7R6Q: ATP-dependent RNA helicase HAS1
State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model. Determined by electron microscopy at 2.98 Å resolution. Released 9 Nov 2022.
- Method
- Electron microscopy
- Resolution
- 2.98 Å
- Organism
- Saccharomyces cerevisiae BY4741
- Chains
- 19
- Atoms
- 29,033
- Mol. weight
- 610.35 kDa
- Released
- 9 Nov 2022
Explore 7R6Q in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7R6Q contains 137 α-helices and 79 β-strands across 16 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 D: 24 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 43 | 1 | 1 |
| α-helix | 44-46 | 3 | |
| α-helix | 51-60 | 10 | |
| β-strand | 64 | 1 | 1 |
| α-helix | 67-70 | 4 | |
| α-helix | 73-77 | 5 | |
| β-strand | 82-84 | 3 | 2 |
| α-helix | 86-87 | 2 | |
| α-helix | 92-107 | 16 | |
| α-helix | 111-113 | 3 | |
| β-strand | 117-120 | 4 | 2 |
| α-helix | 124-137 | 14 | |
| β-strand | 145-148 | 4 | 2 |
| α-helix | 154-163 | 10 | |
| β-strand | 167-170 | 4 | 2 |
| α-helix | 172-181 | 10 | |
| β-strand | 192-195 | 4 | 2 |
| α-helix | 198-204 | 7 | |
| α-helix | 207-216 | 10 | |
| β-strand | 223-227 | 5 | 2 |
| α-helix | 233-240 | 8 | |
| β-strand | 248-249 | 2 | 2 |
| β-strand | 266-270 | 5 | 3 |
| α-helix | 276-286 | 11 | |
| β-strand | 291-296 | 6 | 4 |
| α-helix | 299-311 | 13 | |
| β-strand | 316-319 | 4 | 4 |
| α-helix | 325-335 | 11 | |
| β-strand | 341-346 | 6 | 4 |
| β-strand | 360-363 | 4 | 4 |
| α-helix | 370-383 | 14 | |
| β-strand | 389-392 | 4 | 4 |
| β-strand | 393-394 | 2 | 3 |
| α-helix | 401-407 | 7 | |
| β-strand | 412-415 | 4 | 3 |
| β-strand | 416 | 1 | 5 |
| α-helix | 419-421 | 3 | |
| α-helix | 426-435 | 10 | |
| α-helix | 437-455 | 19 | |
| α-helix | 465-467 | 3 | |
| α-helix | 470-475 | 6 | |
| α-helix | 482-484 | 3 | |
Chain g: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-39 | 5 | |
| α-helix | 59-64 | 6 | |
| α-helix | 67-69 | 3 | |
Chain G: 19 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 48-51 | 4 | |
| α-helix | 54-68 | 15 | |
| β-strand | 71 | 1 | 6 |
| α-helix | 73-76 | 4 | |
| α-helix | 77-79 | 3 | |
| α-helix | 84-94 | 11 | |
| α-helix | 95-97 | 3 | |
| α-helix | 98-101 | 4 | |
| α-helix | 102-118 | 17 | |
| α-helix | 127-129 | 3 | |
| β-strand | 133-134 | 2 | 7 |
| α-helix | 136-144 | 9 | |
| β-strand | 150-154 | 5 | 7 |
| α-helix | 160-162 | 3 | |
| α-helix | 165-172 | 8 | |
| β-strand | 177-180 | 4 | 7 |
| α-helix | 183-188 | 6 | |
| β-strand | 197-200 | 4 | 7 |
| α-helix | 205-207 | 3 | |
| α-helix | 208-218 | 11 | |
| α-helix | 219-223 | 5 | |
| α-helix | 224-226 | 3 | |
| β-strand | 234 | 1 | 6 |
| α-helix | 237-239 | 3 | |
| α-helix | 240-246 | 7 | |
Chain h: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 102-109 | 8 | |
