6NU3 image
Entry Detail
PDB ID:
6NU3
EMDB ID:
Keywords:
Title:
Structural insights into unique features of the human mitochondrial ribosome recycling
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2019-01-30
Release Date:
2019-04-17
Method Details:
Experimental Method:
Resolution:
4.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L32, mitochondrial
Chain IDs:Y (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:Z (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:AA (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:BA (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:CA (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:DA (auth: 5)
Chain Length:394
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L38, mitochondrial
Chain IDs:EA (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:FA (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:GA (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:HA (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:A
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S34, mitochondrial
Chain IDs:CC (auth: A0)
Chain Length:225
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S35, mitochondrial
Chain IDs:DC (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:EC (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:FC (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,mS39
Chain IDs:GC (auth: A4)
Chain Length:474
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:12S rRNA
Chain IDs:CB (auth: AA)
Chain Length:923
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S2, mitochondrial
Chain IDs:DB (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:EB (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:FB (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:GB (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:HB (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:IB (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:JB (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:KB (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:LB (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:MB (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:NB (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:OB (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:PB (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:QB (auth: AO)
Chain Length:185
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S18c, mitochondrial
Chain IDs:RB (auth: AP)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S21, mitochondrial
Chain IDs:SB (auth: AQ)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S22, mitochondrial
Chain IDs:TB (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:UB (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:VB (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:WB (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:XB (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:YB (auth: AW)
Chain Length:187
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S29, mitochondrial
Chain IDs:ZB (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:AC (auth: AY)
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S33, mitochondrial
Chain IDs:BC (auth: AZ)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:mt-tRNAVal
Chain IDs:B
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L2, mitochondrial
Chain IDs:C (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:D (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:E (auth: F)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L9, mitochondrial
Chain IDs:F (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:G (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:H (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L13, mitochondrial
Chain IDs:I (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:J (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:K (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:L (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:M (auth: O)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L18, mitochondrial
Chain IDs:N (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:O (auth: Q)
Chain Length:219
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L20, mitochondrial
Chain IDs:P (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:Q (auth: S)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L22, mitochondrial
Chain IDs:R (auth: T)
Chain Length:28
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L23, mitochondrial
Chain IDs:S (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:T (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:U (auth: W)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L28, mitochondrial
Chain IDs:V (auth: X)
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L47, mitochondrial
Chain IDs:W (auth: Y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L30, mitochondrial
Chain IDs:X (auth: Z)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L42, mitochondrial
Chain IDs:IA (auth: a)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L43, mitochondrial
Chain IDs:JA (auth: b)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L44, mitochondrial
Chain IDs:KA (auth: c)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:cDNA FLJ61100, highly similar to 39S ribosomal protein L45, mitochondrial
Chain IDs:LA (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:MA (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:NA (auth: f)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L49, mitochondrial
Chain IDs:OA (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:PA (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:QA (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:RA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L53, mitochondrial
Chain IDs:SA (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:TA (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:UA (auth: m)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosomal protein 63, mitochondrial
Chain IDs:VA (auth: o)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Chain IDs:WA (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:XA (auth: q)
Chain Length:219
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein S18a, mitochondrial
Chain IDs:YA (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:ZA (auth: s)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Unknown protein/protein extension
Chain IDs:AB (auth: t)
Chain Length:28
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:E-site tRNA
Chain IDs:BB (auth: u)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Structural insights into unique features of the human mitochondrial ribosome recycling.
Proc.Natl.Acad.Sci.USA 116 8283 8288 (2019)
PMID: 30962385 DOI: 10.1073/pnas.1815675116

Abstact

Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRFmt) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRFmt Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRFmt complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRFmt binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling.

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Primary Citation of related structures