7R6Q: ATP-dependent RNA helicase HAS1

Name: PDB 7R6Q: State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model
Published: 2022-11-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

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
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
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

About this viewer

MolViewer shows 7R6Q 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.