7T82: LEUKOCIDIN E/CENTYRIN S26/FAB B438

Crystal Structure of LEUKOCIDIN E/CENTYRIN S26/FAB B438. Determined by X-ray diffraction at 3.5 Å resolution. Released 11 Jan 2023.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Staphylococcaceae, Mus musculus, synthetic construct
Chains: 8
Atoms: 12,610
Mol. weight: 184.74 kDa
Released: 11 Jan 2023

Explore 7T82 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T82 contains 35 α-helices and 154 β-strands across 8 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 B: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	1
β-strand	32-34	3	2
β-strand	39-50	12	2
β-strand	55-66	12	2
β-strand	71-83	13	2
β-strand	87-90	4	3
α-helix	96-98	3
β-strand	99-114	16	3
β-strand	119-125	7	2
β-strand	130	1	3
β-strand	134-142	9	4
β-strand	146-150	5	4
β-strand	161-168	8	4
β-strand	172-179	8	3
β-strand	183-190	8	3
β-strand	192-195	4	5
β-strand	198-201	4	5
β-strand	209	1	6
α-helix	219-222	4
β-strand	223	1	6
α-helix	226-228	3
α-helix	231-234	4
β-strand	236-237	2	2
β-strand	240-248	9	2
β-strand	254-272	19	3
β-strand	278-287	10	3
β-strand	292-299	8	3
β-strand	304-310	7	3

Chain C: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	30	1	15
β-strand	36	1	15
β-strand	38-43	6	14
β-strand	50-54	5	14
β-strand	58-59	2	14
α-helix	60	1
β-strand	67-72	6	13
β-strand	75-80	6	13
α-helix	85-87	3
β-strand	89-95	7	14
α-helix	101	1
β-strand	102-103	2	14
β-strand	107-112	6	14
α-helix	113-115	3
β-strand	116	1	16
β-strand	119-123	5	17
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	17
β-strand	145	1	16
β-strand	150-155	6	18
β-strand	159	1	18
β-strand	164-168	5	17
α-helix	169-172	4
β-strand	178-187	10	17
α-helix	188-192	5
β-strand	196-202	7	18
β-strand	210-215	6	18

Chain D: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	19
β-strand	10-12	3	20
β-strand	17-24	8	19
β-strand	32	1	1
β-strand	34-39	6	20
β-strand	45-51	7	20
β-strand	58-60	3	20
α-helix	62-64	3
β-strand	68-73	6	19
β-strand	78-84	7	19
β-strand	92-100	9	20
β-strand	107-110	4	20
β-strand	114-118	5	20
β-strand	126	1	21
β-strand	129-133	5	22
β-strand	144-154	11	22
β-strand	155	1	21
β-strand	160-163	4	23
α-helix	164-166	3
β-strand	172-174	3	22
α-helix	175-177	3
β-strand	178-179	2	22
β-strand	185-194	10	22
α-helix	195-197	3
β-strand	203-209	7	23
β-strand	214-220	7	23

Chain E: 0 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	24
β-strand	18-23	6	24
β-strand	31-37	7	25
β-strand	46-51	6	25
β-strand	56-59	4	24
β-strand	67-76	10	25
β-strand	79-80	2	25
β-strand	84-89	6	25

Chain F: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	26
β-strand	18-23	6	26
β-strand	31-37	7	27
β-strand	46-51	6	27
β-strand	56-59	4	26
β-strand	67-76	10	27
β-strand	79-80	2	27
α-helix	83	1
β-strand	84-89	6	27

