5TGC: Hetero-trimer of Rtt102-Arp7/9

Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP. Determined by X-ray diffraction at 3.25 Å resolution. Released 6 Sept 2017.

Method: X-ray diffraction
Resolution: 3.25 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 14,208
Mol. weight: 254.24 kDa
Ligands: ATP
Released: 6 Sept 2017

Explore 5TGC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TGC contains 93 α-helices and 93 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: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	34-37	4	2
β-strand	47-48	2	2
α-helix	51-60	10
β-strand	66-69	4	2
α-helix	80-89	10
α-helix	90-95	6
β-strand	104-108	5	1
α-helix	116-124	9
α-helix	125-130	6
β-strand	135-140	6	1
α-helix	141-148	8
β-strand	154-159	6	3
β-strand	164-170	7	3
β-strand	173-174	2	3
β-strand	180-181	2	3
α-helix	186-201	16
α-helix	217-225	9
α-helix	227-234	8
β-strand	237	1	4
α-helix	243-268	26
α-helix	283-285	3
β-strand	287-292	6	5
β-strand	297-302	6	5
α-helix	303-314	12
α-helix	316-318	3
α-helix	325-327	3
α-helix	329-342	14
α-helix	381-390	10
β-strand	392-395	4	3
α-helix	397-400	4
β-strand	402	1	4
α-helix	404-415	12
β-strand	423-425	3	3
α-helix	429-444	16
α-helix	449-451	3
β-strand	454-456	3	1

Chain B: 20 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-13	4	6
β-strand	18-23	6	6
β-strand	35-38	4	6
β-strand	41	1	7
β-strand	42-45	4	8
β-strand	51-54	4	8
β-strand	65	1	7
β-strand	68-69	2	9
β-strand	72-73	2	9
α-helix	76-97	22
α-helix	101-103	3
β-strand	111-115	5	6
α-helix	121-129	9
α-helix	130-134	5
β-strand	139-144	6	6
α-helix	145-152	8
β-strand	159-164	6	10
β-strand	169-175	7	10
β-strand	178-179	2	10
α-helix	181-183	3
β-strand	185-187	3	10
α-helix	191-201	11
α-helix	207-215	9
β-strand	220	1	11
β-strand	282-285	4	12
β-strand	291-294	4	12
α-helix	296-299	4
α-helix	303-318	16
α-helix	323-331	9
β-strand	333-337	5	10
α-helix	339-341	3
β-strand	343	1	11
α-helix	345-357	13
α-helix	363-372	10
α-helix	396-398	3
β-strand	409	1	10
α-helix	410-411	2
α-helix	424-441	18
β-strand	448-450	3	6
α-helix	451-456	6
α-helix	458-462	5

Chain C: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
β-strand	25-30	6	13
α-helix	32	1
β-strand	33	1	14
α-helix	34	1
β-strand	55	1	14
β-strand	60-65	6	13
α-helix	80-83	4
β-strand	88	1	6

Chain D: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	15
β-strand	16-21	6	15
β-strand	29-32	4	15
β-strand	34-39	6	16
β-strand	45-48	4	16
α-helix	51-59	9
β-strand	65-69	5	16
β-strand	71	1	17
β-strand	77	1	17
α-helix	80-89	10
α-helix	90-95	6
β-strand	104-108	5	15
α-helix	116-124	9
α-helix	125-130	6
β-strand	136-140	5	15
α-helix	141-148	8
β-strand	154-159	6	18
β-strand	164-170	7	18
β-strand	173-174	2	18
β-strand	180-181	2	18
α-helix	186-202	17
α-helix	217-223	7
α-helix	224-228	5
α-helix	229-234	6
β-strand	237	1	19
α-helix	243-258	16
α-helix	259-265	7
α-helix	283-285	3
β-strand	287-292	6	20
β-strand	297-302	6	20
α-helix	303-314	12
α-helix	316-318	3
α-helix	325-327	3
α-helix	329-342	14
α-helix	381-390	10
β-strand	392-395	4	18
α-helix	397-400	4
β-strand	402	1	19
α-helix	404-415	12
β-strand	423-424	2	18
α-helix	429-444	16
α-helix	449-451	3
β-strand	454-455	2	15
α-helix	457-462	6

Chain E: 21 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-13	4	21
β-strand	18-23	6	21
β-strand	35-38	4	21
β-strand	41-45	5	22
β-strand	51-54	4	22
β-strand	63-65	3	22
β-strand	68-69	2	23
β-strand	72-73	2	23
α-helix	76-97	22
α-helix	99-103	5
β-strand	111-115	5	21
α-helix	121-129	9
α-helix	130-134	5
β-strand	139-144	6	21
α-helix	145-152	8
β-strand	159-164	6	24
β-strand	169-175	7	24
β-strand	178-179	2	24
β-strand	185-187	3	24
α-helix	191-201	11
α-helix	207-214	8
β-strand	220	1	25
α-helix	276-278	3
β-strand	282-285	4	26
β-strand	291-294	4	26
α-helix	296-299	4
α-helix	303-318	16
α-helix	323-331	9
β-strand	333-337	5	24
α-helix	339-341	3
β-strand	343	1	25
α-helix	345-357	13
α-helix	363-372	10
α-helix	396-399	4
β-strand	400	1	20
β-strand	409	1	24
α-helix	417-419	3
α-helix	425-436	12
α-helix	437-441	5
β-strand	449-450	2	21
α-helix	451-457	7
α-helix	458-463	6

