7MQA image
Deposition Date 2021-05-05
Release Date 2021-09-22
Last Version Date 2024-10-30
Entry Detail
PDB ID:
7MQA
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the human SSU processome, state post-A1
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7MQA validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:5'ETS rRNA
Chain IDs:A (auth: L0)
Chain Length:3617
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:B (auth: L1)
Chain Length:1872
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:C (auth: L2)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Chain IDs:D (auth: L3)
Chain Length:116
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62269 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:E (auth: L4)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62701 Pfam ID:PF08071, PF00900, PF00467, PF16121
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:F (auth: L5)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46782 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:G (auth: L6)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62753 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:H (auth: L7)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62081 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:I (auth: L8)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62241 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:J (auth: L9)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46781 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:K (auth: LA)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P25398 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:L (auth: LC)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62249 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:M (auth: LD)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62280 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:N (auth: LF)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62847 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:O (auth: LG)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62857 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein 75
Gene (Uniprot):WDR75
Chain IDs:P (auth: LH)
Chain Length:830
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IWA0 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 11
Chain IDs:Q (auth: LI)
Chain Length:678
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H8H0 Pfam ID:PF08168, PF20998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 15 homolog
Gene (Uniprot):UTP15
Chain IDs:R (auth: LJ)
Chain Length:518
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TED0 Pfam ID:PF00400, PF09384
Protein Blast
Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein 43
Gene (Uniprot):WDR43
Chain IDs:S (auth: LK), T (auth: LL)
Chain Length:677
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q15061 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:HEAT repeat-containing protein 1
Gene (Uniprot):HEATR1
Chain IDs:U (auth: LM)
Chain Length:2144
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H583 Pfam ID:PF12397, PF08146
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 4 homolog
Gene (Uniprot):UTP4
Chain IDs:V (auth: LN)
Chain Length:686
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q969X6 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Periodic tryptophan protein 2 homolog
Gene (Uniprot):PWP2
Chain IDs:W (auth: LO)
Chain Length:919
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15269 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 6 homolog
Gene (Uniprot):UTP6
Chain IDs:X (auth: LP)
Chain Length:597
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NYH9 Pfam ID:PF08640
Protein Blast
Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein 3
Gene (Uniprot):WDR3
Chain IDs:Y (auth: LQ)
Chain Length:943
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UNX4 Pfam ID:PF12894, PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transducin beta-like protein 3
Gene (Uniprot):TBL3
Chain IDs:Z (auth: LR)
Chain Length:808
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q12788 Pfam ID:PF00400, PF08625
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 18 homolog
Gene (Uniprot):UTP18
Chain IDs:AA (auth: LS)
Chain Length:556
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y5J1 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein 36
Gene (Uniprot):WDR36
Chain IDs:BA (auth: LT)
Chain Length:951
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8NI36 Pfam ID:PF00400, PF12894, PF04192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DDB1- and CUL4-associated factor 13
Gene (Uniprot):DCAF13
Chain IDs:CA (auth: LU)
Chain Length:445
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NV06 Pfam ID:PF00400, PF04158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein 46
Gene (Uniprot):WDR46
Chain IDs:DA (auth: LW)
Chain Length:610
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15213 Pfam ID:PF00400, PF08149
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Active regulator of SIRT1
Gene (Uniprot):RPS19BP1
Chain IDs:EA (auth: LY)
Chain Length:136
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q86WX3 Pfam ID:PF15684
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein IMP3
Gene (Uniprot):IMP3
Chain IDs:FA (auth: LZ)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NV31 Pfam ID:PF00163, PF01479
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein MPP10
Chain IDs:GA (auth: NA)
Chain Length:681
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Something about silencing protein 10
Gene (Uniprot):UTP3
Chain IDs:HA (auth: NB)
Chain Length:479
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NQZ2 Pfam ID:PF04000, PF09368
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 7
Gene (Uniprot):NOL7
Chain IDs:IA (auth: ND)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UMY1 Pfam ID:PF08157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:JA (auth: NF)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62277 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:KA (auth: NG)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62263 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 6
Gene (Uniprot):NOL6
Chain IDs:LA (auth: NH)
Chain Length:1146
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H6R4 Pfam ID:PF03813, PF17403, PF17404, PF17405, PF17406, PF17407
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing protein 7 homolog A
Gene (Uniprot):RRP7A
Chain IDs:MA (auth: NI)
Chain Length:280
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3A4 Pfam ID:PF17799, PF12923
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable dimethyladenosine transferase
Gene (Uniprot):DIMT1
Chain IDs:NA (auth: NL)
