7YKT: ATPase family gene 2 protein

Cryo-EM structure of Drg1 hexamer in helical state treated with ADP/AMPPNP/benzo-diazaborine. Determined by electron microscopy at 5.9 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 5.9 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 34,000
Mol. weight: 513.43 kDa
Ligands: ADP, ATP
Released: 14 Dec 2022

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

Secondary structure: helices and β-sheets

7YKT contains 190 α-helices and 137 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: 29 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	9
β-strand	52-53	2	10
α-helix	55-60	6
β-strand	68-69	2	11
β-strand	70-71	2	12
β-strand	82-83	2	11
β-strand	85-86	2	10
β-strand	95-97	3	9
α-helix	100-105	6
β-strand	113-114	2	9
β-strand	116-117	2	12
α-helix	121-123	3
α-helix	141-143	3
α-helix	147-152	6
α-helix	240-242	3
α-helix	251-265	15
α-helix	269-274	6
β-strand	281-285	5	13
α-helix	292-301	10
β-strand	306-309	4	13
α-helix	322-336	15
β-strand	340-345	6	13
α-helix	347-350	4
β-strand	352	1	14
α-helix	364-374	11
β-strand	383-389	7	13
β-strand	395	1	14
β-strand	407-410	4	13
α-helix	416-430	15
α-helix	432-434	3
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	489-497	9
α-helix	522-545	24
β-strand	552-556	5	15
α-helix	565-574	10
β-strand	578-581	4	15
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	15
α-helix	631-645	15
β-strand	654-659	6	15
β-strand	671	1	16
β-strand	674	1	16
β-strand	677-679	3	15
α-helix	686-696	11
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-756	10
α-helix	763-775	13

Chain B: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	17
β-strand	35	1	18
α-helix	38-39	2
β-strand	52-53	2	19
α-helix	55-60	6
β-strand	68-69	2	20
β-strand	82-83	2	20
β-strand	85-86	2	19
β-strand	95	1	18
α-helix	99-106	8
β-strand	114	1	17
α-helix	121-123	3
β-strand	131	1	21
α-helix	141-144	4
α-helix	147-151	5
β-strand	226	1	21
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	22
α-helix	292-302	11
β-strand	306-309	4	22
α-helix	312-314	3
α-helix	320-336	17
β-strand	340-345	6	22
α-helix	347-350	4
β-strand	352	1	23
β-strand	360	1	24
β-strand	362	1	24
α-helix	364-375	12
β-strand	383-389	7	22
β-strand	395	1	23
α-helix	402-405	4
β-strand	407-410	4	22
α-helix	416-429	14
α-helix	439-448	10
α-helix	454-475	22
α-helix	481-484	4
α-helix	489-498	10
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	25
α-helix	564-574	11
β-strand	579-581	3	25
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	25
α-helix	618-620	3
α-helix	631-645	15
β-strand	654-659	6	25
β-strand	671	1	26
β-strand	674	1	26
β-strand	677-679	3	25
α-helix	686-699	14
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-736	16
α-helix	747-755	9
α-helix	763-775	13

Chain C: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	27
β-strand	35-36	2	28
β-strand	52	1	29
α-helix	55-61	7
β-strand	68-71	4	30
β-strand	81-83	3	30
β-strand	85	1	29
β-strand	95-96	2	28
α-helix	100-105	6
β-strand	114	1	27
β-strand	116-117	2	30
α-helix	121-123	3
β-strand	131	1	31
β-strand	134	1	32
α-helix	141-143	3
α-helix	147-152	6
β-strand	177	1	32
β-strand	226	1	31
α-helix	251-266	16
α-helix	268-272	5
β-strand	281-285	5	33
α-helix	292-302	11
β-strand	306-307	2	33
α-helix	320-336	17
β-strand	340-345	6	33
α-helix	347-350	4
β-strand	352	1	34
α-helix	364-375	12
β-strand	383-389	7	33
α-helix	392-394	3
β-strand	395	1	34
α-helix	402-405	4
β-strand	407-410	4	33
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-475	22
α-helix	481-484	4
α-helix	489-497	9
β-strand	508	1	35
α-helix	515-517	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	35
α-helix	565-574	10
β-strand	578-581	4	35
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	35
α-helix	631-645	15
β-strand	654-659	6	35
α-helix	662-664	3
β-strand	677-679	3	35
α-helix	686-698	13
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-756	10
α-helix	763-775	13

Chain D: 32 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	36
β-strand	35-37	3	37
α-helix	38-39	2
β-strand	52-53	2	38
α-helix	55-61	7
β-strand	68-69	2	39
β-strand	70-71	2	40
β-strand	82-83	2	39
β-strand	85-86	2	38
β-strand	95-97	3	37
α-helix	100-106	7
β-strand	114	1	36
β-strand	116-117	2	40
α-helix	121-123	3
α-helix	141-143	3
α-helix	147-151	5
α-helix	251-262	12
α-helix	268-272	5
β-strand	281-285	5	41
α-helix	292-301	10
β-strand	306-308	3	41
α-helix	320-336	17
β-strand	340-344	5	41
α-helix	347-350	4
α-helix	364-374	11
β-strand	383-389	7	41
α-helix	402-405	4
β-strand	407-410	4	41
α-helix	412-414	3
α-helix	416-434	19
α-helix	439-448	10
α-helix	454-476	23
α-helix	489-498	10
α-helix	515-517	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	42
α-helix	564-574	11
β-strand	578-581	4	42
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	42
α-helix	631-644	14
β-strand	654-659	6	42
α-helix	662-664	3
β-strand	677-679	3	42
α-helix	686-696	11
α-helix	702-705	4
α-helix	711-715	5
α-helix	722-739	18
α-helix	748-756	9
α-helix	763-775	13

