6VZ4: Sth1-Arp7-Arp9-Rtt102
Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state. Determined by electron microscopy at 3.9 Å resolution. Released 2 Dec 2020.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organisms
- Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 14
- Atoms
- 23,950
- Mol. weight
- 444.63 kDa
- Ligands
- ATP, BEF, ADP, MG
- Released
- 2 Dec 2020
Explore 6VZ4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6VZ4 contains 121 α-helices and 81 β-strands across 12 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-57 | 12 | |
| α-helix | 65-77 | 13 | |
| β-strand | 84-85 | 2 | 1 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 2 |
| α-helix | 122-132 | 11 | |
Chain B: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-42 | 11 | |
| β-strand | 46-47 | 2 | 2 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 83 | 1 | |
| α-helix | 84-93 | 10 | |
| β-strand | 97-99 | 3 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 6 |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| β-strand | 54-55 | 2 | 5 |
| α-helix | 57-84 | 28 | |
| β-strand | 89-90 | 2 | 4 |
| α-helix | 92-100 | 9 | |
| α-helix | 105-124 | 20 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-57 | 12 | |
| α-helix | 65-76 | 12 | |
| β-strand | 84-85 | 2 | 7 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 8 |
| α-helix | 122-132 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 8 |
| α-helix | 50-76 | 27 | |
| β-strand | 81-82 | 2 | 7 |
| α-helix | 83 | 1 | |
| α-helix | 84-93 | 10 | |
| β-strand | 97-99 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 3 |
| α-helix | 114-116 | 3 | |
Chain K: 36 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 317-340 | 24 | |
| α-helix | 344-383 | 40 | |
| α-helix | 393-422 | 30 | |
| α-helix | 448-451 | 4 | |
| α-helix | 461-462 | 2 | |
| α-helix | 472-486 | 15 | |
| β-strand | 491-493 | 3 | 11 |
| α-helix | 501-515 | 15 | |
| β-strand | 522-525 | 4 | 11 |
| α-helix | 528-530 | 3 | |
| α-helix | 531-541 | 11 | |
| β-strand | 547-549 | 3 | 11 |
| α-helix | 554-563 | 10 | |
| β-strand | 571-574 | 4 | 11 |
| α-helix | 576-581 | 6 | |
| α-helix | 583-586 | 4 | |
| β-strand | 591 | 1 | 12 |
| β-strand | 593-596 | 4 | 11 |
| α-helix | 599-602 | 4 | |
| α-helix | 608-614 | 7 | |
| β-strand | 619 | 1 | 12 |
| β-strand | 622-625 | 4 | 11 |
| α-helix | 635-644 | 10 | |
| α-helix | 655-658 | 4 | |
| α-helix | 677-681 | 5 | |
| α-helix | 682-690 | 9 | |
| β-strand | 694-695 | 2 | 11 |
| α-helix | 699-702 | 4 | |
| β-strand | 714-716 | 3 | 13 |
| α-helix | 717-719 | 3 | |
| α-helix | 720-732 | 13 | |
| α-helix | 754-764 | 11 | |
| α-helix | 766-768 | 3 | |
| α-helix | 770-776 | 7 | |
| α-helix | 785-788 | 4 | |
| α-helix | 791-805 | 15 | |
| β-strand | 810-814 | 5 | 14 |
| α-helix | 818-829 | 12 | |
| β-strand | 834-837 | 4 | 14 |
| α-helix | 843-854 | 12 | |
| β-strand | 862-866 | 5 | 14 |
| α-helix | 867-870 | 4 | |
| β-strand | 881-884 | 4 | 14 |
| α-helix | 892-899 | 8 | |
| α-helix | 909-910 | 2 | |
| β-strand | 911-914 | 4 | 14 |
| β-strand | 915-917 | 3 | 13 |
| α-helix | 921-932 | 12 | |
| α-helix | 934-942 | 9 | |
| α-helix | 978-984 | 7 | |
| α-helix | 989-1004 | 16 | |
| α-helix | 1045-1051 | 7 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3 | A, E | protein | 136 | Xenopus laevis | Q92133 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B | D, H | protein | 125 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (185-mer) | I | DNA | 185 | synthetic construct | |
| DNA (185-mer) | J | DNA | 185 | synthetic construct | |
| Nuclear protein STH1/NPS1 | K | protein | 813 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32597 |
| Actin-related protein 7 | L | protein | 477 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12406 |
| Actin-like protein ARP9 | M | protein | 467 | Saccharomyces cerevisiae | Q05123 |
| Regulator of Ty1 transposition protein 102 | N | protein | 157 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53330 |
Sequence of entity 1 (A, E), FASTA
