51.2547	11.4707	-19.9727
7	0.6369	0.1711	0.2228	0.8093	0.5317	0.9412	-0.0618	-0.0174	-0.0214	0.1045	0.0969	0.0305	-0.0367	0.0695	-0.0336	0.1199	-0.0026	0.0254	0.103	0.0158	0.0919	-69.9025	10.4397	9.4316
8	1.2205	0.1903	0.0884	0.7694	-0.1471	0.5286	0.0098	-0.1791	0.0156	0.051	-0.0837	-0.1682	-0.091	0.1021	0.0667	0.1739	-0.0158	0.0135	0.2508	-0.0056	0.1561	-39.8284	8.7312	21.072
9	1.1531	-0.0963	0.2181	0.5668	0.0296	0.0987	-0.1791	0.1882	-0.1262	0.0944	0.0508	0.1086	-0.0585	0.0665	0.1074	0.1304	0.0276	0.0131	0.0657	0.0307	0.1805	-11.7633	1.3323	6.3069
10	1.1903	-0.2851	-1.0514	0.1622	0.0943	1.5913	0.0632	-0.1661	-0.3443	0.0851	-0.0958	0.0913	-0.4383	0.0464	0.0686	0.1136	-0.0281	0.0124	0.1083	0.0001	0.169	-80.5953	-0.5699	-2.7399

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain L and resid 1:113
2	X-RAY DIFFRACTION	2	chain L and resid 114:218
3	X-RAY DIFFRACTION	3	chain B and resid 1:113
4	X-RAY DIFFRACTION	4	chain B and resid 114:218
5	X-RAY DIFFRACTION	5	chain H and resid 1:116
6	X-RAY DIFFRACTION	6	chain H and resid 117:218
7	X-RAY DIFFRACTION	7	chain A and resid 1:116
8	X-RAY DIFFRACTION	8	chain A and resid 117:218
9	X-RAY DIFFRACTION	9	chain P
10	X-RAY DIFFRACTION	10	chain C

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