PDB-4gxv: Crystal structure of anti-influenza virus antibody 1F1

ID or keywords:

Entry

Database: PDB / ID: 4gxv

Title

Crystal structure of anti-influenza virus antibody 1F1

Components

Antibody 1F1, heavy chain
Antibody 1F1, light chain

Keywords

IMMUNE SYSTEM / immunoglobulin / immune recognition

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: 1.449 Å

Authors

Ekiert, D.C. / Wilson, I.A.

Citation

Journal: Plos Pathog. / Year: 2012
Title: Influenza Human Monoclonal Antibody 1F1 Interacts with Three Major Antigenic Sites and Residues Mediating Human Receptor Specificity in H1N1 Viruses.
Authors: Tsibane, T. / Ekiert, D.C. / Krause, J.C. / Martinez, O. / Crowe, J.E. / Wilson, I.A. / Basler, C.F.

History

Deposition	Sep 4, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 26, 2012	Group: Database references
Revision 2.0	Dec 25, 2019	Group: Derived calculations / Polymer sequence Category: entity_poly / pdbx_struct_mod_residue / struct_conn Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1	May 26, 2021	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4gxv.cif.gz	366.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4gxv.ent.gz	302.1 KB	Display	PDB format
PDBx/mmJSON format	4gxv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gxv_validation.pdf.gz	456.2 KB	Display	wwPDB validaton report
Full document	4gxv_full_validation.pdf.gz	467.1 KB	Display
Data in XML	4gxv_validation.xml.gz	41.5 KB	Display
Data in CIF	4gxv_validation.cif.gz	60.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gx/4gxv ftp://data.pdbj.org/pub/pdb/validation_reports/gx/4gxv	HTTPS FTP

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Related structure data

Related structure data	4gxuC 4gxxC 1rzfS 2fb4S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ig7-3 5fhb-d 6srv-1 6xli-2 5alb-d 6co3-d 4wht-7 5vzy-d 1igj-1 5ocx-d 4nki-d 4lri-1 4jzo-2 1nd0-3 4h20-d 6c5i-d 4odw-1 4xbe-d 3e8u-d 6qn8-3 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

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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: Antibody 1F1, heavy chain

L: Antibody 1F1, light chain

I: Antibody 1F1, heavy chain

M: Antibody 1F1, light chain

95.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: Antibody 1F1, heavy chain

L: Antibody 1F1, light chain

defined by author&software
47.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: Antibody 1F1, heavy chain

M: Antibody 1F1, light chain

defined by author&software
47.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.789, 99.461, 175.095
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Antibody 1F1, heavy chain Mass: 24914.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody	Antibody 1F1, light chain Mass: 22788.197 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.36 Å³/Da / Density % sol: 47.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG4000, 200 mM sodium phosphate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 70 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.007 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 17, 2009
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.007 Å / Relative weight: 1
Reflection	Resolution: 1.449→50 Å / Num. obs: 160778 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / B_iso Wilson estimate: 22.3 Å² / R_sym value: 0.07 / Net I/σ(I): 10.4
Reflection shell	Resolution: 1.449→1.55 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.4 / R_sym value: 0.58 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2FB4 AND 1RZF

2fb4

1rzf

Resolution: 1.449→36.096 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2072	7896	5.02 %	RANDOM
R_work	0.1807	-	-	-
obs	0.182	157355	97.6 %	-

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.449→36.096 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6618	0	0	740	7358

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	7017
X-RAY DIFFRACTION	f_angle_d	1.324	9611
X-RAY DIFFRACTION	f_dihedral_angle_d	11.935	2521
X-RAY DIFFRACTION	f_chiral_restr	0.075	1086
X-RAY DIFFRACTION	f_plane_restr	0.008	1243

