7Z7H: P. luminescens TccC3-F-actin complex

Name: PDB 7Z7H: Structure of P. luminescens TccC3-F-actin complex
Published: 2022-06-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Structure of P. luminescens TccC3-F-actin complex. Determined by electron microscopy at 3.8 Å resolution. Released 29 Jun 2022.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Oryctolagus cuniculus, Photorhabdus luminescens
Chains: 6
Atoms: 16,111
Mol. weight: 277.15 kDa
Ligands: ADP, MG, APR, NCA
Released: 29 Jun 2022

Explore 7Z7H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z7H contains 129 α-helices and 111 β-strands across 6 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: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	26
β-strand	16-21	6	26
β-strand	29-32	4	26
β-strand	35-38	4	27
β-strand	53-54	2	27
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	27
β-strand	71-72	2	28
β-strand	75-76	2	28
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	26
α-helix	114-127	14
β-strand	131-136	6	26
α-helix	137-143	7
β-strand	149-155	7	29
β-strand	160-166	7	29
β-strand	169-170	2	29
α-helix	172-174	3
β-strand	176-178	3	29
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	30
β-strand	247-250	4	30
α-helix	253-259	7
α-helix	260-262	3
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-295	9
β-strand	297-300	4	29
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	29
α-helix	338-348	11
α-helix	352-355	4
α-helix	356	1
β-strand	357-358	2	26
α-helix	359-365	7
α-helix	368-372	5

Chain B: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	9
β-strand	16-21	6	9
β-strand	22	1	10
β-strand	24	1	10
β-strand	29-32	4	9
β-strand	35-38	4	11
β-strand	53-54	2	11
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	11
β-strand	71-72	2	12
β-strand	75-76	2	12
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	9
α-helix	113-127	15
β-strand	131-136	6	9
α-helix	137-143	7
β-strand	150-155	6	13
β-strand	160-166	7	13
β-strand	169-170	2	13
α-helix	172-174	3
β-strand	176-178	3	13
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	14
β-strand	247-250	4	14
α-helix	253-262	10
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-283	10
α-helix	289-295	7
β-strand	298-300	3	13
α-helix	302-305	4
α-helix	309-320	12
β-strand	330	1	13
α-helix	335-348	14
α-helix	352-355	4
α-helix	356	1
β-strand	357-358	2	9
α-helix	359-365	7
α-helix	368-372	5

Chain C: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	20
β-strand	16-21	6	20
β-strand	22	1	21
β-strand	24	1	21
β-strand	29-32	4	20
β-strand	35-38	4	22
β-strand	53-54	2	22
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	22
β-strand	71-72	2	23
β-strand	75-76	2	23
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	20
α-helix	114-127	14
β-strand	131-136	6	20
α-helix	137-143	7
β-strand	150-155	6	24
β-strand	160-166	7	24
β-strand	169-170	2	24
α-helix	172-174	3
β-strand	176-178	3	24
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	25
β-strand	247-250	4	25
α-helix	253-256	4
α-helix	259-262	4
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-283	10
α-helix	289-295	7
β-strand	298-300	3	24
α-helix	302-305	4
α-helix	309-320	12
β-strand	330	1	24
α-helix	338-348	11
α-helix	352-355	4
α-helix	356	1
β-strand	357-358	2	20
α-helix	359-365	7
α-helix	368-372	5

Chain D: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	1
β-strand	16-21	6	1
β-strand	22	1	2
β-strand	24	1	2
β-strand	29-32	4	1
β-strand	35-38	4	3
β-strand	53-54	2	3
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	114-125	12
β-strand	131-136	6	1
α-helix	137-145	9
β-strand	150-155	6	5
β-strand	160-166	7	5
β-strand	169-170	2	5
α-helix	172-174	3
β-strand	176-178	3	5
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	253-262	10
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-283	10
α-helix	289-295	7
β-strand	297-300	4	5
α-helix	302-305	4
α-helix	309-320	12
β-strand	330	1	5
α-helix	335-348	14
α-helix	352-355	4
α-helix	356	1
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	368-372	5