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	33
β-strand	10-12	3	34
β-strand	18-24	7	33
β-strand	32	1	7
β-strand	34-39	6	34
β-strand	45-51	7	34
β-strand	58-60	3	34
α-helix	62-64	3
β-strand	68-73	6	33
β-strand	78-83	6	33
α-helix	88-90	3
β-strand	92-100	9	34
β-strand	107-110	4	34
β-strand	111	1	33
β-strand	114-118	5	34
β-strand	126	1	35
β-strand	129-133	5	36
β-strand	144-154	11	36
β-strand	155	1	35
β-strand	160-163	4	37
α-helix	164-166	3
β-strand	168	1	37
β-strand	172-174	3	36
α-helix	175-177	3
β-strand	178-179	2	36
β-strand	185-194	10	36
α-helix	195-197	3
β-strand	203-209	7	37
α-helix	210-212	3
β-strand	214-220	7	37

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-14	5	29
β-strand	19-25	7	28
β-strand	30	1	30
β-strand	36	1	30
β-strand	38-43	6	29
β-strand	50-54	5	29
β-strand	58-59	2	29
α-helix	60	1
β-strand	67-72	6	28
β-strand	75-80	6	28
β-strand	89-95	7	29
α-helix	101	1
β-strand	102-103	2	29
β-strand	107-112	6	29
α-helix	113	1
α-helix	115	1
β-strand	119-123	5	31
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	31
β-strand	150-155	6	32
β-strand	159-160	2	32
β-strand	164-168	5	31
α-helix	169-172	4
β-strand	178-187	10	31
α-helix	188-192	5
β-strand	196-202	7	32
β-strand	210-215	6	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leukocidin E	A, B	protein	294	Staphylococcaceae	Q2FXB0 (AlphaFold model)
Antibody Fab Light Chain	C, L	protein	219	Mus musculus
Antibody Fab Heavy Chain	D, H	protein	229	Mus musculus
Centyrin S26	E, F	protein	98	synthetic construct

Sequence of entity 1 (A, B), FASTA

>7T82_1 Leukocidin E (chains A, B)
NSAHHHHHHGSNTNIENIGDGAEVIKRTEDVSSKKWGVTQNVQFDFVKDKKYNKDALIVK
MQGFINSRTSFSDVKGSGYELTKRMIWPFQYNIGLTTKDPNVSLINYLPKNKIETTDVGQ
TLGYNIGGNFQSAPSIGGNGSFNYSKTISYTQKSYVSEVDKQNSKSVKWGVKANEFVTPD
GKKSAHDRYLFVQSPNGPTGSAREYFAPDNQLPPLVQSGFNPSFITTLSHEKGSSDTSEF
ELSYGRNLDITYATLFPRTGIYAERKHNAFVNRNFVVRYKVNWKTHEIKVKGHN

Sequence of entity 2 (C, L), FASTA

>7T82_2 Antibody Fab Light Chain (chains C, L)
DVLMTQTPLSLPVSLGDQASISCRSSQTIVYSDGNTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRVSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (D, H), FASTA

>7T82_3 Antibody Fab Heavy Chain (chains D, H)
QVQLQQSGAELMNPGASVKISCKSTGYKFSSYWIEWVKQRPGHGLEWMGEILPGSGSTNH
NEKFKGKAIFTADASSNTAYMELSSLTSEDSAVYYCARTISTATDWFAYWGQGTLVTVSA
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH

Sequence of entity 4 (E, F), FASTA

>7T82_4 Centyrin S26 (chains E, F)
MLPAPKNLVVSRVTEDSARLSWTAPDAAFDSFHIEYAEPWVWGEAIVLTVPGSERSYDLT
GLKPGTEYVVFIGGVKGGHNSTPLSAIFTTGGHHHHHH

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 Q2FXB0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P8X 1.4 Å, Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a doubly…
7P8T 1.46 Å, Crystal Structure of leukotoxin LukE from Staphylococcus aureus at 1.5 Angstrom resolution
7P93 1.55 Å, Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a…
7P8U 1.6 Å, Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with p-cresyl…
7P8S 1.9 Å, Crystal Structure of leukotoxin LukE from Staphylococcus aureus at 1.9 Angstrom resolution
3ROH 3.2 Å, Crystal Structure of Leukotoxin (LukE) from Staphylococcus aureus subsp. aureus COL.

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