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 (%)
1.449-1.4651	0.3319	229	0.3275	4335	X-RAY DIFFRACTION	86
1.4651-1.4823	0.3924	260	0.3634	4992	X-RAY DIFFRACTION	98
1.4823-1.5004	0.3078	250	0.29	4875	X-RAY DIFFRACTION	98
1.5004-1.5194	0.4073	268	0.3537	4954	X-RAY DIFFRACTION	97
1.5194-1.5393	0.3908	242	0.3763	4910	X-RAY DIFFRACTION	97
1.5393-1.5604	0.2564	258	0.2491	4982	X-RAY DIFFRACTION	98
1.5604-1.5827	0.2725	280	0.2365	4915	X-RAY DIFFRACTION	98
1.5827-1.6064	0.26	229	0.2291	5010	X-RAY DIFFRACTION	98
1.6064-1.6315	0.2496	255	0.2141	4916	X-RAY DIFFRACTION	97
1.6315-1.6582	0.2376	278	0.2086	4887	X-RAY DIFFRACTION	98
1.6582-1.6868	0.2639	266	0.2143	4935	X-RAY DIFFRACTION	97
1.6868-1.7175	0.2564	268	0.2185	4915	X-RAY DIFFRACTION	97
1.7175-1.7505	0.2439	257	0.206	4929	X-RAY DIFFRACTION	98
1.7505-1.7862	0.2289	247	0.2006	4980	X-RAY DIFFRACTION	97
1.7862-1.8251	0.2395	248	0.1964	4954	X-RAY DIFFRACTION	98
1.8251-1.8675	0.2213	270	0.2031	4990	X-RAY DIFFRACTION	98
1.8675-1.9142	0.2439	276	0.2257	4959	X-RAY DIFFRACTION	98
1.9142-1.966	0.2666	258	0.2194	4961	X-RAY DIFFRACTION	98
1.966-2.0238	0.2393	253	0.2017	4958	X-RAY DIFFRACTION	98
2.0238-2.0891	0.2526	268	0.215	4919	X-RAY DIFFRACTION	97
2.0891-2.1638	0.2251	265	0.1843	5037	X-RAY DIFFRACTION	98
2.1638-2.2504	0.1994	303	0.1898	4918	X-RAY DIFFRACTION	97
2.2504-2.3528	0.2132	263	0.1843	5025	X-RAY DIFFRACTION	98
2.3528-2.4768	0.1992	287	0.1776	5083	X-RAY DIFFRACTION	99
2.4768-2.632	0.2135	302	0.1737	5053	X-RAY DIFFRACTION	99
2.632-2.8351	0.2202	274	0.1767	5105	X-RAY DIFFRACTION	100
2.8351-3.1203	0.1804	266	0.1769	5116	X-RAY DIFFRACTION	98
3.1203-3.5715	0.1884	240	0.1655	5171	X-RAY DIFFRACTION	99
3.5715-4.4983	0.16	237	0.1357	5256	X-RAY DIFFRACTION	99
4.4983-36.1076	0.1677	299	0.1536	5419	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	1.9327	0.1315	-0.4745	3.0234	0.6095	2.371	0.1245	0.0111	-0.105	-0.0449	-0.0877	-0.0609	0.0461	0.0798	-0.0422	0.123	-0.0114	-0.0236	0.1636	0.0067	0.1241	57.3214	32.4955	-26.8686
2	0.7461	-0.373	-0.6451	1.9631	1.2222	2.9438	0.0749	-0.0809	0.2178	-0.1216	0.0944	0.3732	-0.2311	-0.1664	-0.0605	0.1923	-0.0214	-0.0165	0.2221	-0.0015	0.1292	36.419	44.0358	2.8447
3	3.1663	0.0179	0.0103	3.3519	0.0888	4.1337	0.0385	-0.2841	-0.0546	0.2069	0.0639	0.3243	0.2354	-0.31	-0.0189	0.1586	-0.0277	-0.0002	0.1863	-0.0042	0.1353	35.065	39.483	8.5884
4	2.5816	-0.1114	-1.3739	4.2435	-2.629	4.0696	-0.0108	0.3429	0.2709	-0.0595	0.1846	0.2719	-0.1311	-0.2169	-0.1593	0.1776	0.0061	-0.0444	0.2533	-0.0014	0.3198	29.5975	28.9121	-28.114
5	3.0575	0.7761	-1.5208	4.2903	-1.0556	2.4089	-0.0209	0.1479	0.0699	-0.3539	0.0722	0.0881	0.0775	0.0175	-0.0524	0.0995	-0.015	-0.0438	0.1244	-0.0239	0.1317	41.5993	29.391	-32.5253
6	3.6707	1.3287	-1.1814	3.9698	0.0085	3.2586	-0.2672	0.2395	-0.0636	-0.3512	0.1876	0.2268	0.1867	-0.1709	0.0905	0.1895	-0.0281	-0.0325	0.2646	-0.0415	0.1787	36.4237	22.1594	-36.1151
7	2.6956	0.5015	-1.0909	1.2228	0.2547	1.6787	0.0317	0.0268	0.028	0.0456	-0.0398	0.2329	-0.0241	-0.0691	-0.0026	0.1278	0.0003	-0.0482	0.1426	-0.007	0.1849	35.9991	29.2	-26.2314