Chain i: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-30 | 3 | |
| α-helix | 35-48 | 14 | |
| α-helix | 52-62 | 11 | |
| α-helix | 82-98 | 17 | |
Chain K: 14 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-48 | 15 | |
| β-strand | 65 | 1 | 5 |
| α-helix | 70-73 | 4 | |
| β-strand | 77-84 | 8 | 8 |
| α-helix | 96 | 1 | |
| β-strand | 97-101 | 5 | 9 |
| α-helix | 107-113 | 7 | |
| β-strand | 123-127 | 5 | 10 |
| α-helix | 137-144 | 8 | |
| α-helix | 145-147 | 3 | |
| β-strand | 153-156 | 4 | 10 |
| α-helix | 167-174 | 8 | |
| β-strand | 179-183 | 5 | 10 |
| α-helix | 187-189 | 3 | |
| α-helix | 190-194 | 5 | |
| α-helix | 198-200 | 3 | |
| β-strand | 207-209 | 3 | 10 |
| β-strand | 212-213 | 2 | 11 |
| β-strand | 216-217 | 2 | 11 |
| α-helix | 219-232 | 14 | |
| β-strand | 233-237 | 5 | 9 |
| β-strand | 243-250 | 8 | 8 |
| α-helix | 256-273 | 18 | |
| β-strand | 276-283 | 8 | 8 |
| β-strand | 289-293 | 5 | 8 |
| α-helix | 295-300 | 6 | |
| α-helix | 328-334 | 7 | |
Chain L: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 77-82 | 6 | |
| α-helix | 106-116 | 11 | |
Chain m: 13 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 241-243 | 3 | |
| α-helix | 259-262 | 4 | |
| α-helix | 263-265 | 3 | |
| α-helix | 271-284 | 14 | |
| α-helix | 291-297 | 7 | |
| α-helix | 330-332 | 3 | |
| α-helix | 334-336 | 3 | |
| β-strand | 337 | 1 | 14 |
| α-helix | 342-344 | 3 | |
| α-helix | 346-347 | 2 | |
| α-helix | 348-356 | 9 | |
| α-helix | 377-380 | 4 | |
| α-helix | 384-396 | 13 | |
| β-strand | 399-405 | 7 | 20 |
| α-helix | 409-412 | 4 | |
8 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 |
|---|
| ITS-2 | 6 | RNA | 87 | Saccharomyces cerevisiae BY4741 | |
| ATP-dependent RNA helicase HAS1 | D | protein | 505 | Saccharomyces cerevisiae BY4741 | Q03532 (AlphaFold model) |
| 60S ribosomal protein L8-A | G | protein | 256 | Saccharomyces cerevisiae BY4741 | P17076 (AlphaFold model) |
| Proteasome-interacting protein CIC1 | K | protein | 376 | Saccharomyces cerevisiae BY4741 | P38779 (AlphaFold model) |
| Pescadillo homolog | n | protein | 605 | Saccharomyces cerevisiae BY4741 | P53261 (AlphaFold model) |
| Ribosome biogenesis protein 15 | o | protein | 220 | Saccharomyces cerevisiae BY4741 | P53927 |
| Ribosome biogenesis protein RLP7 | t | protein | 322 | Saccharomyces cerevisiae BY4741 | P40693 |
| 60S ribosomal protein L25 | X | protein | 142 | Saccharomyces cerevisiae BY4741 | P04456 |
| Ribosome biogenesis protein ERB1 | m | protein | 807 | Saccharomyces cerevisiae BY4741 | Q04660 |
| 25S rRNA | 1 | RNA | 295 | Saccharomyces cerevisiae BY4741 | |
| Nucleolar protein 16 | v | protein | 231 | Saccharomyces cerevisiae BY4741 | P40007 |
| 5.8S rRNA | 2 | RNA | 57 | Saccharomyces cerevisiae BY4741 | |
7 more molecules are not listed.