>6VZ4_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCGIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6VZ4_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6VZ4_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>6VZ4_4 Histone H2B (chains D, H)
MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSA
Sequence of entity 5 (I), FASTA
>6VZ4_5 DNA (185-MER) (chains I)
ATCACCCTAGGTCTCTGATGCTCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGACACGCGGTGAACA
GCGAT
Sequence of entity 6 (J), FASTA
>6VZ4_6 DNA (185-MER) (chains J)
ATCGCTGTTCACCGCGAGTCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGT
AATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGA
GCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAGCATCAGAGACCTAGG
GTGAT
Sequence of entity 7 (K), FASTA
>6VZ4_7 Nuclear protein STH1/NPS1 (chains K)
MGSSHHHHHHSQDPNSVRLAEELERQQLLEKRKKERNLHLQKINSIIDFIKERQSEQWSR
QERCFQFGRLGASLHNQMEKDEQKRIERTAKQRLAALKSNDEEAYLKLLDQTKDTRITQL
LRQTNSFLDSLSEAVRAQQNEAKILHGEEVQPITDEEREKTDYYEVAHRIKEKIDKQPSI
LVGGTLKEYQLRGLEWMVSLYNNHLNGILADEMGLGKTIQSISLITYLYEVKKDIGPFLV
IVPLSTITNWTLEFEKWAPSLNTIIYKGTPNQRHSLQHQIRVGNFDVLLTTYEYIIKDKS
LLSKHDWAHMIIDEGHRMKNAQSKLSFTISHYYRTRNRLILTGTPLQNNLPELWALLNFV
LPKIFNSAKTFEDWFNTPFANTGTQEKLELTEEETLLIIRRLHKVLRPFLLRRLKKEVEK
DLPDKVEKVIKCKLSGLQQQLYQQMLKHNALFVGAGTEGATKGGIKGLNNKIMQLRKICN
HPFVFDEVEGVVNPSRGNSDLLFRVAGKFELLDRVLPKFKASGHRVLMFFQMTQVMDIME
DFLRMKDLKYMRLDGSTKTEERTEMLNAFNAPDSDYFCFLLSTRAGGLGLNLQTADTVII
FDTDWNPHQDLQAQDRAHRIGQKNEVRILRLITTDSVEEVILERAMQKLDIDGKVIQAGK
FDNKSTAEEQEAFLRRLIESETNRDDDDKAELDDDELNDTLARSADEKILFDKIDKERMN
QERADAKAQGLRVPPPRLIQLDELPKVFREDIEEHFKKEDSEPLGRIRQKKRVYYDDGLT
EEQFLEAVEDDNMSLEDAIKKRREARERRRLRQ
Sequence of entity 8 (L), FASTA
>6VZ4_8 Actin-related protein 7 (chains L)
MTLNRKCVVIHNGSHRTVAGFSNVELPQCIIPSSYIKRTDEGGEAEFIFGTYNMIDAAAE
KRNGDEVYTLVDSQGLPYNWDALEMQWRYLYDTQLKVSPEELPLVITMPATNGKPDMAIL
ERYYELAFDKLNVPVFQIVIEPLAIALSMGKSSAFVIDIGASGCNVTPIIDGIVVKNAVV
RSKFGGDFLDFQVHERLAPLIKEENDMENMADEQKRSTDVWYEASTWIQQFKSTMLQVSE
KDLFELERYYKEQADIYAKQQEQLKQMDQQLQYTALTGSPNNPLVQKKNFLFKPLNKTLT
LDLKECYQFAEYLFKPQLISDKFSPEDGLGPLMAKSVKKAGASINSMKANTSTNPNGLGT
SHINTNVGDNNSTASSSNISPEQVYSLLLTNVIITGSTSLIEGMEQRIIKELSIRFPQYK
LTTFANQVMMDRKIQGWLGALTMANLPSWSLGKWYSKEDYETLKRDRKQSQATNATN
Sequence of entity 9 (M), FASTA
>6VZ4_9 Actin-like protein ARP9 (chains M)
MAPFRQDSILIIYPRSQTTLVQFGLNEETFTVPELEIPTQIYRTTRQDGSYTYHSTNKDN
KAELIKPIQNGEIIDISAFTQFLRLIFVSILSDRANKNQDAFEAELSNIPLLLITHHSWS
QSDLEIITQYVFESLEINNLIQLPASLAATYSMISLQNCCIIDVGTHHTDIIPIVDYAQL
DHLVSSIPMGGQSINDSLKKLLPQWDDDQIESLKKSPIFEVLSDDAKKLSSFDFGNENED
EDEGTLNVAEIITSGRDTREVLEERERGQKVKNVKNSDLEFNTFWDEKGNEIKVGKQRFQ
GCNNLIKNISNRVGLTLDNIDDINKAKAVWENIIIVGGTTSISGFKEALLGQLLKDHLII
EPEEEKSKREEEAKSVLPAATKKKSKFMTNSTAFVPTIEYVQCPTVIKLAKYPDYFPEWK
KSGYSEIIFLGAQIVSKQIFTHPKDTFYITREKYNMKGPAALWDVQF
Sequence of entity 10 (N), FASTA
>6VZ4_10 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 |
| BEF | Beryllium trifluoride ion | Be F3 | 1 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| MG | Magnesium ion | Mg | 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 Q92133 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3MEA 1.26 Å, Crystal structure of the SGF29 in complex with H3K4me3
- 3MEU 1.28 Å, Crystal structure of SGF29 in complex with H3R2me2sK4me3
- 3ME9 1.37 Å, Crystal structure of SGF29 in complex with H3K4me3 peptide
- 3H91 1.5 Å, Crystal structure of the complex of human chromobox homolog 2 (CBX2) and H3K27 peptide
- 3O7A 1.67 Å, Crystal structure of PHF13 in complex with H3K4me3
- 3MEV 1.83 Å, Crystal structure of SGF29 in complex with R2AK4me3
- 3GL6 1.9 Å, Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide
- 4HSU 1.99 Å, Crystal structure of LSD2-NPAC with H3(1-26)in space group P21
- 3MET 2.0 Å, Crystal structure of SGF29 in complex with H3K4me2
- 7CRQ 3.15 Å, NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
- 7CRP 3.2 Å, NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)
- 7UNK 3.45 Å, Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex
Browse structure collections
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