8	7.2201	5.1672	3.3546	9.3432	4.9413	6.0423	-0.1827	-0.0929	0.178	0.3845	0.0873	-0.1067	-0.2897	-0.1785	0.1131	0.3628	0.0744	-0.0604	0.2496	-0.0443	0.2813	29.4339	50.0716	2.1235
9	1.0621	1.0392	0.0411	6.0218	2.2543	3.0101	-0.047	-0.0054	0.0892	-0.1135	-0.1102	0.1512	-0.348	-0.1664	0.167	0.2398	0.0221	-0.0422	0.2201	-0.0139	0.2251	27.4493	41.102	-8.7548
10	9.7483	-2.6232	1.1018	8.1226	-1.2867	8.6665	0.1981	0.8226	0.747	-0.9986	-0.0692	0.0237	-0.7608	-0.4078	-0.1184	0.5655	-0.0247	-0.075	0.3805	0.0879	0.3396	29.3943	52.9564	-13.3287
11	4.1406	0.4094	0.4347	6.7211	2.7658	4.1975	-0.0719	0.023	-0.015	-0.0256	0.0574	-0.3169	-0.1312	-0.0768	-0.01	0.2056	0.0168	-0.0519	0.2079	0.0088	0.089	31.3201	42.8995	-5.9504
12	2.723	-1.1105	-0.6884	0.9008	-0.3749	1.1857	-0.1727	-0.0813	0.4067	-0.4995	-0.278	0.9064	-0.5	-0.4905	0.353	0.37	0.0955	-0.1615	0.3046	-0.0497	0.4032	21.3574	47.5092	-9.5872
13	1.3418	-0.554	-0.3749	0.4644	-0.3568	1.2957	0.2015	0.1468	-1.2073	-0.6926	-0.2557	0.7669	0.4219	-0.0399	-0.8883	0.6468	0.008	-0.452	0.1566	-0.0104	1.0338	-25.9611	75.6656	26.0627
14	2.8147	-1.063	0.5544	1.8567	-1.1623	0.957	0.4231	0.018	-0.7212	-0.3848	-0.1394	0.5912	0.2635	-0.0302	0.0951	0.2415	0.0081	-0.1581	0.17	-0.0105	0.3823	-21.2819	87.318	30.0709
15	0.1645	0.1251	-0.6499	3.9707	0.7863	3.4412	-0.0393	-0.1847	0.3791	-0.2268	-0.1759	-0.3129	-0.4958	0.1981	0.1117	0.2851	-0.0001	-0.0463	0.2351	-0.0443	0.2715	-1.7113	55.8248	16.1165
16	3.2327	-0.2593	-0.008	5.5381	0.5096	3.7443	0.0188	-0.2304	0.0301	0.1809	-0.1603	-0.3257	-0.1787	0.0234	0.1484	0.2536	-0.0409	-0.0334	0.2589	-0.0136	0.2092	-0.4443	50.6028	20.3352
17	2.566	-2.0673	0.4363	2.7284	-0.2778	0.5739	0.3298	0.038	0.0085	-0.2517	-0.2998	-0.0463	0.0099	0.2893	-0.0156	0.1255	0.0036	-0.0175	0.2524	0.0458	0.1264	-1.3019	88.3555	32.673
18	3.8817	-2.9089	0.4494	4.6847	-4.0679	5.6268	-0.2731	0.2113	0.3202	1.0539	0.4442	0.0883	-1.1239	0.3151	-0.1065	0.3767	-0.1209	0.0065	0.4099	0.0042	0.2713	-5.1433	93.5819	44.2328
19	2.0615	-1.1534	0.0753	2.7154	-0.0684	1.793	0.2992	-0.1504	0.0096	-0.1943	-0.2419	-0.0981	-0.0804	0.3383	0.0572	0.1264	-0.004	0.0074	0.2548	0.0451	0.1305	-2.6383	90.0205	33.0158
20	2.4095	-2.4236	0.2029	3.7849	1.888	3.2417	0.3371	-0.1935	-0.6189	-0.0441	0.2814	0.0394	0.7864	0.036	-0.5881	0.315	0.0201	-0.135	0.2777	0.0304	0.2902	9.6819	73.858	35.3287
21	9.103	5.1131	6.3366	7.4407	4.804	4.7423	0.0349	-0.0714	-0.1507	-0.2489	0.0584	-0.3956	-0.0435	-0.374	-0.0965	0.3926	-0.062	0.0381	0.2605	-0.0403	0.3017	4.4712	56.4363	8.6057
22	2.5213	1.2622	2.7634	1.8528	3.1185	5.4504	-0.0602	0.0363	-0.2235	-0.0817	-0.0268	-0.6539	-0.1365	0.1797	-0.0524	0.5121	-0.0987	-0.0895	0.2165	0.0175	0.332	7.8255	67.5894	20.0724
23	3.0175	1.6778	0.5557	3.6623	-0.3144	0.2916	-0.1051	-0.0601	0.1591	-0.2446	-0.0012	-0.123	-0.9811	0.0456	-0.0418	0.6169	-0.0564	-0.023	0.2449	-0.0051	0.3387	4.127	66.8057	15.2479
24	2.0823	0.5369	0.8828	2.585	2.3668	3.7038	-0.3089	0.5686	-0.2185	-0.1958	0.5353	-0.7212	-0.2143	0.3955	-0.0553	0.7668	-0.3244	-0.0174	0.4208	-0.0168	0.4129	12.6122	68.2499	9.4051
25	0.3428	-0.1583	0.9753	2.7878	2.5946	6.1033	0.0086	-0.0586	-0.1746	0.2361	0.4526	-0.6472	-0.5823	0.3956	-0.3853	0.4384	-0.1608	0.0035	0.3206	-0.1176	0.4824	15.3005	67.4053	15.5778

