7Z11: Substrate bound DRG1

Structure of substrate bound DRG1 (AFG2). Determined by electron microscopy at 3.2 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 7
Atoms: 34,079
Mol. weight: 516.58 kDa
Ligands: AGS
Released: 21 Sept 2022

Explore 7Z11 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z11 contains 247 α-helices and 190 β-strands across 7 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: 42 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	1
α-helix	46-49	4
β-strand	50-53	4	1
α-helix	55-60	6
β-strand	68-71	4	1
β-strand	73	1	1
β-strand	78	1	2
β-strand	79-85	7	1
β-strand	95-98	4	1
α-helix	100-106	7
β-strand	113-114	2	1
β-strand	117-118	2	1
β-strand	125	1	3
β-strand	128-132	5	4
α-helix	139-141	3
α-helix	145-155	11
β-strand	164-165	2	5
β-strand	177-178	2	5
β-strand	179-183	5	4
β-strand	210	1	2
β-strand	216	1	3
β-strand	223-226	4	4
α-helix	232-233	2
α-helix	251-266	16
α-helix	268-272	5
α-helix	277-279	3
β-strand	281-285	5	6
α-helix	292-302	11
β-strand	306-309	4	6
α-helix	322-336	15
β-strand	340-345	6	6
α-helix	347-349	3
β-strand	352	1	7
α-helix	361-375	15
α-helix	378-380	3
β-strand	383-389	7	6
α-helix	392-394	3
β-strand	395	1	7
α-helix	397-399	3
β-strand	402	1	8
β-strand	404	1	8
β-strand	407-410	4	6
α-helix	412-414	3
α-helix	416-427	12
α-helix	428-433	6
α-helix	439-448	10
α-helix	455-473	19
α-helix	481-483	3
α-helix	488-497	10
α-helix	501-503	3
α-helix	515-517	3
α-helix	522-532	11
α-helix	534-537	4
α-helix	539-545	7
α-helix	548-550	3
β-strand	552-556	5	9
β-strand	559	1	10
β-strand	561	1	10
α-helix	564-573	10
β-strand	579-581	3	9
β-strand	590	1	11
α-helix	593-607	15
β-strand	612-616	5	9
α-helix	618-620	3
α-helix	623-624	2
α-helix	631-648	18
β-strand	654-659	6	9
α-helix	662-664	3
α-helix	667-670	4
β-strand	672	1	12
β-strand	674	1	12
β-strand	677-680	4	9
α-helix	686-697	12
α-helix	702-705	4
α-helix	709-715	7
α-helix	721-738	18
α-helix	747-754	8
α-helix	763-772	10

Chain B: 41 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	13
α-helix	46-49	4
β-strand	50-52	3	13
β-strand	53	1	14
α-helix	55-61	7
β-strand	68-73	6	13
β-strand	78	1	15
β-strand	79-82	4	13
β-strand	85	1	14
α-helix	86-87	2
β-strand	95-98	4	13
α-helix	100-103	4
α-helix	108-109	2
β-strand	113-118	6	13
β-strand	125	1	16
β-strand	128-133	6	17
α-helix	139-142	4
α-helix	145-152	8
β-strand	157-158	2	16
β-strand	163	1	17
β-strand	167-168	2	18
β-strand	175-176	2	18
β-strand	178-184	7	17
β-strand	210	1	15
β-strand	215-216	2	16
β-strand	223-226	4	17
α-helix	234-236	3
α-helix	238-242	5
α-helix	244-246	3
α-helix	248-250	3
α-helix	251-266	16
α-helix	269-274	6
α-helix	277-279	3
β-strand	281-285	5	19
α-helix	292-302	11
β-strand	306-311	6	19
β-strand	319	1	20
α-helix	322-336	15
β-strand	340-345	6	19
α-helix	347-349	3
α-helix	361-373	13
β-strand	383-389	7	19
α-helix	392-394	3
β-strand	407-410	4	19
α-helix	416-428	13
α-helix	441-448	8
α-helix	455-475	21
α-helix	481-483	3
α-helix	488-495	8
α-helix	501-503	3
α-helix	522-532	11
α-helix	534-537	4
α-helix	539-545	7
α-helix	548-550	3
β-strand	552-556	5	21
α-helix	564-573	10
β-strand	577-581	5	21
α-helix	584-586	3
β-strand	590	1	22
α-helix	593-607	15
β-strand	611-616	6	21
α-helix	618-621	4
α-helix	631-644	14
β-strand	653-659	7	21
α-helix	662-664	3
β-strand	677-680	4	21
α-helix	686-696	11
α-helix	702-705	4
α-helix	709-715	7
α-helix	721-738	18
α-helix	747-754	8
α-helix	763-775	13