Chain Length:313
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UNQ2 Pfam ID:PF00398
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:OA (auth: NM)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61247 Pfam ID:PF01015
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:PA (auth: NO)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62244 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:QA (auth: NP)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P39019 Pfam ID:PF01090
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:RA (auth: NQ)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42677 Pfam ID:PF01667
Polymer Type:polypeptide(L)
Molecule:RRP12-like protein
Chain IDs:SA (auth: NR)
Chain Length:861
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable ATP-dependent RNA helicase DHX37
Gene (Uniprot):DHX37
Chain IDs:TA (auth: NS)
Chain Length:1157
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IY37 Pfam ID:PF00270, PF00271, PF04408, PF21010, PF07717
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S27a
Gene (Uniprot):RPS27A
Chain IDs:UA (auth: NT)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62979 Pfam ID:PF00240, PF01599
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:VA (auth: NU)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08708 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Exosome component 10
Gene (Uniprot):EXOSC10
Chain IDs:WA (auth: NV)
Chain Length:885
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q01780 Pfam ID:PF08066, PF01612, PF00570
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 56
Gene (Uniprot):NOP56
Chain IDs:XA (auth: SA)
Chain Length:594
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00567 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 58
Gene (Uniprot):NOP58
Chain IDs:YA (auth: SB)
Chain Length:529
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y2X3 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA 2'-O-methyltransferase fibrillarin
Gene (Uniprot):FBL
Chain IDs:ZA (auth: SC), AB (auth: SD)
Chain Length:321
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P22087 Pfam ID:PF01269
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NHP2-like protein 1
Gene (Uniprot):SNU13
Chain IDs:BB (auth: SE), CB (auth: SF)
Chain Length:128
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P55769 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-interacting protein 2
Gene (Uniprot):RRP9
Chain IDs:DB (auth: SG)
Chain Length:475
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43818 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA 3'-terminal phosphate cyclase-like protein
Gene (Uniprot):RCL1
Chain IDs:EB (auth: SH)
Chain Length:373
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y2P8 Pfam ID:PF01137, PF05189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BMS1 homolog
Gene (Uniprot):BMS1
Chain IDs:FB (auth: SI)
Chain Length:1282
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14692 Pfam ID:PF08142, PF04950
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA small subunit methyltransferase NEP1
Gene (Uniprot):EMG1
Chain IDs:GB (auth: SJ), HB (auth: SK)
Chain Length:244
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q92979 Pfam ID:PF03587 EC:2.1.1.257
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein FCF1 homolog
Gene (Uniprot):FCF1
Chain IDs:IB (auth: SL)
Chain Length:198
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y324 Pfam ID:PF04900
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein IMP4
Gene (Uniprot):IMP4
Chain IDs:JB (auth: SM)
Chain Length:291
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96G21 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small subunit processome component 20 homolog
Gene (Uniprot):UTP20
Chain IDs:KB (auth: SP)
Chain Length:2785
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75691 Pfam ID:PF07539, PF20416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Deoxynucleotidyltransferase terminal-interacting protein 2
Gene (Uniprot):DNTTIP2
Chain IDs:LB (auth: SQ)
Chain Length:756
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5QJE6 Pfam ID:PF08698
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:MB (auth: SR)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62266 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 14 homolog A
Gene (Uniprot):UTP14A
Chain IDs:NB (auth: SS)
Chain Length:771
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BVJ6 Pfam ID:PF04615
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 14
Chain IDs:OB (auth: ST)
Chain Length:632
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P78316 Pfam ID:PF04147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 4 homolog
Chain IDs:PB (auth: SU)
Chain Length:472
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BVI4 Pfam ID:PF03914
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA-binding protein PNO1
Gene (Uniprot):PNO1
Chain IDs:QB (auth: SW)
Chain Length:252
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NRX1 Pfam ID:PF22891
Polymer Type:polypeptide(L)
Molecule:Unassigned peptides
Chain IDs:RB (auth: SX)
Chain Length:228
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable U3 small nucleolar RNA-associated protein 11
Gene (Uniprot):UTP11
Chain IDs:SB (auth: SY)
Chain Length:253
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3A2 Pfam ID:PF03998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bystin
Chain IDs:TB (auth: SZ)
Chain Length:304
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13895 Pfam ID:PF05291
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A2M B A modified residue
OMC B C modified residue
OMG B G modified residue
OMU B U modified residue
PSU B U modified residue
Ligand Molecules
ATP
GTP
MG
SAH
ZN
Primary Citation
Nucleolar maturation of the human small subunit processome.
Science 373 eabj5338 eabj5338 (2021)
PMID: 34516797 DOI: 10.1126/science.abj5338

Abstact

The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution cryo–electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms. These structures reveal the molecular mechanisms that enable crucial progressions during SSU processome maturation. RNA folding states within these particles are communicated to and coordinated with key enzymes that drive irreversible steps such as targeted exosome-mediated RNA degradation, protein-guided site-specific endonucleolytic RNA cleavage, and tightly controlled RNA unwinding. These conserved mechanisms highlight the SSU processome’s impressive structural plasticity, which endows this 4.5-megadalton nucleolar assembly with the distinctive ability to mature the small ribosomal subunit from within.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
7MQA