PDB-4fnl: Crystal structure of broadly neutralizing antibody C05

ID or keywords:

Entry

Database: PDB / ID: 4fnl

Title

Crystal structure of broadly neutralizing antibody C05

Components

Antibody C05, Heavy Chain
Antibody C05, 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: 2.297 Å

Authors

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

Citation

Journal: Nature / Year: 2012
Title: Cross-neutralization of influenza A viruses mediated by a single antibody loop.
Authors: Damian C Ekiert / Arun K Kashyap / John Steel / Adam Rubrum / Gira Bhabha / Reza Khayat / Jeong Hyun Lee / Michael A Dillon / Ryann E O'Neil / Aleksandr M Faynboym / Michael Horowitz / ...
Abstract: Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that ...

History

Deposition	Jun 19, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 3, 2012	Group: Database references
Revision 1.2	Oct 10, 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 19, 2021	Group: Database references / Derived calculations / Source and taxonomy Category: entity_src_gen / pdbx_database_related / struct_site Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_related.content_type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fnl.cif.gz	365.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4fnl.ent.gz	301.2 KB	Display	PDB format
PDBx/mmJSON format	4fnl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fnl_validation.pdf.gz	465.7 KB	Display	wwPDB validaton report
Full document	4fnl_full_validation.pdf.gz	472.9 KB	Display
Data in XML	4fnl_validation.xml.gz	38.4 KB	Display
Data in CIF	4fnl_validation.cif.gz	55.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fn/4fnl ftp://data.pdbj.org/pub/pdb/validation_reports/fn/4fnl	HTTPS FTP

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Related structure data

Related structure data	2138C 2139C 2140C 4fnkC 4fp8C 4fqrC 1aqkS 1vgeS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5vkk-2 3l1o-d 1q9l-1 1gpo-2 6dzr-d 5mv3-5 4nrz-2 3okm-d 6e8v-7 6l8t-3 2r23-d 4c83-2 2hkf-d 5ur8-d 2gsi-1 6axl-2 3u46-2 4m61-1 5ik3-2 4xce-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 C05, Heavy Chain

L: Antibody C05, Light Chain

I: Antibody C05, Heavy Chain

M: Antibody C05, Light Chain

hetero molecules

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

1

H: Antibody C05, Heavy Chain

L: Antibody C05, Light Chain

hetero molecules

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

2

I: Antibody C05, Heavy Chain

M: Antibody C05, Light Chain

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

Unit cell

Length a, b, c (Å)	160.130, 160.130, 135.520
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Antibody	Antibody C05, Heavy Chain Mass: 26303.262 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody	Antibody C05, Light Chain Mass: 23367.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 519 / 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: 4.37 Å³/Da / Density % sol: 71.87 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 1.8 M ammonium sulfate, 100 mM sodium acetate, pH 5.4, 50 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2011
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 2.297→50 Å / Num. obs: 78741 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / R_sym value: 0.19 / Net I/σ(I): 20.4
Reflection shell	Resolution: 2.297→2.4 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.2 / R_sym value: 0.8 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
Blu-Ice	Epics	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.2_869)	refinement
HKL-2000		data reduction
XPREP		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AQK AND 1VGE

1aqk

1vge

Resolution: 2.297→49.219 Å / SU ML: 0.98 / σ(F): 1.34 / Phase error: 25.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2401	3937	5.03 %	RANDOM
R_work	0.2124	-	-	-
obs	0.2138	78237	99.38 %	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.597 Å² / k_sol: 0.331 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.9419 Å²	-0 Å²	0 Å²
2-	-	-0.9419 Å²	0 Å²
3-	-	-	1.8838 Å²

Refinement step

Cycle: LAST / Resolution: 2.297→49.219 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6753	0	8	519	7280

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7001
X-RAY DIFFRACTION	f_angle_d	0.993	9509
X-RAY DIFFRACTION	f_dihedral_angle_d	14.379	2532
X-RAY DIFFRACTION	f_chiral_restr	0.072	1062
X-RAY DIFFRACTION	f_plane_restr	0.005	1235