Chain F: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
α-helix	19-21	3
β-strand	25-30	6	27
α-helix	32	1
β-strand	33	1	28
α-helix	34	1
β-strand	55	1	28
β-strand	60-65	6	27
α-helix	84-87	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 7	A, D	protein	490	Saccharomyces cerevisiae	Q12406 (AlphaFold model)
Actin-like protein ARP9	B, E	protein	467	Saccharomyces cerevisiae	Q05123 (AlphaFold model)
Regulator of Ty1 transposition protein 102	C, F	protein	158	Saccharomyces cerevisiae	P53330 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5TGC_1 Actin-related protein 7 (chains A, D)
MMTLNRKCVVIHNGSHRTVAGFSNVELPQCIIPSSYIKRTDEGGEAEFIFGTYNMIDAAA
EKRNGDEVYTLVDSQGLPYNWDALEMQWRYLYDTQLKVSPEELPLVITMPATNGKPDMAI
LERYYELAFDKLNVPVFQIVIEPLAIALSMGKSSAFVIDIGASGCNVTPIIDGIVVKNAV
VRSKFGGDFLDFQVHERLAPLIKEENDMENMADEQKRSTDVWYEASTWIQQFKSTMLQVS
EKDLFELERYYKEQADIYAKQQEQLKQMDQQLQYTALTGSPNNPLVQKKNFLFKPLNKTL
TLDLKECYQFAEYLFKPQLISDKFSPEDGLGPLMAKSVKKAGASINSMKANTSTNPNGLG
TSHINTNVGDNNSTASSSNISPEQVYSLLLTNVIITGSTSLIEGMEQRIIKELSIRFPQY
KLTTFANQVMMDRKIQGWLGALTMANLPSWSLGKWYSKEDYETLKRDRKQSQATNATNLV
PRGSHHHHHH

Sequence of entity 2 (B, E), FASTA

>5TGC_2 Actin-like protein ARP9 (chains B, E)
MAPFRQDSILIIYPRSQTTLVQFGLNEETFTVPELEIPTQIYRTTRQDGSYTYHSTNKDN
KAELIKPIQNGEIIDISAFTQFLRLIFVSILSDRANKNQDAFEAELSNIPLLLITHHSWS
QSDLEIITQYVFESLEINNLIQLPASLAATYSMISLQNCCIIDVGTHHTDIIPIVDYAQL
DHLVSSIPMGGQSINDSLKKLLPQWDDDQIESLKKSPIFEVLSDDAKKLSSFDFGNENED
EDEGTLNVAEIITSGRDTREVLEERERGQKVKNVKNSDLEFNTFWDEKGNEIKVGKQRFQ
GCNNLIKNISNRVGLTLDNIDDINKAKAVWENIIIVGGTTSISGFKEALLGQLLKDHLII
EPEEEKSKREEEAKSVLPAATKKKSKFMTNSTAFVPTIEYVQCPTVIKLAKYPDYFPEWK
KSGYSEIIFLGAQIVSKQIFTHPKDTFYITREKYNMKGPAALWDVQF

Sequence of entity 3 (C, F), FASTA

>5TGC_3 Regulator of Ty1 transposition protein 102 (chains C, F)
SMDPQTLITKANKVSYYGNPTSKESWRYDWYQPSKVSSNVQQPQQQLGDMENNLEKYPFR
YKTWLRNQEDEKNLQRESCEDILDLKEFDRRILKKSLMTSHTKGDTSKATGAPSANQGDE
ALSVDDIRGAVGNSEAIPGLSAGVNNDNTKESKDVKMN

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase. Turegun, B., Baker, R.W., Leschziner, A.E. et al. Commun Biol (2018) 1. DOI 10.1038/s42003-017-0002-6 · PubMed

Other PDB entries of the same protein (UniProt Q12406 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4I6M 2.8 Å, Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.
7C4J 2.89 Å, Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome free state
3WEE 3.1 Å, Structure of the full-length yeast Arp7-Arp9 Heterodimer
6VZ4 3.9 Å, Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium…
9PB3 4.0 Å, ARP of SWI/SNF of PIC-Med-SWI/SNF
6VZG 4.2 Å, Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102
7EGP 6.9 Å, The structure of SWI/SNF-nucleosome complex
6KW3 7.13 Å, The ClassA RSC-Nucleosome Complex
6KW4 7.55 Å, The ClassB RSC-Nucleosome Complex
6UXW 8.96 Å, SWI/SNF nucleosome complex with ADP-BeFx
6KW5 10.13 Å, The ClassC RSC-Nucleosome Complex
6TDA 15.0 Å, Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome

Browse structure collections

About this viewer

MolViewer shows 5TGC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.