7QI4 image
Entry Detail
PDB ID:
7QI4
EMDB ID:
Keywords:
Title:
Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2021-12-14
Release Date:
2022-07-13
Method Details:
Experimental Method:
Resolution:
2.21 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L32, mitochondrial
Chain IDs:GB (auth: 0)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L33, mitochondrial
Chain IDs:HB (auth: 1)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L34, mitochondrial
Chain IDs:IB (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L35, mitochondrial
Chain IDs:JB (auth: 3)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L36, mitochondrial
Chain IDs:KB (auth: 4)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L37, mitochondrial
Chain IDs:LB (auth: 5)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L38, mitochondrial
Chain IDs:MB (auth: 6)
Chain Length:380
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L39, mitochondrial
Chain IDs:NB (auth: 7)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L40, mitochondrial
Chain IDs:OB (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L41, mitochondrial
Chain IDs:PB (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:16S mitochondrial rRNA
Chain IDs:IA (auth: A)
Chain Length:1558
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S34, mitochondrial
Chain IDs:AA (auth: A0)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S35, mitochondrial
Chain IDs:BA (auth: A1)
Chain Length:323
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
Chain IDs:CA (auth: A2)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Aurora kinase A-interacting protein
Chain IDs:DA (auth: A3)
Chain Length:199
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Chain IDs:EA (auth: A4)
Chain Length:689
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:12S mitochondrial rRNA
Chain IDs:A (auth: AA)
Chain Length:954
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S2, mitochondrial
Chain IDs:B (auth: AB)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S24, mitochondrial
Chain IDs:C (auth: AC)
Chain Length:167
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S5, mitochondrial
Chain IDs:D (auth: AD)
Chain Length:430
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S6, mitochondrial
Chain IDs:E (auth: AE)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S7, mitochondrial
Chain IDs:F (auth: AF)
Chain Length:242
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S9, mitochondrial
Chain IDs:G (auth: AG)
Chain Length:396
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S10, mitochondrial
Chain IDs:H (auth: AH)
Chain Length:201
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S11, mitochondrial
Chain IDs:I (auth: AI)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S12, mitochondrial
Chain IDs:J (auth: AJ)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S14, mitochondrial
Chain IDs:K (auth: AK)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S15, mitochondrial
Chain IDs:L (auth: AL)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S16, mitochondrial
Chain IDs:M (auth: AM)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S17, mitochondrial
Chain IDs:N (auth: AN)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S18b, mitochondrial
Chain IDs:O (auth: AO)
Chain Length:258
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S18c, mitochondrial
Chain IDs:P (auth: AP)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:MRPS21 isoform 1
Chain IDs:Q (auth: AQ)
Chain Length:87
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S22, mitochondrial
Chain IDs:R (auth: AR)
Chain Length:360
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S23, mitochondrial
Chain IDs:S (auth: AS)
Chain Length:190
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S25, mitochondrial
Chain IDs:T (auth: AT)
Chain Length:173
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S26, mitochondrial
Chain IDs:U (auth: AU)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S27, mitochondrial
Chain IDs:V (auth: AV)
Chain Length:414
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S28, mitochondrial
Chain IDs:W (auth: AW)
Chain Length:22
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S29, mitochondrial
Chain IDs:X (auth: AX)
Chain Length:398
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S31, mitochondrial
Chain IDs:Y (auth: AY)
Chain Length:52
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S33, mitochondrial
Chain IDs:Z (auth: AZ)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:A/A-tRNA
Chain IDs:FA (auth: Aw)
Chain Length:22
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:P/P-tRNA
Chain IDs:GA (auth: Ax)
Chain Length:398
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:E/E-tRNA
Chain IDs:PC (auth: Ay)
Chain Length:52
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:HA (auth: Az)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:mitochondrial tRNAVal
Chain IDs:JA (auth: B)
Chain Length:72
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L2, mitochondrial
Chain IDs:KA (auth: D)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L3, mitochondrial
Chain IDs:LA (auth: E)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L4, mitochondrial
Chain IDs:MA (auth: F)
Chain Length:311
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L9, mitochondrial
Chain IDs:NA (auth: H)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L10, mitochondrial
Chain IDs:OA (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L11, mitochondrial
Chain IDs:PA (auth: J)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L13, mitochondrial
Chain IDs:QA (auth: K)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L14, mitochondrial
Chain IDs:RA (auth: L)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L15, mitochondrial
Chain IDs:SA (auth: M)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L16, mitochondrial
Chain IDs:TA (auth: N)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L17, mitochondrial
Chain IDs:UA (auth: O)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L18, mitochondrial
Chain IDs:VA (auth: P)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L19, mitochondrial
Chain IDs:WA (auth: Q)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L20, mitochondrial
Chain IDs:XA (auth: R)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L21, mitochondrial
Chain IDs:YA (auth: S)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L22, mitochondrial
Chain IDs:ZA (auth: T)
Chain Length:198
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L23, mitochondrial
Chain IDs:AB (auth: U)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L24, mitochondrial
Chain IDs:BB (auth: V)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L27, mitochondrial
Chain IDs:CB (auth: W)
Chain Length:198
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L28, mitochondrial
Chain IDs:DB (auth: X)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L47, mitochondrial
Chain IDs:EB (auth: Y)
Chain Length:198
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L30, mitochondrial
Chain IDs:FB (auth: Z)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L42, mitochondrial
Chain IDs:QB (auth: a)
Chain Length:1558
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L43, mitochondrial
Chain IDs:RB (auth: b)
Chain Length:72
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L44, mitochondrial
Chain IDs:SB (auth: c)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L45, mitochondrial
Chain IDs:TB (auth: d)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L46, mitochondrial
Chain IDs:UB (auth: e)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L48, mitochondrial
Chain IDs:VB (auth: f)
Chain Length:311
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L49, mitochondrial
Chain IDs:WB (auth: g)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L50, mitochondrial
Chain IDs:XB (auth: h)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L51, mitochondrial
Chain IDs:YB (auth: i)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L52, mitochondrial
Chain IDs:ZB (auth: j)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L53, mitochondrial
Chain IDs:AC (auth: k)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L54, mitochondrial
Chain IDs:BC (auth: l)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L55, mitochondrial
Chain IDs:CC (auth: m)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosomal protein 63, mitochondrial
Chain IDs:DC (auth: o)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Chain IDs:EC (auth: p)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Growth arrest and DNA damage-inducible proteins-interacting protein 1
Chain IDs:FC (auth: q)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein S18a, mitochondrial
Chain IDs:GC (auth: r)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein S30, mitochondrial
Chain IDs:HC (auth: s)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L12, mitochondrial
Chain IDs:IC (auth: t), JC (auth: u), KC (auth: v), LC (auth: w), MC (auth: x), NC (auth: y)
Chain Length:198
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L1, mitochondrial
Chain IDs:OC (auth: z)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA IA A modified residue
2MG JA G modified residue
AYA Q ALA modified residue
OMG IA G modified residue
OMU IA U modified residue
PSU IA U modified residue
SAC QA SER modified residue
THC RB THR modified residue
Primary Citation

Abstact

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.

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Disease

Primary Citation of related structures