Chain C: 37 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	23
α-helix	46-49	4
β-strand	50-53	4	23
α-helix	55-60	6
β-strand	68-73	6	23
β-strand	78	1	24
β-strand	79-85	7	23
β-strand	95-98	4	23
α-helix	100-106	7
β-strand	113-118	6	23
β-strand	125	1	25
β-strand	128-133	6	26
α-helix	139-142	4
α-helix	145-154	10
β-strand	157-158	2	25
β-strand	163-168	6	26
β-strand	175-184	10	26
β-strand	210	1	24
β-strand	215-216	2	25
β-strand	223-224	2	26
α-helix	238-242	5
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-274	7
α-helix	277-279	3
β-strand	281-285	5	27
α-helix	292-302	11
β-strand	306-311	6	27
β-strand	319	1	28
α-helix	322-336	15
β-strand	340-345	6	27
α-helix	361-374	14
β-strand	383-389	7	27
α-helix	392-394	3
β-strand	407-410	4	27
α-helix	412-414	3
α-helix	416-430	15
α-helix	440-448	9
α-helix	455-475	21
α-helix	481-483	3
α-helix	488-495	8
α-helix	501-503	3
α-helix	522-532	11
α-helix	534-537	4
α-helix	539-545	7
α-helix	548-550	3
β-strand	552-556	5	29
α-helix	563-573	11
β-strand	577-581	5	29
α-helix	583-586	4
β-strand	590	1	30
α-helix	593-607	15
β-strand	611-616	6	29
α-helix	618-620	3
α-helix	631-644	14
β-strand	653-659	7	29
α-helix	662-664	3
α-helix	667-670	4
β-strand	677-680	4	29
α-helix	686-696	11
α-helix	709-715	7
α-helix	721-738	18
α-helix	747-756	10
α-helix	763-773	11

Chain D: 43 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	31
β-strand	50-53	4	31
α-helix	55-60	6
β-strand	68-73	6	31
β-strand	78	1	32
β-strand	79-85	7	31
α-helix	86-87	2
β-strand	95-98	4	31
α-helix	100-106	7
α-helix	108-109	2
β-strand	113-118	6	31
α-helix	123-124	2
β-strand	125	1	33
α-helix	126	1
β-strand	128-133	6	34
α-helix	139-142	4
α-helix	145-155	11
β-strand	158	1	35
β-strand	163-168	6	34
α-helix	170-172	3
β-strand	175-184	10	34
β-strand	210	1	32
β-strand	215	1	35
β-strand	216	1	33
β-strand	223-226	4	34
α-helix	234-236	3
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-274	7
β-strand	282-285	4	36
α-helix	292-302	11
β-strand	306-310	5	36
α-helix	312-315	4
β-strand	319	1	37
α-helix	322-336	15
β-strand	340-345	6	36
α-helix	347-350	4
α-helix	361-374	14
β-strand	383-389	7	36
α-helix	392-394	3
α-helix	397-399	3
β-strand	407-410	4	36
α-helix	416-428	13
α-helix	440-448	9
α-helix	455-475	21
α-helix	481-483	3
α-helix	488-495	8
α-helix	501-503	3
α-helix	515-517	3
α-helix	522-528	7
α-helix	529-533	5
α-helix	534-537	4
α-helix	539-545	7
α-helix	548-550	3
β-strand	552-556	5	38
α-helix	563-571	9
β-strand	577-581	5	38
α-helix	584-586	3
α-helix	593-607	15
β-strand	611-616	6	38
α-helix	636-644	9
β-strand	653-659	7	38
α-helix	662-664	3
β-strand	677-680	4	38
α-helix	686-696	11
α-helix	703-705	3
α-helix	709-715	7
α-helix	721-738	18
α-helix	747-754	8
α-helix	763-775	13

