3V56: PDB entry 3V56

Re-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold - reveals an additonal copy of the peptide. Determined by X-ray diffraction at 3.0 Å resolution. Released 28 Mar 2012.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 13
Atoms: 7,446
Mol. weight: 147.83 kDa
Released: 28 Mar 2012

Explore 3V56 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V56 contains 11 α-helices and 104 β-strands across 13 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and D: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	1
α-helix	156-157	2
β-strand	158	1	2
β-strand	164-165	2	2
α-helix	166-167	2
β-strand	168-174	7	1
β-strand	178-181	4	2
β-strand	184-187	4	2
β-strand	191-201	11	1
β-strand	207-208	2	3
β-strand	211-215	5	2
β-strand	226-231	6	2
β-strand	234-235	2	3
β-strand	243-253	11	1
β-strand	258-263	6	2
β-strand	270-271	2	1
β-strand	278-283	6	1

Chain B: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	4
β-strand	158-160	3	5
β-strand	163-165	3	5
α-helix	166-167	2
β-strand	168-174	7	4
β-strand	178-181	4	5
β-strand	184-187	4	5
β-strand	191-201	11	4
β-strand	207-208	2	6
β-strand	211-215	5	5
β-strand	226-231	6	5
β-strand	234-235	2	6
β-strand	243-253	11	4
β-strand	258-263	6	5
β-strand	270-271	2	4
β-strand	278-283	6	4

Chains C, E and F: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	7
α-helix	156-157	2
β-strand	158-160	3	8
β-strand	163-165	3	8
α-helix	166-167	2
β-strand	168-174	7	7
β-strand	178-181	4	8
β-strand	184-187	4	8
β-strand	191-201	11	7
β-strand	207-208	2	9
β-strand	211-215	5	8
β-strand	226-231	6	8
β-strand	234-235	2	9
β-strand	243-253	11	7
β-strand	258-263	6	8
β-strand	270-271	2	7
β-strand	278-283	6	7

Chains G, H, I, J, K, L and Z: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	19
β-strand	31-33	3	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor ligand superfamily member 13B	A, B, C, D, E, F	protein	208	Homo sapiens	Q9Y275 (AlphaFold model)
BR3 derived peptive	G, H, I, J, K, L, Z	protein	14		Q96RJ3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>3V56_1 Tumor necrosis factor ligand superfamily member 13B (chains A, B, C, D, E, F)
GSHMELQGHHAEKLPAGAGAPKAGLEEAPAVTAGLKIFEPPAPGEGNSSQNSRNKRAVQG
PEETVTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYG
QVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGD
ELQLAIPRENAQISLDGDVTFFGALKLL

Sequence of entity 2 (G, H, I, J, K, L, Z), FASTA

>3V56_2 BR3 derived peptive (chains G, H, I, J, K, L, Z)
XCHWDLLVRHWVCX

Primary citation

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. Smart, O.S., Womack, T.O., Flensburg, C. et al. Acta Crystallogr D Biol Crystallogr (2012) 68:368-380. DOI 10.1107/S0907444911056058 · PubMed

Other PDB entries of the same protein (UniProt Q9Y275 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KXG 2.0 Å, The 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator.
5Y9J 2.05 Å, BAFF in complex with belimumab
4ZCH 2.43 Å, Single-chain human APRIL-BAFF-BAFF Heterotrimer
1OQE 2.5 Å, Crystal structure of sTALL-1 with BAFF-R
8ZUJ 2.58 Å, Pentagonal cluster of BAFF-BAFFR ectodomain complex
1OQD 2.6 Å, Crystal structure of sTALL-1 and BCMA
1KD7 2.8 Å, Crystal structure of an extracellular domain fragment of human BAFF
6FXN 2.9 Å, Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody…
1JH5 3.0 Å, Crystal Structure of sTALL-1 of TNF family ligand
1OSG 3.0 Å, Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold
4V46 3.3 Å, Crystal structure of the BAFF-BAFF-R complex

Browse structure collections

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