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 (%)
2.297-2.325	0.5569	127	0.5399	2413	X-RAY DIFFRACTION	92
2.325-2.3545	0.4215	156	0.4883	2585	X-RAY DIFFRACTION	98
2.3545-2.3854	0.4301	137	0.4229	2584	X-RAY DIFFRACTION	98
2.3854-2.4181	0.4391	129	0.3842	2614	X-RAY DIFFRACTION	99
2.4181-2.4527	0.4377	141	0.3828	2619	X-RAY DIFFRACTION	100
2.4527-2.4893	0.4051	142	0.3231	2642	X-RAY DIFFRACTION	100
2.4893-2.5282	0.3317	123	0.3104	2630	X-RAY DIFFRACTION	100
2.5282-2.5696	0.3413	119	0.2979	2661	X-RAY DIFFRACTION	100
2.5696-2.6139	0.327	149	0.2901	2643	X-RAY DIFFRACTION	100
2.6139-2.6614	0.337	142	0.2712	2610	X-RAY DIFFRACTION	99
2.6614-2.7126	0.334	144	0.2854	2584	X-RAY DIFFRACTION	98
2.7126-2.768	0.2883	126	0.2242	2662	X-RAY DIFFRACTION	100
2.768-2.8282	0.2478	142	0.2094	2632	X-RAY DIFFRACTION	100
2.8282-2.894	0.2549	125	0.2092	2663	X-RAY DIFFRACTION	100
2.894-2.9663	0.2364	118	0.2012	2689	X-RAY DIFFRACTION	100
2.9663-3.0465	0.2469	126	0.2054	2642	X-RAY DIFFRACTION	100
3.0465-3.1361	0.2473	158	0.2017	2666	X-RAY DIFFRACTION	100
3.1361-3.2373	0.2261	135	0.2042	2650	X-RAY DIFFRACTION	100
3.2373-3.353	0.2619	149	0.2154	2658	X-RAY DIFFRACTION	100
3.353-3.4872	0.25	157	0.2274	2654	X-RAY DIFFRACTION	100
3.4872-3.6459	0.2207	153	0.1987	2661	X-RAY DIFFRACTION	100
3.6459-3.8381	0.2335	134	0.1926	2677	X-RAY DIFFRACTION	100
3.8381-4.0784	0.2117	161	0.1809	2653	X-RAY DIFFRACTION	100
4.0784-4.3931	0.1653	140	0.1452	2698	X-RAY DIFFRACTION	100
4.3931-4.8349	0.1505	141	0.1274	2729	X-RAY DIFFRACTION	100
4.8349-5.5337	0.1594	160	0.1493	2717	X-RAY DIFFRACTION	100
5.5337-6.9687	0.2154	157	0.1911	2750	X-RAY DIFFRACTION	100
6.9687-49.2304	0.2077	146	0.2029	2914	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	0.9712	-0.053	0.0992	2.5093	0.2381	0.9578	-0.0136	-0.0104	0.0425	0.0039	0.0165	0.153	-0.0024	-0.2835	0.0347	0.0825	-0.0504	-0.0126	0.1265	0.0126	0.1462	42.3697	-23.3843	30.2828
2	2.9602	0.2714	0.2427	2.2062	0.3706	3.0311	0.1545	-0.2832	-0.3241	0.2431	0.0458	-0.4189	0.1598	0.3388	-0.0536	0.1873	-0.031	-0.0769	0.1928	-0.026	0.2605	65.3028	-42.2968	45.0962
3	4.3618	0.0848	2.6327	4.0578	0.6811	6.2223	0.1075	-0.6461	-0.0153	0.3349	-0.058	-0.1331	0.0165	0.0334	0.0141	0.2018	-0.0463	-0.035	0.2275	-0.0293	0.1769	61.3557	-42.1182	47.1932
4	2.4916	-0.8621	1.2123	3.1096	0.3483	1.8895	0.1339	-0.8657	-0.4211	0.5916	-0.1764	-0.3884	0.4252	0.1588	-0.0188	0.3946	-0.159	-0.0452	0.5328	0.1661	0.3534	59.3653	-49.1948	50.7578
5	5.4107	-1.1681	3.4946	1.3135	-1.1862	4.8281	-0.0422	0.2911	0.0835	-0.1572	-0.071	-0.1263	-0.2129	0.3932	0.0599	0.1416	-0.0274	0.0379	0.1373	0.0102	0.1575	67.5591	-11.3016	29.6127
6	2.842	-0.8476	0.5215	1.9203	-1.0882	4.0435	0.0567	0.1721	0.1659	-0.3753	-0.0963	-0.2237	0.0195	-0.0963	0.0239	0.1496	-0.0258	0.0138	0.0842	0.0129	0.1159	55.786	-8.1566	26.7483
7	3.2134	0.0554	1.9583	6.24	-0.7196	3.9492	0.0322	-0.1697	-0.001	0.3111	-0.2672	-0.0894	-0.0609	0.112	0.1988	0.1249	-0.0196	0.0563	0.1961	0.0107	0.1551	55.9655	-10.6992	39.2374
8	2.5128	-0.2667	1.5027	0.8933	-0.1157	2.2711	0.0292	-0.0485	-0.0406	0.019	0.0969	0.0615	-0.1052	0.0838	-0.099	0.1878	-0.0497	0.0063	0.1575	0.0337	0.1604	60.154	-10.7561	31.3082
