PDB-6fxn: Crystal structure of human BAFF in complex with Fab fragment of a...

ID or keywords:

Entry

Database: PDB / ID: 6fxn

Title

Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody belimumab

Components

Tumor necrosis factor ligand superfamily member 13B
belimumab heavy chain
belimumab light chain

Keywords

IMMUNE SYSTEM / Immunology / B cell / cytokine / BAFF / antibody / Proteros

Function / homology

Function and homology information

positive regulation of germinal center formation / B cell costimulation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / germinal center formation / tumor necrosis factor receptor binding / skin development / B cell proliferation / B cell homeostasis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Lammens, A. / Maskos, K. / Willen, L. / Jiang, X. / Schneider, P.

Citation

Journal: Nat Commun / Year: 2018
Title: A loop region of BAFF controls B cell survival and regulates recognition by different inhibitors.
Authors: Vigolo, M. / Chambers, M.G. / Willen, L. / Chevalley, D. / Maskos, K. / Lammens, A. / Tardivel, A. / Das, D. / Kowalczyk-Quintas, C. / Schuepbach-Mallepell, S. / Smulski, C.R. / Eslami, M. / ...

History

Deposition	Mar 9, 2018	Deposition site: PDBE / Processing site: PDBE
Supersession	Apr 4, 2018	ID: 6ERX
Revision 1.0	Apr 4, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6fxn.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb6fxn.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	6fxn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6fxn_validation.pdf.gz	518.7 KB	Display	wwPDB validaton report
Full document	6fxn_full_validation.pdf.gz	524 KB	Display
Data in XML	6fxn_validation.xml.gz	108.2 KB	Display
Data in CIF	6fxn_validation.cif.gz	152.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fx/6fxn ftp://data.pdbj.org/pub/pdb/validation_reports/fx/6fxn	HTTPS FTP

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Related structure data

Related structure data	1kd7S 7fabS S: Starting model for refinement
Similar structure data	3nt2-2 3ntr-2 3nt5-2 3nt4-2 4aln-d 5cjq-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 - 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

A: Tumor necrosis factor ligand superfamily member 13B

B: Tumor necrosis factor ligand superfamily member 13B

C: Tumor necrosis factor ligand superfamily member 13B

D: belimumab heavy chain

E: belimumab light chain

F: belimumab heavy chain

G: belimumab light chain

H: belimumab heavy chain

I: belimumab light chain

J: Tumor necrosis factor ligand superfamily member 13B

K: Tumor necrosis factor ligand superfamily member 13B

L: Tumor necrosis factor ligand superfamily member 13B

M: belimumab heavy chain

N: belimumab light chain

O: belimumab heavy chain

P: belimumab light chain

Q: belimumab heavy chain

R: belimumab light chain

389 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tumor necrosis factor ligand superfamily member 13B

B: Tumor necrosis factor ligand superfamily member 13B

C: Tumor necrosis factor ligand superfamily member 13B

D: belimumab heavy chain

E: belimumab light chain

F: belimumab heavy chain

G: belimumab light chain

H: belimumab heavy chain

I: belimumab light chain

defined by author&software
Evidence: homology
195 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

J: Tumor necrosis factor ligand superfamily member 13B

K: Tumor necrosis factor ligand superfamily member 13B

L: Tumor necrosis factor ligand superfamily member 13B

M: belimumab heavy chain

N: belimumab light chain

O: belimumab heavy chain

P: belimumab light chain

Q: belimumab heavy chain

R: belimumab light chain

defined by author&software
195 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	135.687, 135.499, 138.180
Angle α, β, γ (deg.)	90.00, 91.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Tumor necrosis factor ligand superfamily member 13B / B lymphocyte stimulator / BLyS / B-cell-activating factor / BAFF / Dendritic cell-derived TNF-like ...B lymphocyte stimulator / BLyS / B-cell-activating factor / BAFF / Dendritic cell-derived TNF-like molecule / TNF- and APOL-related leukocyte expressed ligand 1 / TALL-1 Mass: 18394.908 Da / Num. of mol.: 6 / Mutation: H218A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: TNFSF13B, BAFF, BLYS, TALL1, TNFSF20, ZTNF4, UNQ401/PRO738 Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y275
#2: Antibody	belimumab heavy chain Mass: 23704.645 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody	belimumab light chain Mass: 22764.932 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 270 / 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: 3.26 Å³/Da / Density % sol: 62.29 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 9% (w/v) PEG4000, 0.1 M MgCl2, 0.1 M HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.9→138.11 Å / Num. obs: 109365 / % possible obs: 98.7 % / Redundancy: 3.36 % / Net I/σ(I): 11.24
Reflection shell	Resolution: 2.9→3.15 Å / Mean I/σ(I) obs: 3.05 / Num. unique obs: 23126 / % possible all: 95.4