Sequence of entity 1 (6), FASTA
>7R6Q_1 ITS-2 (chains 6)
CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCU
GGCCUUUAGGCGAACAAUGUUCUUAAA
Sequence of entity 2 (D), FASTA
>7R6Q_2 ATP-dependent RNA helicase HAS1 (chains D)
MATPSNKRSRDSESTEEPVVDEKSTSKQNNAAPEGEQTTCVEKFEELKLSQPTLKAIEKM
GFTTMTSVQARTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIELLHSLKFKPRNGTGIIVI
TPTRELALQIFGVARELMEFHSQTFGIVIGGANRRQEAEKLMKGVNMLIATPGRLLDHLQ
NTKGFVFKNLKALIIDEADRILEIGFEDEMRQIIKILPNEDRQSMLFSATQTTKVEDLAR
ISLRPGPLFINVVPETDNSTADGLEQGYVVCDSDKRFLLLFSFLKRNQKKKIIVFLSSCN
SVKYYAELLNYIDLPVLELHGKQKQQKRTNTFFEFCNAERGILICTDVAARGLDIPAVDW
IIQFDPPDDPRDYIHRVGRTARGTKGKGKSLMFLTPNELGFLRYLKASKVPLNEYEFPEN
KIANVQSQLEKLIKSNYYLHQTAKDGYRSYLQAYASHSLKTVYQIDKLDLAKVAKSYGFP
VPPKVNITIGASGKTPNTKRRKTHK
Sequence of entity 3 (G), FASTA
>7R6Q_3 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA
Sequence of entity 4 (K), FASTA
>7R6Q_4 Proteasome-interacting protein CIC1 (chains K)
MAKKSNSKKSTPVSTPSKEKKKVIEKKSSTAIPRERVIKAVNELIKFTSKPQDENNEEGN
NGKKNLLEDDEEELKKDLQLIVVNNKSFTGTSKSFKLKLLNVKHSFYKPWKEASATAVKD
FKVLLILKDSDIKKVSEDDLFDQLDSEGIKVDEIICGKDLKTVYKAYEARNAFISQFSLI
LADDSIVTSLPKLMGGKAYNKVETTPISIRTHANKEFSLTTLTNNIKKVYMNQLPVKLPR
GTTLNVHLGNLEWLRPEEFVDNVELISEQLIKAYQIRSIFIKTNRSPVLPLYYNQDVLDE
LEAKKDKIEETHEDDMVTIDGVQVHLSTFNKGLMEIANPSELGSIFSKQINNAKKRSSSE
LEKESSESEAVKKAKS
Sequence of entity 5 (n), FASTA
>7R6Q_5 Pescadillo homolog (chains n)
MRIKKKNTRGNARNFITRSQAVRKLQVSLADFRRLCIFKGIYPREPRNKKKANKGSTAPT
TFYYAKDIQYLMHEPVLAKFREHKTFARKLTRALGRGEVSSAKRLEENRDSYTLDHIIKE
RYPSFPDAIRDIDDALNMLFLFSNLPSTNQVSSKIINDAQKICNQWLAYVAKERLVRKVF
VSIKGVYYQANIKGEEVRWLVPFKFPENIPSDVDFRIMLTFLEFYSTLLHFVLYKLYTDS
GLIYPPKLDLKKDKIISGLSSYILESRQEDSLLKLDPTEIEEDVKVESLDASTLKSALNA
DEANTDETEKEEEQEKKQEKEQEKEQNEETELDTFEDNNKNKGDILIQPSKYDSPVASLF
SAFVFYVSREVPIDILEFLILSCGGNVISEAAMDQIENKKDIDMSKVTHQIVDRPVLKNK
VAGRTYIQPQWIFDCINKGELVPANKYLPGEALPPHLSPWGDAIGYDPTAPVEEGEEEES
ESESESEDQVEEEDQEVVAGEEDDDDDEELQAQKELELEAQGIKYSETSEADKDVNKSKN
KKRKVDEEEEEKKLKMIMMSNKQKKLYKKMKYSNAKKEEQAENLKKKKKQIAKQKAKLNK
LDSKK
Sequence of entity 6 (o), FASTA
>7R6Q_6 Ribosome biogenesis protein 15 (chains o)
MVKSTSKTSTKETVTKQPTEEKPIQEKEELALETSSSSSDEEDEKDEDEIEGLAASDDEQ
SGTHKIKRLNPKKQANEKKSKDKKTLEEYSGIIYVSRLPHGFHEKELSKYFAQFGDLKEV
RLARNKKTGNSRHYGFLEFVNKEDAMIAQESMNNYLLMGHLLQVRVLPKGAKIEKLYKYK
KRVLVEKGITKPVKQLKDNMKQKHEERIKKLAKSGIEFKW
Sequence of entity 7 (t), FASTA
>7R6Q_7 Ribosome biogenesis protein RLP7 (chains t)
MSSTQDSKAQTLNSNPEILLRKRRNADRTRIERQELAKKKREEQIKKKRSNKNKFVRAES
IVAKTLATSREKERIKRVSILEDKKAKNETQHIASGKDFILKITEKANGAEENSVDLEET
EEEEDDGLIREKTTYDGKPALLFIVRVRGPLAVNIPNKAFKILSLLRLVETNTGVFVKLT
KNVYPLLKVIAPYVVIGKPSLSSIRSLIQKRGRIIYKGENEAEPHEIVLNDNNIVEEQLG
DHGIICVEDIIHEIATMGESFSVCNFFLQPFKLNREVSGFGSLNRLRKIKQREAESRTRQ
FSNAATAPVIEVDIDSLLAKLN
Sequence of entity 8 (X), FASTA
>7R6Q_8 60S ribosomal protein L25 (chains X)
MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSY
KVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI
Sequence of entity 9 (m), FASTA