Chain E: 31 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	43
β-strand	52-53	2	44
α-helix	55-60	6
β-strand	68-69	2	45
β-strand	82-83	2	45
β-strand	85-86	2	44
β-strand	95	1	43
α-helix	99-105	7
β-strand	113-114	2	43
α-helix	121-123	3
α-helix	147-153	7
α-helix	240-242	3
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	46
α-helix	292-302	11
β-strand	306-309	4	46
α-helix	312-314	3
α-helix	321-336	16
β-strand	340-345	6	46
α-helix	347-350	4
α-helix	364-375	12
β-strand	383-389	7	46
α-helix	402-405	4
β-strand	409-410	2	46
α-helix	416-429	14
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	488-498	11
α-helix	522-537	16
α-helix	540-545	6
β-strand	553-556	4	47
α-helix	563-574	12
β-strand	581	1	47
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	47
α-helix	618-620	3
α-helix	631-645	15
β-strand	654-659	6	47
β-strand	671	1	48
β-strand	674	1	48
β-strand	677-679	3	47
α-helix	686-697	12
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-756	10
α-helix	763-775	13

Chain F: 34 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	1
β-strand	35	1	2
β-strand	52-53	2	3
α-helix	55-60	6
β-strand	68-71	4	4
β-strand	79-83	5	4
β-strand	85-86	2	3
β-strand	95	1	2
α-helix	99-105	7
α-helix	108-109	2
β-strand	114	1	1
β-strand	116-117	2	4
α-helix	121-123	3
α-helix	141-143	3
α-helix	147-153	7
α-helix	240-242	3
α-helix	251-265	15
α-helix	268-272	5
β-strand	281-285	5	5
α-helix	292-302	11
β-strand	306-309	4	5
α-helix	312-314	3
α-helix	320-336	17
β-strand	340-345	6	5
α-helix	347-350	4
β-strand	352	1	6
α-helix	364-375	12
β-strand	383-388	6	5
β-strand	395	1	6
α-helix	402-405	4
β-strand	407-410	4	5
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	488-496	9
α-helix	510-512	3
α-helix	515-517	3
α-helix	525-537	13
α-helix	539-545	7
β-strand	553-555	3	7
α-helix	563-574	12
β-strand	578-581	4	7
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	7
α-helix	631-644	14
β-strand	654-658	5	7
α-helix	662-664	3
β-strand	671	1	8
β-strand	674	1	8
β-strand	677-679	3	7
α-helix	686-696	11
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-756	10
α-helix	763-775	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATPase family gene 2 protein	A, B, C, D, E, F	protein	780	Saccharomyces cerevisiae	P32794 (AlphaFold model)

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

>7YKT_1 ATPase family gene 2 protein (chains A, B, C, D, E, F)
MAPKSSSSGSKKKSSASSNSADAKASKFKLPAEFITRPHPSKDHGKETCTAYIHPNVLSS
LEINPGSFCTVGKIGENGILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQ
VQPPYATKVTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESIDVVI
TDASDDSLPDVSQLDLNMDDMYGGLDNLFYLSPPFIFRKGSTHITFSKETQANRKYNLPE
PLSYAAVGGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGKTMLLRVVA
NTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSIIFIDEIDSIAPNRANDDSG
EVESRVVATLLTLMDGMGAAGKVVVIAATNRPNSVDPALRRPGRFDQEVEIGIPDVDARF
DILTKQFSRMSSDRHVLDSEAIKYIASKTHGYVGADLTALCRESVMKTIQRGLGTDANID
KFSLKVTLKDVESAMVDIRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASE
TFARLGISAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVGESERAIRE
IFRKARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLLNEIDGVEELKGVVIVAATN
RPDEIDAALLRPGRLDRHIYVGPPDVNARLEILKKCTKKFNTEESGVDLHELADRTEGYS
GAEVVLLCQEAGLAAIMEDLDVAKVELRHFEKAFKGIARGITPEMLSYYEEFALRSGSSS

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	6

Primary citation

Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition. Ma, C., Wu, D., Chen, Q. et al. Nat Commun (2022) 13:6765-6765. DOI 10.1038/s41467-022-34511-2 · PubMed

Other PDB entries of the same protein (UniProt P32794 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z11 3.2 Å, Structure of substrate bound DRG1 (AFG2)
7NKU 3.4 Å, diazaborine bound Drg1(AFG2)
7WBB 3.6 Å, Cryo-EM structure of substrate engaged Drg1 hexamer
7WD3 3.8 Å, Cryo-EM structure of Drg1 hexamer treated with ATP and benzo-diazaborine
7Z34 3.8 Å, Structure of pre-60S particle bound to DRG1(AFG2).
7YKZ 4.3 Å, Cryo-EM structure of Drg1 hexamer in the planar state treated with ADP/AMPPNP/Diazaborine
7YKL 5.6 Å, Cryo-EM structure of Drg1 hexamer treated with AMPPNP
7YKK 5.9 Å, Cryo-EM structure of Drg1 hexamer treated with ADP

Browse structure collections

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