7R7A image
Deposition Date 2021-06-24
Release Date 2022-11-09
Last Version Date 2024-06-05
Entry Detail
PDB ID:
7R7A
Keywords:
RIBOSOME
Title:
State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
Biological Source:
Source Organism:
Saccharomyces cerevisiae BY4741 (Taxon ID: 1247190)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.04 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7R7A validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA gene and internal transcribed spacer 2
Chain IDs:ZA (auth: 6)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal subunit assembly/export protein LOC1
Gene (Uniprot):LOC1
Chain IDs:C (auth: 7)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P43586
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 2
Gene (Uniprot):NOC2
Chain IDs:LA (auth: 8)
Chain Length:710
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P39744 Pfam ID:PF03715
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BRX1
Gene (Uniprot):BRX1
Chain IDs:D (auth: A)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q08235 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:E (auth: B)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P14126 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:F (auth: C)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase HAS1
Gene (Uniprot):HAS1
Chain IDs:AB (auth: D)
Chain Length:505
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q03532 Pfam ID:PF00270, PF00271, PF13959
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:G (auth: E)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q02326 Pfam ID:PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:H (auth: F)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:QA (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P17076 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:I (auth: H)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05738 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex-associated protein 3
Gene (Uniprot):NOC3
Chain IDs:MA (auth: I)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q07896 Pfam ID:PF07540, PF03914
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein EBP2
Gene (Uniprot):EBP2
Chain IDs:J
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P36049 Pfam ID:PF05890
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome-interacting protein CIC1
Gene (Uniprot):CIC1
Chain IDs:NA (auth: K)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P38779 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:K (auth: L)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12690 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:L (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:M (auth: N)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05748 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:N (auth: O)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P26784 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:O (auth: P)
Chain Length:460
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05740 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:P (auth: Q)
Chain Length:618
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX49 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:PA (auth: R)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX82 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:Q (auth: S)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX23 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:R (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q02753 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:SA (auth: U)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05749 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:OA (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX41 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor MRT4
Gene (Uniprot):MRT4
Chain IDs:S (auth: W)
Chain Length:841
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P33201 Pfam ID:PF00466, PF17777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:T (auth: X)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:U (auth: Y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:RA (auth: Z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0C2H6 Pfam ID:PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Chain IDs:DB (auth: a)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX43 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):NOG1
Chain IDs:V (auth: b)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q02892 Pfam ID:PF17835, PF06858, PF08155
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:TA (auth: c)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P14120 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:W (auth: d)
Chain Length:505
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0C2H8 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:X (auth: e)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P38061 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:Y (auth: f)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05744 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:UA (auth: g)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P87262 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:Z (auth: h)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX84 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:AA (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05745 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:BA (auth: j)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P49166 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:VA (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P49167 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosome subunit biogenesis protein NIP7
Gene (Uniprot):NIP7
Chain IDs:CA (auth: l)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q08962 Pfam ID:PF17833, PF03657
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein ERB1
Gene (Uniprot):ERB1
Chain IDs:DA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q04660 Pfam ID:PF08145, PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Gene (Uniprot):NOP7
Chain IDs:WA (auth: n)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53261 Pfam ID:PF06732, PF16589
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein 15
Gene (Uniprot):NOP15
Chain IDs:BB (auth: o)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53927 Pfam ID:PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:YTM1 isoform 1
Chain IDs:XA (auth: p)
Chain Length:460
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12024 Pfam ID:PF08154, PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:25S rRNA (cytosine(2870)-C(5))-methyltransferase
Gene (Uniprot):NOP2
Chain IDs:EA (auth: q)
Chain Length:618
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40991 Pfam ID:PF01189 EC:2.1.1.310
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2
Chain IDs:FA (auth: r)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40078 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nuclear GTP-binding protein NUG1
Gene (Uniprot):NUG1
Chain IDs:GA (auth: s)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40010 Pfam ID:PF08701, PF01926
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP7
Gene (Uniprot):RLP7
Chain IDs:YA (auth: t)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40693 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:HA (auth: u)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q07915 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 16
Gene (Uniprot):NOP16
Chain IDs:IA (auth: v)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40007 Pfam ID:PF09420
Protein Blast
Polymer Type:polypeptide(L)
Molecule:27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
Gene (Uniprot):SPB1
Chain IDs:CB (auth: w)
Chain Length:841
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P25582 Pfam ID:PF01728, PF11861, PF07780 EC:2.1.1.167
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent rRNA helicase SPB4
Chain IDs:EB (auth: x)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P25808 Pfam ID:PF00270, PF00271, PF13959
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:JA (auth: y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12522 Pfam ID:PF01912
Protein Blast
Polymer Type:polypeptide(L)
Molecule:UPF0642 protein YBL028C
Gene (Uniprot):YBL0423
Chain IDs:KA (auth: z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P38202 Pfam ID:PF10338
Ligand Molecules
ZN
Primary Citation
Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
Nat.Struct.Mol.Biol. 29 1228 1238 (2022)
PMID: 36482249 DOI: 10.1038/s41594-022-00874-9

Abstact

DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.

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Protein

Chemical

Disease

Primary Citation of related structures
7NAC
7NAD
7NAF
7R6K
7R6Q
7R72