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 2 through 108 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 109 through 148 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 149 through 215 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 2 through 22 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 23 through 48 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 49 through 75 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 76 through 113 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 114 through 129 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 130 through 150 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 151 through 161 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 162 through 187 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 188 through 209 )
13	X-RAY DIFFRACTION	13	chain 'I' and (resid 2 through 21 )
14	X-RAY DIFFRACTION	14	chain 'I' and (resid 22 through 110 )
15	X-RAY DIFFRACTION	15	chain 'I' and (resid 111 through 150 )
16	X-RAY DIFFRACTION	16	chain 'I' and (resid 151 through 215 )
17	X-RAY DIFFRACTION	17	chain 'M' and (resid 1 through 48 )
18	X-RAY DIFFRACTION	18	chain 'M' and (resid 49 through 61 )
19	X-RAY DIFFRACTION	19	chain 'M' and (resid 62 through 101 )
20	X-RAY DIFFRACTION	20	chain 'M' and (resid 102 through 113 )
21	X-RAY DIFFRACTION	21	chain 'M' and (resid 114 through 129 )
22	X-RAY DIFFRACTION	22	chain 'M' and (resid 130 through 150 )
23	X-RAY DIFFRACTION	23	chain 'M' and (resid 151 through 187 )
24	X-RAY DIFFRACTION	24	chain 'M' and (resid 188 through 197 )
25	X-RAY DIFFRACTION	25	chain 'M' and (resid 198 through 209 )

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About Yorodumi

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Yorodumi