6VZG: Sth1-Arp7-Arp9-Rtt102

Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102. Determined by electron microscopy at 4.2 Å resolution. Released 2 Dec 2020.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae
Chains: 4
Atoms: 7,408
Mol. weight: 220.4 kDa
Ligands: ATP
Released: 2 Dec 2020

Explore 6VZG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VZG contains 51 α-helices and 45 β-strands across 4 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 K: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	317-340	24
α-helix	344-376	33

Chain L: 24 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	34-38	5	2
β-strand	46-48	3	2
α-helix	51-60	10
β-strand	66-69	4	2
β-strand	71	1	3
β-strand	77	1	3
α-helix	80-93	14
β-strand	104-108	5	1
α-helix	116-124	9
α-helix	125-130	6
β-strand	136-140	5	1
α-helix	141-148	8
β-strand	154-159	6	4
β-strand	164-169	6	4
β-strand	174	1	4
β-strand	180-182	3	4
α-helix	186-197	12
α-helix	198-200	3
α-helix	215-223	9
α-helix	224-228	5
α-helix	229-234	6
α-helix	243-255	13
α-helix	283-285	3
β-strand	287-292	6	5
α-helix	293-295	3
β-strand	297-302	6	5
α-helix	303-311	9
α-helix	316-318	3
α-helix	325-327	3
α-helix	329-342	14
α-helix	381-388	8
β-strand	392-395	4	4
α-helix	398-400	3
α-helix	404-415	12
β-strand	423-424	2	4
α-helix	429-433	5
α-helix	435-444	10
α-helix	449-451	3
β-strand	455	1	1
α-helix	457-464	8

Chain M: 24 helices, 21 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	26	1	7
β-strand	29	1	7
β-strand	35-38	4	6
β-strand	41-45	5	8
α-helix	47-49	3
β-strand	51-54	4	8
α-helix	58-60	3
β-strand	63-65	3	8
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	116	1
α-helix	121-133	13
β-strand	140-144	5	6
α-helix	145-152	8
β-strand	159-164	6	10
β-strand	169-175	7	10
β-strand	178-179	2	10
β-strand	185-187	3	10
α-helix	191-201	11
α-helix	207-215	9
α-helix	276-278	3
β-strand	282-285	4	11
α-helix	290	1
β-strand	291-294	4	11
α-helix	296-299	4
α-helix	303-317	15
α-helix	323-330	8
β-strand	333-336	4	10
α-helix	338-341	4
α-helix	345-357	13
α-helix	364-373	10
β-strand	409	1	10
α-helix	410-413	4
α-helix	417-422	6
α-helix	427-440	14
β-strand	449	1	6
α-helix	451-457	7
α-helix	458-461	4
α-helix	462-465	4

Chain N: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
β-strand	25-30	6	12
β-strand	33	1	13
β-strand	55	1	13
β-strand	60-65	6	12
β-strand	88	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 7	L	protein	477	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12406 (AlphaFold model)
Actin-like protein ARP9	M	protein	467	Saccharomyces cerevisiae	Q05123 (AlphaFold model)
Nuclear protein STH1/NPS1	K	protein	813	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32597 (AlphaFold model)
Regulator of Ty1 transposition protein 102	N	protein	157	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53330 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>6VZG_1 Actin-related protein 7 (chains L)
MTLNRKCVVIHNGSHRTVAGFSNVELPQCIIPSSYIKRTDEGGEAEFIFGTYNMIDAAAE
KRNGDEVYTLVDSQGLPYNWDALEMQWRYLYDTQLKVSPEELPLVITMPATNGKPDMAIL
ERYYELAFDKLNVPVFQIVIEPLAIALSMGKSSAFVIDIGASGCNVTPIIDGIVVKNAVV
RSKFGGDFLDFQVHERLAPLIKEENDMENMADEQKRSTDVWYEASTWIQQFKSTMLQVSE
KDLFELERYYKEQADIYAKQQEQLKQMDQQLQYTALTGSPNNPLVQKKNFLFKPLNKTLT
LDLKECYQFAEYLFKPQLISDKFSPEDGLGPLMAKSVKKAGASINSMKANTSTNPNGLGT
SHINTNVGDNNSTASSSNISPEQVYSLLLTNVIITGSTSLIEGMEQRIIKELSIRFPQYK
LTTFANQVMMDRKIQGWLGALTMANLPSWSLGKWYSKEDYETLKRDRKQSQATNATN