9	4.9811	-5.6246	5.6153	6.3403	-6.3261	6.4314	0.2176	0.1861	-0.2035	0.1423	-0.0527	0.0906	0.1167	0.2144	0.0154	0.1446	-0.0187	0.0016	0.2152	-0.0315	0.1719	76.2706	-21.6526	41.3122
10	2.6466	2.4234	1.7247	3.0292	3.2104	4.4002	0.3891	-0.1269	-0.5813	0.3109	-0.1045	0.0933	1.0015	-0.0816	-0.2018	0.3666	0.021	-0.1791	0.1781	0.0232	0.6858	71.6199	-51.782	45.559
11	1.4575	-0.2841	-0.1572	1.0246	0.1613	1.4603	0.0618	0.2449	-0.6912	-0.2828	0.2356	-0.0474	-0.0057	0.0626	-0.1521	0.2357	0.0292	-0.0467	0.252	-0.114	0.3448	78.7085	-39.1735	40.6184
12	4.7646	-3.4018	-1.1743	4.9558	1.2279	0.9292	0.0659	0.1219	-0.6815	-0.17	0.2733	-0.6623	0.325	0.5753	-0.2812	0.3379	0.0627	-0.0396	0.3762	-0.1468	0.5563	80.1533	-46.0308	34.6189
13	7.3849	-0.4874	-0.5148	2.5894	2.9922	4.3355	-0.0324	0.0611	-0.4267	-0.0432	0.0221	0.5686	-0.3465	-0.4125	0.0246	0.1895	0.0114	0.0074	0.2285	-0.0346	0.2473	70.9996	-26.0065	44.3442
14	0.4599	0.075	0.3629	1.1577	0.4987	0.549	0.227	0.0465	-0.9996	-0.0376	0.055	-0.3816	0.297	0.2756	-0.0257	0.2388	0.1177	-0.1206	0.1783	-0.0808	0.6327	81.6511	-48.4563	42.1477
15	1.831	-0.6851	-0.0717	2.2546	-0.0566	1.3858	0.0776	-0.1259	0.0101	0.159	-0.0045	0.2611	0.0867	-0.5763	0.0327	0.1555	-0.0427	0.0617	0.4274	0.0619	0.2445	41.5592	-22.085	66.86
16	3.6277	-0.129	-0.1042	2.9326	1.0279	3.9296	-0.1016	-0.2446	0.51	0.0706	0.188	0.3773	-0.4324	-0.2332	-0.081	0.2803	0.0816	0.097	0.2942	-0.0113	0.4299	35.5751	7.0481	52.3531
17	5.7318	0.4148	-0.3524	5.1922	-1.1792	6.2145	0.0425	0.0058	0.0565	-0.4713	0.1254	0.5925	-0.024	-0.2098	-0.1536	0.2903	0.1226	0.0302	0.357	-0.0087	0.4514	31.1837	3.9992	48.4774
18	1.1885	1.0341	-0.6015	6.0451	-3.9147	4.9511	0.0342	-0.2877	0.111	0.4163	0.0156	0.0081	-0.4833	0.2438	-0.0622	0.2164	-0.0318	0.0304	0.3095	-0.0476	0.212	64.2003	-5.7478	67.4862
19	1.0426	-0.4417	1.3379	3.6556	-2.3348	4.8507	-0.053	-0.2519	0.0143	0.0692	0.1911	-0.0742	-0.0273	-0.418	-0.117	0.1674	-0.0162	0.0381	0.3292	0.0362	0.1914	61.3709	-17.6148	70.3741
20	6.321	-1.2015	-0.7356	4.5213	-1.7214	4.3046	-0.0794	0.0022	0.1088	-0.2396	0.0088	0.1254	-0.075	-0.1772	0.0559	0.1597	-0.0513	0.0015	0.1678	-0.0302	0.097	59.2011	-16.237	57.8708
21	0.4503	0.1977	-0.1899	3.2796	-1.7677	2.9906	0.0399	-0.0499	0.0662	0.074	0.1421	0.1344	-0.1643	-0.12	-0.1468	0.1725	-0.0195	0.0061	0.3374	0.0102	0.1806	61.1579	-12.5255	65.8138
22	0.7449	-1.9938	2.3748	5.329	-6.3485	7.5737	0.0781	-0.0704	0.115	0.2457	-0.0277	0.2685	-0.2107	-0.065	0.0354	0.2459	0.0047	0.0488	0.2009	-0.0308	0.169	59.1822	6.8232	55.8078
23	4.6725	-0.479	-4.5753	1.5766	0.3771	5.6741	-0.0121	0.4134	0.313	0.0133	0.0233	0.8674	-0.2764	-0.9672	-0.0811	0.3981	0.1994	0.1086	0.4829	-0.0109	0.8515	30.4221	17.1087	52.27
24	2.2165	-1.5981	0.1119	2.6397	0.6842	0.5279	0.0018	-0.5265	0.2184	0.3241	0.1439	0.3873	-0.1663	-0.1596	0.299	0.4524	0.1317	0.3365	0.2654	-0.1833	0.2491	45.0276	17.1983	56.8854
25	2.4505	-1.8336	-0.5435	8.1541	1.431	2.0995	-0.1269	-0.4092	0.7727	0.4798	0.235	0.8663	-0.8643	-0.1191	-0.0754	0.7566	0.1039	0.1289	0.4662	-0.1207	0.6061	39.7902	21.5335	63.0795
26	2.9977	-1.0114	-0.51	0.7241	0.7583	1.7687	0.0406	-0.1711	0.408	0.3105	0.0944	0.566	-0.3281	-0.2065	-0.0164	0.4768	0.1177	0.2035	0.31	-0.0226	0.6393	41.5396	19.6957	54.9723

