7YKZ: ATPase family gene 2 protein

Cryo-EM structure of Drg1 hexamer in the planar state treated with ADP/AMPPNP/Diazaborine. Determined by electron microscopy at 4.3 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 4.3 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 34,146
Mol. weight: 516.51 kDa
Ligands: NDT, ATP, ADP
Released: 14 Dec 2022

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

Secondary structure: helices and β-sheets

7YKZ contains 195 α-helices and 140 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: 33 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	35
β-strand	35-36	2	36
β-strand	52-53	2	37
α-helix	55-60	6
β-strand	68-69	2	38
β-strand	70-71	2	39
β-strand	82-83	2	38
β-strand	85-86	2	37
β-strand	95-96	2	36
α-helix	99-105	7
β-strand	114	1	35
β-strand	116-117	2	39
α-helix	121-123	3
β-strand	134	1	40
α-helix	141-144	4
α-helix	147-153	7
β-strand	177	1	40
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-272	5
β-strand	281-285	5	41
α-helix	292-301	10
β-strand	306-309	4	41
α-helix	320-336	17
β-strand	340-345	6	41
α-helix	347-350	4
β-strand	352	1	42
α-helix	364-375	12
β-strand	383-389	7	41
β-strand	395	1	42
α-helix	402-405	4
β-strand	408-410	3	41
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-471	18
α-helix	472-476	5
α-helix	481-484	4
α-helix	489-496	8
α-helix	510-512	3
α-helix	515-517	3
α-helix	522-533	12
α-helix	539-545	7
β-strand	552-556	5	43
α-helix	565-574	10
β-strand	578-581	4	43
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	43
α-helix	631-645	15
β-strand	654-659	6	43
β-strand	671	1	44
β-strand	674	1	44
β-strand	677-679	3	43
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	763-774	12