Chain E: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	15
β-strand	16-21	6	15
β-strand	29-32	4	15
β-strand	35-38	4	16
β-strand	53-54	2	16
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	16
β-strand	71-72	2	17
β-strand	75-76	2	17
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	15
α-helix	114-127	14
β-strand	131-136	6	15
α-helix	137-143	7
β-strand	149-155	7	18
β-strand	160-166	7	18
β-strand	169-170	2	18
α-helix	172-174	3
β-strand	176-178	3	18
α-helix	182-196	15
α-helix	202-216	15
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	19
β-strand	247-250	4	19
α-helix	253-259	7
α-helix	260-262	3
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	289-295	7
β-strand	298-300	3	18
α-helix	302-305	4
α-helix	309-320	12
β-strand	330	1	18
α-helix	335-348	14
α-helix	352-355	4
α-helix	356	1
β-strand	357-358	2	15
α-helix	359-365	7
α-helix	368-372	5

Chain F: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	107-114	8	7
α-helix	119-125	7
β-strand	130	1	8
α-helix	135-137	3
α-helix	138-147	10
α-helix	159-167	9
α-helix	173-183	11
β-strand	192-195	4	7
β-strand	209-221	13	7
β-strand	226-228	3	7
β-strand	240-243	4	7
α-helix	248-250	3
β-strand	254-258	5	7
β-strand	265-268	4	7
β-strand	272	1	8
α-helix	274-276	3
β-strand	277-280	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B, C, D, E	protein	377	Oryctolagus cuniculus	P68135 (AlphaFold model)
Maltose/maltodextrin-binding periplasmic protein,TccC3	F	protein	578	Photorhabdus luminescens	P0AEX9 (AlphaFold model), Q8GF97 (AlphaFold model)

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

>7Z7H_1 Actin, alpha skeletal muscle (chains A, B, C, D, E)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Sequence of entity 2 (F), FASTA

>7Z7H_2 Maltose/maltodextrin-binding periplasmic protein,TccC3 (chains F)
MGSSHHHHHHSSGLVPRGSHMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEH
PDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRY
NGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWP
LIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNK
GETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEF
LENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAF
WYAVRTAVINAASGRQTVDEALKDAQTNSGSSGSSGSTNLQKKSFTLYRADNRSFEEMQS
KFPEGFKAWTPLDTKMARQFASIFIGQKDTSNLPKETVKNISTWGAKPKLKDLSNYIKYT
KDKSTVWVSTAINTEAGGQSSGAPLHKIDMDLYEFAIDGQKLNPLPEGRTKNMVPSLLLD
TPQIETSSIIALNHGPVNDASISFLTTIPLKNVKPHKR

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5
MG	Magnesium ion	Mg	5
APR	Adenosine-5-diphosphoribose	C15 H23 N5 O14 P2	1
NCA	Nicotinamide	C6 H6 N2 O	1

Primary citation

Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin. Belyy, A., Lindemann, F., Roderer, D. et al. Nat Commun (2022) 13:4202-4202. DOI 10.1038/s41467-022-31836-w · PubMed

Other PDB entries of the same protein (UniProt P68135 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4B1Y 1.29 Å, Structure of the Phactr1 RPEL-3 bound to G-actin
2FXU 1.35 Å, X-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution.
4K41 1.4 Å, Crystal structure of actin in complex with marine macrolide kabiramide C
1QZ5 1.45 Å, Structure of rabbit actin in complex with kabiramide C
1WUA 1.45 Å, The structure of Aplyronine A-actin complex
2Q0U 1.45 Å, Structure of Pectenotoxin-2 and Latrunculin B Bound to Actin
2V52 1.45 Å, Structure of MAL-RPEL2 complexed to G-actin
3MN5 1.5 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
2PBD 1.5 Å, Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP*
5ZZA 1.53 Å, OdinProfilin/Rabbit Actin Complex
1J6Z 1.54 Å, Uncomplexed actin
1QZ6 1.6 Å, Structure of rabbit actin in complex with jaspisamide A

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