Chain E: 40 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-37	3	39
β-strand	52-53	2	40
α-helix	55-60	6
β-strand	67-71	5	41
β-strand	73	1	42
α-helix	77	1
β-strand	78	1	43
β-strand	79-83	5	41
β-strand	84-85	2	40
β-strand	95-97	3	39
α-helix	100-103	4
β-strand	113	1	39
β-strand	114	1	42
β-strand	117-118	2	41
α-helix	122-124	3
β-strand	125	1	44
β-strand	128-133	6	45
α-helix	139-142	4
α-helix	145-155	11
β-strand	157-158	2	44
β-strand	163-164	2	45
β-strand	168	1	46
β-strand	175	1	46
β-strand	178-184	7	45
β-strand	210	1	43
β-strand	215-216	2	44
β-strand	223-226	4	45
α-helix	238-241	4
α-helix	244-246	3
α-helix	251-265	15
α-helix	269-272	4
β-strand	281-285	5	47
α-helix	292-302	11
β-strand	306-309	4	47
α-helix	323-336	14
β-strand	340-345	6	47
α-helix	347-349	3
β-strand	352	1	48
α-helix	361-374	14
β-strand	383-389	7	47
α-helix	392-394	3
β-strand	395	1	48
α-helix	397-399	3
β-strand	402	1	49
β-strand	404	1	49
β-strand	407-410	4	47
α-helix	412-414	3
α-helix	419-426	8
α-helix	427-430	4
α-helix	431-434	4
α-helix	440-448	9
α-helix	455-475	21
α-helix	481-483	3
α-helix	488-495	8
α-helix	522-528	7
α-helix	529-533	5
α-helix	534-537	4
α-helix	540-543	4
α-helix	548-550	3
β-strand	556	1	50
α-helix	565-570	6
β-strand	577	1	51
β-strand	580	1	52
α-helix	597-607	11
β-strand	611	1	51
β-strand	614	1	52
α-helix	618-621	4
α-helix	636-644	9
β-strand	653	1	51
α-helix	662-664	3
α-helix	667-670	4
β-strand	680	1	50
α-helix	686-696	11
α-helix	710-712	3
α-helix	724-738	15
α-helix	747-756	10
α-helix	763-776	14

Chain F: 42 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	53
α-helix	46-49	4
β-strand	50-53	4	53
α-helix	55-60	6
β-strand	67-73	7	53
β-strand	78-85	8	53
β-strand	95-98	4	53
α-helix	100-106	7
α-helix	112	1
β-strand	113-118	6	53
α-helix	122-124	3
β-strand	125	1	54
α-helix	126	1
β-strand	128-133	6	55
α-helix	139-141	3
α-helix	145-155	11
β-strand	157-158	2	54
β-strand	163-168	6	55
β-strand	175-184	10	55
β-strand	210	1	53
β-strand	215-216	2	54
β-strand	223-227	5	55
α-helix	234-236	3
α-helix	251-261	11
α-helix	262-266	5
α-helix	269-272	4
α-helix	276-278	3
β-strand	282-285	4	56
α-helix	292-302	11
β-strand	306-308	3	56
α-helix	309-310	2
α-helix	322-333	12
β-strand	340-344	5	56
α-helix	347-350	4
β-strand	352	1	57
α-helix	362-373	12
β-strand	385-389	5	56
α-helix	392-394	3
β-strand	395	1	57
α-helix	397-400	4
β-strand	407-408	2	56
α-helix	416-427	12
α-helix	442-448	7
α-helix	455-475	21
α-helix	481-483	3
α-helix	488-497	10
α-helix	501-504	4
α-helix	515-517	3
α-helix	522-528	7
α-helix	529-533	5
α-helix	534-537	4
α-helix	539-545	7
β-strand	553-556	4	58
α-helix	563-572	10
β-strand	577-581	5	58
α-helix	583-586	4
α-helix	593-605	13
β-strand	611-615	5	58
α-helix	618-620	3
α-helix	635-646	12
β-strand	653-659	7	58
α-helix	662-664	3
β-strand	677-680	4	58
α-helix	686-696	11
α-helix	702-705	4
α-helix	709-715	7
α-helix	722-738	17
α-helix	747-754	8

Chain G: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	-1	1	20
β-strand	1	1	28
α-helix	2	1
β-strand	3	1	37
α-helix	4	1
β-strand	10	1	11
β-strand	12	1	22
β-strand	14	1	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATPase family gene 2 protein	A, B, C, D, E, F	protein	780	Saccharomyces cerevisiae S288C	P32794 (AlphaFold model)
peptide substrate	G	protein	20	Saccharomyces cerevisiae S288C

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

>7Z11_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

Sequence of entity 2 (G), FASTA

>7Z11_2 peptide substrate (chains G)
XXXXXXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	11

Primary citation

Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Prattes, M., Grishkovskaya, I., Hodirnau, V.V. et al. Nat Struct Mol Biol (2022) 29:942-953. DOI 10.1038/s41594-022-00832-5 · PubMed

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

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
7YKT 5.9 Å, Cryo-EM structure of Drg1 hexamer in helical state treated with…

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