7XNX image
Entry Detail
PDB ID:
7XNX
EMDB ID:
Keywords:
Title:
High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-04-30
Release Date:
2023-04-05
Method Details:
Experimental Method:
Resolution:
2.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:tRNA
Chain IDs:BC (auth: CC)
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:28S rRNA
Chain IDs:A (auth: L1)
Chain Length:5070
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:B (auth: L2)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:C (auth: L3)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8
Chain IDs:D (auth: LA)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:E (auth: LB)
Chain Length:159
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4
Chain IDs:F (auth: LC)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:G (auth: LD)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:H (auth: LE)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7
Chain IDs:I (auth: LF)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:J (auth: LG)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:K (auth: LH)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosomal protein L10 isoform A
Chain IDs:L (auth: LI)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11
Chain IDs:M (auth: LJ)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13
Chain IDs:N (auth: LL)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14
Chain IDs:O (auth: LM)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15
Chain IDs:P (auth: LN)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13a
Chain IDs:Q (auth: LO)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17
Chain IDs:R (auth: LP)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18
Chain IDs:S (auth: LQ)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19
Chain IDs:T (auth: LR)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18a
Chain IDs:U (auth: LS)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:V (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22
Chain IDs:W (auth: LU)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23
Chain IDs:X (auth: LV)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24
Chain IDs:Y (auth: LW)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23a
Chain IDs:Z (auth: LX)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26
Chain IDs:AA (auth: LY)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:BA (auth: LZ), CA (auth: La)
Chain Length:257
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:DA (auth: Lb)
Chain Length:159
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:EA (auth: Lc)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:FA (auth: Ld)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:GA (auth: Le)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35a
Chain IDs:HA (auth: Lf)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:IA (auth: Lg)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35
Chain IDs:JA (auth: Lh)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:KA (auth: Li)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37
Chain IDs:LA (auth: Lj)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:MA (auth: Lk)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:NA (auth: Ll)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin-60S ribosomal protein L40
Chain IDs:OA (auth: Lm)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41
Chain IDs:PA (auth: Ln)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36a
Chain IDs:QA (auth: Lo)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37a
Chain IDs:RA (auth: Lp)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:SA (auth: Lr)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:TA (auth: S2)
Chain Length:1869
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein SA
Chain IDs:UA (auth: SA)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3a
Chain IDs:VA (auth: SB)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:PB (auth: SC)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3
Chain IDs:WA (auth: SD)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4, X isoform
Chain IDs:XA (auth: SE)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S5
Chain IDs:YA (auth: SF)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6
Chain IDs:QB (auth: SG)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:ZA (auth: SH)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:AB (auth: SI)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9
Chain IDs:RB (auth: SJ)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S10
Chain IDs:BB (auth: SK)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11
Chain IDs:CB (auth: SL)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S12
Chain IDs:SB (auth: SM)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S13
Chain IDs:TB (auth: SN)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S14
Chain IDs:UB (auth: SO)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15
Chain IDs:DB (auth: SP)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S16
Chain IDs:EB (auth: SQ)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17
Chain IDs:FB (auth: SR)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18
Chain IDs:GB (auth: SS)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19
Chain IDs:HB (auth: ST)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S20
Chain IDs:IB (auth: SU)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21
Chain IDs:JB (auth: SV)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15a
Chain IDs:VB (auth: SW)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S23
Chain IDs:KB (auth: SX)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:WB (auth: SY)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:XB (auth: SZ)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26
Chain IDs:LB (auth: Sa)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27
Chain IDs:YB (auth: Sb)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28
Chain IDs:MB (auth: Sc)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S29
Chain IDs:NB (auth: Sd)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30
Chain IDs:ZB (auth: Se)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin-40S ribosomal protein S27a
Chain IDs:AC (auth: Sf), CC (auth: CE)
Chain Length:133
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Receptor of activated protein C kinase 1
Chain IDs:OB (auth: Sg)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MLZ QA LYS modified residue
Primary Citation

Abstact

UNLABELLED The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2'-O-methylation regulate leukemia stem cell (LSC) activity in vivo. A comprehensive analysis of the rRNA 2'-O-methylation landscape of 94 patients with acute myeloid leukemia (AML) revealed dynamic 2'-O-methylation specifically at exterior sites of ribosomes. The rRNA 2'-O-methylation pattern is closely associated with AML development stage and LSC gene expression signature. Forced expression of the 2'-O-methyltransferase fibrillarin (FBL) induced an AML stem cell phenotype and enabled engraftment of non-LSC leukemia cells in NSG mice. Enhanced 2'-O-methylation redirected the ribosome translation program toward amino acid transporter mRNAs enriched in optimal codons and subsequently increased intracellular amino acid levels. Methylation at the single site 18S-guanosine 1447 was instrumental for LSC activity. Collectively, our work demonstrates that dynamic 2'-O-methylation at specific sites on rRNAs shifts translational preferences and controls AML LSC self-renewal. SIGNIFICANCE We establish the complete rRNA 2'-O-methylation landscape in human AML. Plasticity of rRNA 2'-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process constitutes a novel concept of how cancers reprogram cell fate and function. This article is highlighted in the In This Issue feature, p. 247.

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Disease

Primary Citation of related structures