7T87: Leukocidin ab/centyrin S17/FAB 214F complex

Crystal structure of leukocidin ab/centyrin S17/FAB 214F complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 11 Jan 2023.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Staphylococcaceae, Mus musculus, synthetic construct
Chains: 5
Atoms: 8,641
Mol. weight: 133.39 kDa
Released: 11 Jan 2023

Explore 7T87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T87 contains 27 α-helices and 104 β-strands across 5 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.

Chain A: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	19-27	9	1
β-strand	34-35	2	2
β-strand	36-44	9	1
β-strand	50-57	8	1
β-strand	60-62	3	2
β-strand	66-67	2	3
β-strand	75-90	16	3
β-strand	97-103	7	1
β-strand	112-119	8	4
β-strand	123-126	4	5
β-strand	128	1	6
β-strand	131	1	6
α-helix	135-137	3
β-strand	142-149	8	4
β-strand	153-157	5	3
β-strand	165-172	8	3
β-strand	175-177	3	7
β-strand	180-182	3	7
β-strand	195-196	2	3
β-strand	200	1	8
α-helix	209-212	4
β-strand	213	1	8
α-helix	214-215	2
α-helix	216-218	3
α-helix	221-224	4
β-strand	226-227	2	2
β-strand	231-238	8	1
β-strand	244-265	22	3
β-strand	268-291	24	3
β-strand	296-302	7	3

Chain B: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	43-55	13	5
β-strand	60-70	11	5
β-strand	77-88	12	5
β-strand	92-95	4	9
β-strand	103-118	16	9
β-strand	123-129	7	5
β-strand	133-134	2	9
β-strand	138-145	8	10
α-helix	147-149	3
β-strand	151-153	3	10
β-strand	167-172	6	10
β-strand	176-180	5	9
β-strand	188-195	8	9
β-strand	197-200	4	11
β-strand	203-206	4	11
β-strand	214	1	12
α-helix	225-228	4
β-strand	229	1	12
α-helix	232-234	3
α-helix	237-240	4
β-strand	242-243	2	5
β-strand	247-253	7	5
β-strand	259-275	17	9
β-strand	285-302	18	9
β-strand	307-317	11	9

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	24
β-strand	6	1	25
β-strand	11	1	26
β-strand	18-21	4	26
β-strand	23	1	25
β-strand	31-38	8	27
α-helix	42-44	3
β-strand	46-51	6	27
β-strand	56-59	4	26
β-strand	67-75	9	27
β-strand	80	1	27
β-strand	81	1	24
β-strand	84-89	6	27

Chain H: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
α-helix	7	1
β-strand	10-12	3	15
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-52	8	15
β-strand	57-60	4	15
α-helix	62-64	3
β-strand	65	1	19
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-100	9	15
β-strand	103	1	20
β-strand	106	1	20
β-strand	110-114	5	15
β-strand	118-122	5	15
α-helix	126-127	2
β-strand	128	1	21
α-helix	129-130	2
β-strand	131-135	5	22
β-strand	146-156	11	22
β-strand	157	1	21
β-strand	162-165	4	23
α-helix	166-168	3
β-strand	174-176	3	22
α-helix	177-179	3
β-strand	180-181	2	22
β-strand	187-196	10	22
α-helix	197-199	3
β-strand	205-211	7	23
α-helix	212-214	3
β-strand	216-222	7	23

