7NXV: Complex of DNase I/G-actin/PPP1R15A_582-621

Crystal structure of the complex of DNase I/G-actin/PPP1R15A_582-621. Determined by X-ray diffraction at 2.55 Å resolution. Released 29 Sept 2021.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Oryctolagus cuniculus, Bos taurus, Homo sapiens
Chains: 6
Atoms: 10,650
Mol. weight: 153.54 kDa
Ligands: CA, ATP
Released: 29 Sept 2021

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

Secondary structure: helices and β-sheets

7NXV contains 79 α-helices and 78 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: 25 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	7	1
β-strand	8-12	5	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	42-44	3	4
α-helix	48-50	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	5
β-strand	75-76	2	5
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-144	8
β-strand	150-155	6	6
β-strand	160-166	7	6
β-strand	169-170	2	6
α-helix	172-174	3
β-strand	176-178	3	6
α-helix	182-195	14
α-helix	203-206	4
α-helix	208-216	9
α-helix	223-232	10
β-strand	238-241	4	7
β-strand	247-250	4	7
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	6
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	6
α-helix	338-346	9
α-helix	351-354	4
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-373	5

Chain B: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	4
α-helix	13-17	5
α-helix	19-29	11
β-strand	34-40	7	4
α-helix	46-55	10
β-strand	64-67	4	4
α-helix	68-70	3
β-strand	71	1	8
β-strand	78	1	8
β-strand	79-84	6	4
β-strand	90-96	7	9
α-helix	112-113	2
β-strand	114-119	6	9
β-strand	127-132	6	9
α-helix	137-139	3
α-helix	140-158	19
β-strand	163-168	6	9
α-helix	178-183	6
α-helix	185-188	4
β-strand	192-194	3	9
β-strand	203	1	10
β-strand	212-217	6	9
α-helix	219-224	6
β-strand	225	1	11
β-strand	231-232	2	4
α-helix	235-238	4
α-helix	243-249	7
β-strand	252	1	10
β-strand	255-258	4	4
β-strand	259	1	11

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	583-602	20
α-helix	604-606	3
α-helix	609-618	10

Chain D: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	12
β-strand	16-21	6	12
β-strand	29-32	4	12
β-strand	35-38	4	13
β-strand	42-44	3	14
α-helix	48-50	3
β-strand	53-54	2	13
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	13
β-strand	71-72	2	15
β-strand	75-76	2	15
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	12
α-helix	113-125	13
β-strand	131-136	6	12
α-helix	137-144	8
β-strand	150-155	6	16
β-strand	160-166	7	16
β-strand	169-170	2	16
α-helix	172-174	3
β-strand	176-178	3	16
α-helix	182-194	13
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	17
β-strand	247-250	4	17
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	16
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	16
α-helix	338-346	9
α-helix	350-354	5
β-strand	357-358	2	12
α-helix	359-365	7
α-helix	369-373	5

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	584-603	20
α-helix	604-607	4
α-helix	609-619	11

Chain F: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	14
α-helix	13-17	5
α-helix	19-30	12
β-strand	34-40	7	14
α-helix	46-55	10
β-strand	64-67	4	14
α-helix	68-70	3
β-strand	71	1	18
β-strand	78	1	18
β-strand	79-84	6	14
β-strand	90-96	7	19
β-strand	114-119	6	19
β-strand	127-132	6	19
α-helix	137-139	3
α-helix	140-158	19
β-strand	163-168	6	19
α-helix	178-183	6
α-helix	185-188	4
β-strand	192-194	3	19
β-strand	203	1	20
β-strand	212-217	6	19
α-helix	219-224	6
β-strand	225	1	21
β-strand	231-232	2	14
α-helix	235-238	4
α-helix	243-249	7
β-strand	252	1	20
β-strand	255-258	4	14
β-strand	259	1	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle, intermediate form	A, D	protein	375	Oryctolagus cuniculus	P68135 (AlphaFold model)
Deoxyribonuclease-1	B, F	protein	260	Bos taurus	P00639 (AlphaFold model)
Protein phosphatase 1 regulatory subunit 15A	C, E	protein	40	Homo sapiens	O75807 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>7NXV_1 Actin, alpha skeletal muscle, intermediate form (chains A, D)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (B, F), FASTA

>7NXV_2 Deoxyribonuclease-1 (chains B, F)
LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDP
NTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSS
HSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQ
WSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYG
LSNEMALAISDHYPVEVTLT

Sequence of entity 3 (C, E), FASTA

>7NXV_3 Protein phosphatase 1 regulatory subunit 15A (chains C, E)
WEQLARDRSRFARRITQAQEELSPCLTPAARARAWARLRN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Higher-order phosphatase-substrate contacts terminate the integrated stress response. Yan, Y., Harding, H.P., Ron, D. Nat Struct Mol Biol (2021) 28:835-846. DOI 10.1038/s41594-021-00666-7 · 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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