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Processing

Software

Name	Classification
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1KD7 , 7FAB

1kd7

7fab

Resolution: 2.9→138.11 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.907 / SU B: 31.652 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 1.124 / ESU R Free: 0.328 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23128	654	0.6 %	RANDOM
R_work	0.19082	-	-	-
obs	0.19106	108711	99.01 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 59.251 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.89 Å²	0 Å²	-1.56 Å²
2-	-	0.29 Å²	0 Å²
3-	-	-	-1.08 Å²

Refinement step

Cycle: 1 / Resolution: 2.9→138.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25879	0	0	270	26149

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	25944
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	23679
X-RAY DIFFRACTION	r_angle_refined_deg	1.524	1.948	35416
X-RAY DIFFRACTION	r_angle_other_deg	1.197	3	54474
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.616	5	3402
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.688	24.684	980
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.846	15	3851
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.333	15	87
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	4063
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	29817
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	5746
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.222	3.904	13668
X-RAY DIFFRACTION	r_mcbond_other	2.222	3.904	13667
X-RAY DIFFRACTION	r_mcangle_it	3.571	6.582	17050
X-RAY DIFFRACTION	r_mcangle_other	3.571	6.582	17051
X-RAY DIFFRACTION	r_scbond_it	3.125	4.17	12276
X-RAY DIFFRACTION	r_scbond_other	3.125	4.17	12277
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.689	6.903	18367
X-RAY DIFFRACTION	r_long_range_B_refined	6.105	34.152	25075
X-RAY DIFFRACTION	r_long_range_B_other	6.104	34.15	25070
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.903→2.978 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	34	-
R_work	0.333	7410	-
obs	-	-	91.2 %