Chain B: 32 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	17
β-strand	35-36	2	18
β-strand	52-53	2	19
α-helix	55-61	7
β-strand	68-69	2	20
β-strand	70-71	2	21
β-strand	82-83	2	20
β-strand	85-86	2	19
β-strand	95-96	2	18
α-helix	100-105	6
α-helix	108-109	2
β-strand	114	1	17
β-strand	116-117	2	21
α-helix	121-123	3
α-helix	141-143	3
α-helix	147-152	6
α-helix	251-266	16
α-helix	269-274	6
β-strand	281-285	5	22
α-helix	292-302	11
β-strand	306-309	4	22
α-helix	320-336	17
β-strand	340-345	6	22
α-helix	347-350	4
α-helix	364-375	12
β-strand	383-389	7	22
α-helix	402-405	4
β-strand	407-410	4	22
α-helix	416-429	14
α-helix	439-448	10
α-helix	454-471	18
α-helix	472-476	5
α-helix	481-484	4
α-helix	489-496	8
β-strand	508	1	23
α-helix	510-512	3
α-helix	522-536	15
α-helix	539-545	7
β-strand	552-556	5	23
α-helix	565-574	10
β-strand	578-581	4	23
α-helix	584-586	3
α-helix	593-607	15
β-strand	612-615	4	23
α-helix	631-645	15
β-strand	654-659	6	23
β-strand	671	1	24
β-strand	674	1	24
β-strand	677-679	3	23
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 C: 33 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	45
α-helix	38-39	2
α-helix	55-60	6
β-strand	68-69	2	46
β-strand	70-71	2	47
β-strand	82-83	2	46
β-strand	95	1	45
α-helix	99-105	7
β-strand	113-114	2	45
β-strand	116-117	2	47
α-helix	122-123	2
α-helix	141-143	3
α-helix	147-152	6
α-helix	231-233	3
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	48
α-helix	292-302	11
β-strand	306-309	4	48
α-helix	320-336	17
β-strand	340-344	5	48
α-helix	347-350	4
α-helix	364-374	11
β-strand	383-389	7	48
α-helix	392-394	3
α-helix	402-405	4
β-strand	407-410	4	48
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	488-497	10
α-helix	515-517	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	553-556	4	49
α-helix	565-569	5
α-helix	570-574	5
β-strand	578-581	4	49
α-helix	593-607	15
β-strand	612-615	4	49
α-helix	631-644	14
β-strand	654-659	6	49
α-helix	662-664	3
β-strand	677-679	3	49
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 D: 34 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	1
β-strand	35-37	3	2
β-strand	52-53	2	3
α-helix	55-60	6
β-strand	68-71	4	4
β-strand	81-83	3	4
β-strand	85-86	2	3
β-strand	95-97	3	2
α-helix	100-105	6
β-strand	114	1	1
β-strand	116-117	2	4
α-helix	122-123	2
β-strand	134	1	5
α-helix	147-152	6
β-strand	177	1	5
α-helix	234-236	3
α-helix	240-242	3
α-helix	251-265	15
α-helix	268-272	5
β-strand	281-285	5	6
α-helix	292-302	11
β-strand	306-309	4	6
α-helix	312-314	3
α-helix	320-336	17
β-strand	339-345	7	6
α-helix	347-350	4
α-helix	364-375	12
β-strand	382-389	8	6
α-helix	402-405	4
β-strand	407-410	4	6
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	488-497	10
α-helix	510-512	3
α-helix	515-517	3
α-helix	522-536	15
α-helix	539-545	7
β-strand	552-556	5	7
α-helix	565-574	10
β-strand	578-581	4	7
α-helix	584-586	3
α-helix	593-607	15
β-strand	612-615	4	7
α-helix	631-645	15
β-strand	654-659	6	7
α-helix	662-664	3
β-strand	677-679	3	7
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 E: 34 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	33-37	5	25
β-strand	52-53	2	26
α-helix	55-60	6
β-strand	68-69	2	27
β-strand	70-71	2	28
β-strand	82-83	2	27
β-strand	85-86	2	26
β-strand	95-97	3	25
α-helix	100-105	6
β-strand	113-115	3	25
β-strand	116-117	2	28
α-helix	121-123	3
β-strand	131	1	29
β-strand	134	1	30
α-helix	141-143	3
α-helix	147-152	6
β-strand	177	1	30
β-strand	226	1	29
α-helix	234-236	3
α-helix	238-242	5
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	31
α-helix	292-302	11
β-strand	306-308	3	31
α-helix	313-315	3
α-helix	322-336	15
β-strand	339-345	7	31
α-helix	347-350	4
β-strand	352	1	32
α-helix	364-375	12
β-strand	382-389	8	31
β-strand	395	1	32
α-helix	402-405	4
β-strand	407-410	4	31
α-helix	416-430	15
β-strand	435	1	33
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
β-strand	486	1	33
α-helix	489-497	9
β-strand	508	1	34
α-helix	510-512	3
α-helix	522-536	15
α-helix	539-545	7
β-strand	552-556	5	34
α-helix	563-574	12
β-strand	578-581	4	34
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	34
α-helix	631-645	15
β-strand	654-659	6	34
α-helix	662-664	3
β-strand	677-679	3	34
α-helix	686-697	12
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-755	9
α-helix	763-775	13

Chain F: 29 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	8
β-strand	35	1	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	1	9
α-helix	100-106	7
β-strand	114	1	8
β-strand	116-117	2	12
α-helix	121-123	3
α-helix	141-143	3
α-helix	147-153	7
α-helix	251-266	16
α-helix	268-274	7
β-strand	282-285	4	13
α-helix	292-302	11
β-strand	306-308	3	13
α-helix	322-336	15
β-strand	340-344	5	13
α-helix	347-350	4
β-strand	352	1	14
α-helix	364-375	12
β-strand	383-389	7	13
β-strand	395	1	14
α-helix	402-405	4
β-strand	408-410	3	13
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	489-497	9
β-strand	508	1	15
α-helix	510-512	3
α-helix	522-545	24
β-strand	552-556	5	15
α-helix	564-574	11
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	686-697	12
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-755	9
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

>7YKZ_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
NDT	2-(toluene-4-sulfonyl)-2H-BENZO[D][1,2,3]DIAZABORININ-1-ol	C14 H13 B N2 O3 S	6
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	6
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	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).
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
7YKT 5.9 Å, Cryo-EM structure of Drg1 hexamer in helical state treated with…

Browse structure collections

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