Sequence of entity 2 (M), FASTA

>6VZG_2 Actin-like protein ARP9 (chains M)
MAPFRQDSILIIYPRSQTTLVQFGLNEETFTVPELEIPTQIYRTTRQDGSYTYHSTNKDN
KAELIKPIQNGEIIDISAFTQFLRLIFVSILSDRANKNQDAFEAELSNIPLLLITHHSWS
QSDLEIITQYVFESLEINNLIQLPASLAATYSMISLQNCCIIDVGTHHTDIIPIVDYAQL
DHLVSSIPMGGQSINDSLKKLLPQWDDDQIESLKKSPIFEVLSDDAKKLSSFDFGNENED
EDEGTLNVAEIITSGRDTREVLEERERGQKVKNVKNSDLEFNTFWDEKGNEIKVGKQRFQ
GCNNLIKNISNRVGLTLDNIDDINKAKAVWENIIIVGGTTSISGFKEALLGQLLKDHLII
EPEEEKSKREEEAKSVLPAATKKKSKFMTNSTAFVPTIEYVQCPTVIKLAKYPDYFPEWK
KSGYSEIIFLGAQIVSKQIFTHPKDTFYITREKYNMKGPAALWDVQF

Sequence of entity 3 (K), FASTA

>6VZG_3 Nuclear protein STH1/NPS1 (chains K)
MGSSHHHHHHSQDPNSVRLAEELERQQLLEKRKKERNLHLQKINSIIDFIKERQSEQWSR
QERCFQFGRLGASLHNQMEKDEQKRIEKTAKQRLAALKSNDEEAYLKLLDQTKDTRITQL
LRQTNSFLDSLSEAVRAQQNEAKILHGEEVQPITDEEREKTDYYEVAHRIKEKIDKQPSI
LVGGTLKEYQLRGLEWMVSLYNNHLNGILADEMGLGKTIQSISLITYLYEVKKDIGPFLV
IVPLSTITNWTLEFEKWAPSLNTIIYKGTPNQRHSLQHQIRVGNFDVLLTTYEYIIKDKS
LLSKHDWAHMIIDEGHRMKNAQSKLSFTISHYYRTRNRLILTGTPLQNNLPELWALLNFV
LPKIFNSAKTFEDWFNTPFANTGTQEKLELTEEETLLIIRRLHKVLRPFLLRRLKKEVEK
DLPDKVEKVIKCKLSGLQQQLYQQMLKHNALFVGAGTEGATKGGIKGLNNKIMQLRKICN
HPFVFDEVEGVVNPSRGNSDLLFRVAGKFELLDRVLPKFKASGHRVLMFFQMTQVMDIME
DFLRMKDLKYMRLDGSTKTEERTEMLNAFNAPDSDYFCFLLSTRAGGLGLNLQTADTVII
FDTDWNPHQDLQAQDRAHRIGQKNEVRILRLITTDSVEEVILERAMQKLDIDGKVIQAGK
FDNKSTAEEQEAFLRRLIESETNRDDDDKAELDDDELNDTLARSADEKILFDKIDKERMN
QERADAKAQGLRVPPPRLIQLDELPKVFREDIEEHFKKEDSEPLGRIRQKKRVYYDDGLT
EEQFLEAVEDDNMSLEDAIKKRREARERRRLRQ

Sequence of entity 4 (N), FASTA

>6VZG_4 Regulator of Ty1 transposition protein 102 (chains N)
MDPQTLITKANKVSYYGNPTSKESWRYDWYQPSKVSSNVQQPQQQLGDMENNLEKYPFRY
KTWLRNQEDEKNLQRESCEDILDLKEFDRRILKKSLMTSHTKGDTSKATGAPSANQGDEA
LSVDDIRGAVGNSEAIPGLSAGVNNDNTKESKDVKMN

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Structural insights into assembly and function of the RSC chromatin remodeling complex. Baker, R.W., Reimer, J.M., Carman, P.J. et al. Nat Struct Mol Biol (2021) 28:71-80. DOI 10.1038/s41594-020-00528-8 · 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
5TGC 3.25 Å, Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP
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
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

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