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	3.1552	-2.0008	-0.6585	4.7333	0.8792	3.4542	-0.0309	0.0778	-0.2636	0.0676	-0.0645	0.1232	0.3489	-0.2119	0.0954	0.0872	-0.0543	-0.0625	0.0351	0.0357	0.1163	10.033	108.312	17.173
2	2.4586	-1.1542	-0.2845	2.9261	1.3933	4.6579	0.0822	0.3539	0.0555	-0.4577	-0.0335	-0.0731	-0.1621	0.0821	-0.0487	0.0999	-0.005	-0.0407	0.0869	0.0334	0.1794	17.116	126.361	4.256
3	5.0213	-0.6495	-1.8999	2.6641	1.0263	3.5972	0.0032	-0.1666	-0.0605	0.0862	0.0896	-0.4355	-0.0657	0.2643	-0.0928	0.072	0.0021	-0.1066	0.0203	-0.017	0.2028	28.96	120.455	23.511
4	4.2387	-0.1116	-4.1775	2.4528	-2.5572	7.4298	-0.1322	-0.2313	-0.0997	0.3515	0.4186	0.5631	-0.1697	-0.6154	-0.2865	0.1923	0.002	0.0102	0.6701	-0.0012	0.443	-6.517	109.724	47.198
5	3.8261	0.667	0.7732	2.2669	-0.5611	3.1006	-0.1122	-0.0425	1.022	0.4231	-0.0776	0.3213	-0.4362	-0.1222	0.1899	0.679	0.108	0.1851	0.2652	0.0587	0.929	-6.239	107.665	79.593
6	5.0477	-1.8835	2.0258	3.5814	-2.1504	5.3103	-0.2615	-1.0162	-0.6094	0.2168	0.1509	-0.0192	0.4118	-0.0202	0.1107	0.2127	0.0049	0.0334	0.5117	0.1705	0.309	12.069	96.807	49.324
7	8.7956	-1.5481	-1.9352	2.581	0.0835	5.6888	0.4118	-0.2078	0.3365	0.463	-0.2071	0.3346	-0.3202	-0.4029	-0.2048	0.4361	-0.1172	0.0802	0.1011	0.0305	0.4415	-2.855	91.677	84.45
8	5.6694	-3.6891	2.8016	6.3067	-1.7951	2.0698	-0.1064	-0.4526	0.195	0.117	0.0676	0.0781	-0.1037	-0.1619	0.0387	0.034	0.0158	-0.0426	0.0819	-0.0244	0.1583	-12.642	143.057	2.739
9	7.1538	3.5347	-1.0295	7.422	0.3391	2.1776	0.1109	-0.5082	-0.1444	1.3711	0.0949	-0.3181	0.5238	0.1737	-0.2058	0.4598	0.0935	-0.1257	0.1856	-0.0282	0.1887	-42.497	142.023	4.001
10	6.315	0.3589	2.5987	2.1373	1.1609	5.1456	0.2393	0.1447	-0.4961	-0.2809	-0.1019	-0.2217	0.195	0.1238	-0.1374	0.2002	0.0788	-0.0619	0.0423	0.0045	0.1999	-13.886	124.005	-8.069
11	5.6898	-2.9782	-1.3468	8.1789	2.8281	3.8524	0.0001	0.0973	0.1085	0.0857	0.0421	0.2969	-0.1083	-0.1641	-0.0421	0.0984	-0.06	-0.0815	0.0775	0.0672	0.1487	-49.991	137.52	-10.69
12	2.4306	2.7661	2.1112	4.8147	3.7152	6.4176	0.1003	-0.2124	0.1703	0.2059	-0.1549	0.2598	-0.0343	-0.2597	0.0547	0.1683	0.0577	-0.0588	0.071	0.0064	0.1318	29.975	150.943	38.648
13	2.1544	-1.1088	-1.6177	4.3683	-1.4484	8.3764	-0.4703	0.2678	-0.3493	0.3928	-0.106	0.5815	1.0177	-1.6955	0.5764	0.3848	-0.3322	0.1812	0.5571	-0.2637	0.4819	31.11	181.848	37.549
14	3.762	1.9018	-1.1907	6.262	0.6026	2.89	-0.0328	0.1994	-0.1017	-0.4521	0.2361	-0.3637	-0.0458	0.2675	-0.2034	0.1725	0.0186	-0.0539	0.1149	-0.0646	0.135	41.841	151.167	20.173
15	3.411	-0.3038	-2.4496	4.7915	3.6028	8.6207	-0.2606	-0.2019	0.1044	0.2746	-0.0633	0.1322	0.1872	0.258	0.3238	0.1727	-0.0597	-0.0916	0.1144	0.0342	0.168	46.678	187.374	32.875
16	2.0854	-1.3355	0.8008	3.6194	-0.5903	3.4119	-0.0565	0.0343	0.2289	-0.0322	0.0324	-0.0512	-0.3778	0.0468	0.024	0.1001	-0.0268	-0.0638	0.024	0.0235	0.1008	54.657	166.783	84.992
17	2.7146	-1.2258	0.7418	2.918	-1.6305	4.551	0.0975	0.2752	-0.0161	-0.2417	-0.1008	0.0676	0.249	0.0138	0.0034	0.0624	0.0244	-0.0799	0.0371	-0.0366	0.1492	49.05	148.076	71.987
18	3.7404	0.0529	0.8683	2.8758	-0.9919	2.6095	-0.0591	-0.0577	0.107	0.1076	0.2142	0.5545	-0.1307	-0.5075	-0.155	0.1144	0.039	0.0119	0.1093	0.0536	0.1697	35.897	153.972	90.42
19	5.3876	1.8583	4.0947	1.9719	3.2039	5.9106	0.0988	-0.0666	-0.2025	0.2669	0.046	-0.194	0.4293	0.2949	-0.1448	0.1021	0.0312	-0.0505	0.2143	0.0573	0.2113	69.652	167.181	115.58
20	6.9041	0.0702	-2.2216	2.3888	-0.0998	3.7016	-0.121	0.2219	-1.1698	0.1419	-0.1593	-0.025	0.5655	0.2102	0.2802	0.2884	0.0853	-0.0634	0.0957	-0.1039	0.49	67.806	167.677	147.178
21	1.9401	-1.6591	-0.3519	5.0186	2.8961	7.0772	-0.1142	-0.2088	0.2152	0.0213	-0.1671	0.1139	-0.4575	-0.3049	0.2812	0.1116	-0.0129	-0.1181	0.248	-0.0295	0.1753	50.907	178.417	116.103
22	7.2402	-1.3168	1.9515	2.3599	0.2083	5.6037	0.0811	-0.1996	0.0679	0.1927	-0.0706	-0.1422	0.1566	0.1925	-0.0106	0.0771	-0.0037	-0.0064	0.0266	0.0056	0.1858	63.514	183.307	152.464
23	4.0154	3.1478	-1.7948	5.8451	-3.4573	5.2751	0.2641	-0.5258	-0.2927	0.4625	-0.2098	-0.084	0.1743	-0.1509	-0.0542	0.3785	-0.0281	-0.1049	0.2124	0.0157	0.1946	35.319	124.078	106.666
24	1.1811	-0.9482	0.0413	2.9304	2.1498	6.3914	-0.0008	-0.3425	-0.0109	-0.0206	0.2253	-0.5201	-0.3408	1.1149	-0.2245	0.5204	-0.3587	-0.0563	0.7513	-0.0176	0.6491	34.735	92.297	106.587
25	4.6003	1.6827	0.7394	6.6589	0.3023	2.7031	0.0501	0.1876	0.0434	-0.2035	0.0793	0.3001	0.1354	-0.545	-0.1293	0.2023	-0.0258	-0.0858	0.2959	0.1284	0.1763	23.674	122.779	88.058
26	3.4416	-0.2207	0.8576	4.5673	-1.9353	5.8153	-0.0108	-0.6972	-0.1673	0.3237	-0.1137	-0.1249	0.0474	-0.006	0.1246	0.4578	-0.3217	-0.016	0.4739	-0.0288	0.3588	18.96	86.928	102.695
27	5.7791	-3.8437	-2.9483	5.7101	1.033	2.0873	-0.1436	-0.4438	-0.1815	0.1425	0.1474	0.0553	0.082	0.2935	-0.0037	0.1337	0.0013	-0.134	0.0435	0.0175	0.1805	79.132	132.379	72.316
28	5.5246	3.5709	0.4465	6.9833	-0.2882	2.1032	0.508	-0.4867	0.1102	1.1579	-0.2375	0.4289	-0.2669	0.1239	-0.2704	0.4761	0.0331	0.0656	0.2263	-0.0286	0.3428	109.484	133.458	73.227
29	7.0389	0.6155	-1.9261	3.136	-1.061	3.7637	0.2483	0.3707	0.3357	-0.2653	-0.1801	-0.1511	-0.2224	0.0298	-0.0682	0.2254	0.1019	-0.0147	0.0694	0.0211	0.1723	80.363	150.9	60.564
30	5.0203	-2.389	0.5782	6.9419	-2.5176	3.7033	0.1246	0.0823	-0.0356	-0.1969	-0.034	-0.1696	0.0724	0.1467	-0.0907	0.2375	0.0122	-0.0212	0.0963	-0.1128	0.2953	116.467	137.068	58.127