>7R6Q_9 Ribosome biogenesis protein ERB1 (chains m)
MMAKNNKTTEAKMSKKRAASEESDVEEDEDKLLSVDGLIDAEASESDEDDDEYESAVEEK
ESSSDKEAQDDSDDDSDAELNKLLAEEEGDGEEDYDSSEFSDDTTSLTDRLSGVKLQTIV
DPNIYSKYADGSDRIIKPEINPVYDSDDSDAETQNTIGNIPLSAYDEMPHIGYDINGKRI
MRPAKGSALDQLLDSIELPEGWTGLLDKNSGSSLNLTKEELELISKIQRNEQTDDSINPY
EPLIDWFTRHEEVMPLTAVPEPKRRFVPSKNEAKRVMKIVRAIREGRIIPPKKLKEMKEK
EKIENYQYDLWGDSTETNDHVMHLRAPKLPPPTNEESYNPPEEYLLSPEEKEAWENTEYS
ERERNFIPQKYSALRKVPGYGESIRERFERSLDLYLAPRVRKNKLNIDPNSLIPELPSPK
DLRPFPIRCSTIYAGHKGKVRTLSIDPSGLWLATGSDDGTVRVWEILTGREVYRTTLIDD
EENPDYHIECIEWNPDANNGILAVAVGENIHLIVPPIFGYDIENNGKTKIEDGFGYDTFG
TVKKSNLEVNENGDGDEDGENESAKNAVKKQVAQWNKPSQKQLEKDICITISCKKTVKKL
SWHRKGDYFVTVQPDSGNTSVLIHQVSKHLTQSPFKKSKGIIMDAKFHPFKPQLFVCSQR
YVRIYDLSQQILVKKLLPGARWLSKIDIHPRGDNLIASSFDKRVLWHDLDLASTPYKTLR
YHEKAVRSVNFHKKLPLFSSAADDGTIHVFHATVYDDMMKNPMIVPLKKLTGHKVINSLG
VLDAIWHPREAWLFSAGADNTARLWTT
Sequence of entity 10 (1), FASTA
>7R6Q_10 25S rRNA (chains 1)
GUUUGACCUCAAAUCAGGUAGGAAAGCUCAAAUUUGAAAUCUGGUACCUUCGGUGCCCGA
GUUGUAAUUUGGAGAGGGCAACUUUGGGUUUGUAAAGUGCCUUCGAAGAGUCGCUAAGUG
GGUGGUCCAUCUAAAGCUAAUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAGGC
CUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCUUCCGGAACCUGGAUAUGGAUUCUU
CACACUGAAUGUGGAGAAAAUCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUA
Sequence of entity 11 (v), FASTA
>7R6Q_11 Nucleolar protein 16 (chains v)
MTSVRKRKMNRSSVGKATRRNKDKQRKINIQSNPIIAANWDYSLTMAQNYKKLGLRAKLQ
TPAGGKEADLSKVVKRIPLTKPVLDEDEDEDEGEDEQNDYNAATVELDENEIPEGGARIQ
RDKNGDVVRVVYGKKKNFDADEDVNEIKARDTTEETEVVKKLEELASRPVIRKERSQSER
EEEWLEKLYKKHGDDYKKMFFDKKLNIYQQSEGDLKRRLLRWKKRNGIASK
Sequence of entity 12 (2), FASTA
>7R6Q_12 5.8S rRNA (chains 2)
UGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Primary citation
Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Cruz, V.E., Sekulski, K., Peddada, N. et al. Nat Struct Mol Biol (2022) 29:1228-1238. DOI 10.1038/s41594-022-00874-9 · PubMed
Other PDB entries of the same protein (UniProt Q03532 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8V83 2.53 Å, 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
- 8V87 2.66 Å, 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
- 8V84 2.7 Å, 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
- 11AA 2.78 Å, Yeast co-transcriptional pre-60S assembly intermediate Nop12 RNP
- 7NAC 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
- 7R7A 3.04 Å, State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
- 6EM3 3.2 Å, State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of…
- 6ELZ 3.3 Å, State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S…
- 7OHX 3.3 Å, Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34…
- 7OHW 3.5 Å, Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25…
- 6EM1 3.6 Å, State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S…
- 5Z3G 3.65 Å, Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP)
Browse structure collections
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