Chain L: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	34-39	6	14
β-strand	46-50	5	14
β-strand	54-55	2	14
α-helix	56	1
β-strand	63-68	6	13
β-strand	71-76	6	13
α-helix	81-83	3
β-strand	85-91	7	14
α-helix	97	1
β-strand	98	1	15
β-strand	99	1	14
β-strand	103-107	5	14
β-strand	112	1	16
β-strand	115-119	5	17
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	17
β-strand	141	1	16
β-strand	146-151	6	18
β-strand	155	1	18
β-strand	160-164	5	17
α-helix	165-168	4
β-strand	174-183	10	17
α-helix	184-188	5
β-strand	192-198	7	18
β-strand	206-211	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leukocidin B	A	protein	309	Staphylococcaceae	Q2FWP0 (AlphaFold model)
Leukocidin A	B	protein	332	Staphylococcaceae	Q2FWN9 (AlphaFold model)
Antibody Fab B214 Light Chain	L	protein	213	Mus musculus
Antibody Fab B214 Heavy Chain	H	protein	233	Mus musculus
Centyrin S17	C	protein	98	synthetic construct

Sequence of entity 1 (A), FASTA

>7T87_1 Leukocidin B (chains A)
KINSEIKQVSEKNLDGDTKMYTRTATTSDSQKNITQSLQFNFLTEPNYDKETVFIKAKGT
IGSGLRILDPNGYWNSTLRWPGSYSVSIQNVDDNNNTNVTDFAPKNQDESREVKYTYGYK
TGGDFSINRGGLTGNITKESNYSETISYQQPSYRTLLDQSTSHKGVGWKVEAHLINNMGH
DHTRQLTNDSDNRTKSEIFSLTRNGNLWAKDNFTPKDKMPVTVSEGFNPEFLAVMSHDKK
DKGKSQFVVHYKRSMDEFKIDWNRHGFWGYWSGENHVDKKEEKLSALYEVDWKTHNVKFV
KVLNDNEKK

Sequence of entity 2 (B), FASTA

>7T87_2 Leukocidin A (chains B)
NSAHHHHHHGSHKDSQDQNKKEHVDKSQQKDKRNVTNKDKNSTAPDDIGKNGKITKRTET
VYDEKTNILQNLQFDFIDDPTYDKNVLLVKKQGSIHSNLKFESHKEEKNSNWLKYPSEYH
VDFQVKRNRKTEILDQLPKNKISTAKVDSTFSYSSGGKFDSTKGIGRTSSNSYSKTISYN
QQNYDTIASGKNNNWHVHWSVIANDLKYGGEVKNRNDELLFYRNTRIATVENPELSFASK
YRYPALVRSGFNPEFLTYLSNEKSNEKTQFEVTYTRNQDILKNRPGIHYAPPILEKNKDG
QRLIVTYEVDWKNKTVKVVDKYSDDNKPYKEG

Sequence of entity 3 (L), FASTA

>7T87_3 Antibody Fab B214 Light Chain (chains L)
DIVMTQSPTTMAASPGERITITCSAHSNLISNYLHWYQQKPGFSPKLLIYRTSNLASGVP
ARFSGSGSGTSYSLTIGTMEAEDVATYFCQQGSSIPFTFGSGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 4 (H), FASTA

>7T87_4 Antibody Fab B214 Heavy Chain (chains H)
EVQLQQSGAELVKPGASVKISCKASGYAFSSSWMNWLKQRPGKGLEWIGRIYPGDGDTNY
NGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCARYGYDYDGEYYYAMDYWGQGTSV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH

Sequence of entity 5 (C), FASTA

>7T87_5 Centyrin S17 (chains C)
MLPAPKNLVVSRVTEDSARLSWTAPDAAFDSFWITYEEKFYRGEAIVLTVPGSERSYDLT
GLKPGTEYKVWIVGVKGGQGSWPLSAIFTTGGHHHHHH

Primary citation

Multivalent human antibody-centyrin fusion protein to prevent and treat Staphylococcus aureus infections. Buckley, P.T., Chan, R., Fernandez, J. et al. Cell Host Microbe (2023) 31:751-765.e11. DOI 10.1016/j.chom.2023.04.004 · PubMed

Other PDB entries of the same protein (UniProt Q2FWP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RHV 2.29 Å, Crystal structure of mouse CD11b I-domain (CD11b-I) in complex with Staphylococcus…
6RHW 2.75 Å, Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus…
5K59 2.84 Å, Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising…

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