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 500
2	X-RAY DIFFRACTION	2	B	1 - 500
3	X-RAY DIFFRACTION	3	C	1 - 500
4	X-RAY DIFFRACTION	4	D	1 - 123
5	X-RAY DIFFRACTION	5	D	124 - 300
6	X-RAY DIFFRACTION	6	E	1 - 109
7	X-RAY DIFFRACTION	7	E	110 - 300
8	X-RAY DIFFRACTION	8	F	1 - 123
9	X-RAY DIFFRACTION	9	F	124 - 300
10	X-RAY DIFFRACTION	10	G	1 - 109
11	X-RAY DIFFRACTION	11	G	110 - 300
12	X-RAY DIFFRACTION	12	H	1 - 123
13	X-RAY DIFFRACTION	13	H	124 - 300
14	X-RAY DIFFRACTION	14	I	1 - 109
15	X-RAY DIFFRACTION	15	I	110 - 300
16	X-RAY DIFFRACTION	16	J	1 - 500
17	X-RAY DIFFRACTION	17	K	1 - 500
18	X-RAY DIFFRACTION	18	L	1 - 500
19	X-RAY DIFFRACTION	19	M	1 - 123
20	X-RAY DIFFRACTION	20	M	124 - 300
21	X-RAY DIFFRACTION	21	N	1 - 109
22	X-RAY DIFFRACTION	22	N	110 - 300
23	X-RAY DIFFRACTION	23	O	1 - 123
24	X-RAY DIFFRACTION	24	O	124 - 300
25	X-RAY DIFFRACTION	25	P	1 - 109
26	X-RAY DIFFRACTION	26	P	110 - 300
27	X-RAY DIFFRACTION	27	Q	1 - 123
28	X-RAY DIFFRACTION	28	Q	124 - 300
29	X-RAY DIFFRACTION	29	R	1 - 109
30	X-RAY DIFFRACTION	30	R	110 - 300

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