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resseq 2:119)
2	X-RAY DIFFRACTION	2	chain 'H' and (resseq 120:175)
3	X-RAY DIFFRACTION	3	chain 'H' and (resseq 176:203)
4	X-RAY DIFFRACTION	4	chain 'H' and (resseq 204:214)
5	X-RAY DIFFRACTION	5	chain 'L' and (resseq 1:25)
6	X-RAY DIFFRACTION	6	chain 'L' and (resseq 26:38)
7	X-RAY DIFFRACTION	7	chain 'L' and (resseq 39:61)
8	X-RAY DIFFRACTION	8	chain 'L' and (resseq 62:101)
9	X-RAY DIFFRACTION	9	chain 'L' and (resseq 102:113)
10	X-RAY DIFFRACTION	10	chain 'L' and (resseq 114:128)
11	X-RAY DIFFRACTION	11	chain 'L' and (resseq 129:150)
12	X-RAY DIFFRACTION	12	chain 'L' and (resseq 151:163)
13	X-RAY DIFFRACTION	13	chain 'L' and (resseq 164:174)
14	X-RAY DIFFRACTION	14	chain 'L' and (resseq 175:213)
15	X-RAY DIFFRACTION	15	chain 'I' and (resseq 2:119)
16	X-RAY DIFFRACTION	16	chain 'I' and (resseq 120:175)
17	X-RAY DIFFRACTION	17	chain 'I' and (resseq 176:213)
18	X-RAY DIFFRACTION	18	chain 'M' and (resseq 1:25)
19	X-RAY DIFFRACTION	19	chain 'M' and (resseq 26:38)
20	X-RAY DIFFRACTION	20	chain 'M' and (resseq 39:61)
21	X-RAY DIFFRACTION	21	chain 'M' and (resseq 62:101)
22	X-RAY DIFFRACTION	22	chain 'M' and (resseq 102:113)
23	X-RAY DIFFRACTION	23	chain 'M' and (resseq 114:128)
24	X-RAY DIFFRACTION	24	chain 'M' and (resseq 129:150)
25	X-RAY DIFFRACTION	25	chain 'M' and (resseq 151:163)
26	X-RAY DIFFRACTION	26	chain 'M' and (resseq 164:213)

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