ISDA

Deposition Date 2014-08-26

Release Date 2014-10-15

Last Version Date 2024-05-29

Entry Detail

PDB ID:

3J7Y

Keywords:

RIBOSOME

Title:

Structure of the large ribosomal subunit from human mitochondria

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL32
Gene (Uniprot):MRPL32
Chain IDs:Y (auth: 0)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYC8 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL33
Gene (Uniprot):MRPL33
Chain IDs:Z (auth: 1)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75394 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL34
Gene (Uniprot):MRPL34
Chain IDs:AA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BQ48 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL35
Gene (Uniprot):MRPL35
Chain IDs:BA (auth: 3)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NZE8 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL36
Gene (Uniprot):MRPL36
Chain IDs:CA (auth: 4)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P0J6 Pfam ID:PF00444

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL37
Gene (Uniprot):MRPL37
Chain IDs:DA (auth: 5)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BZE1 Pfam ID:PF07147

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL38
Gene (Uniprot):MRPL38
Chain IDs:EA (auth: 6)
Chain Length:380
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96DV4 Pfam ID:PF01161

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL39
Gene (Uniprot):MRPL39
Chain IDs:FA (auth: 7)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NYK5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL40
Gene (Uniprot):MRPL40
Chain IDs:GA (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NQ50 Pfam ID:PF09812

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL41
Gene (Uniprot):MRPL41
Chain IDs:HA (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8IXM3 Pfam ID:PF09809

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:mt-tRNAVal
Chain IDs:B
Chain Length:155
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL2
Gene (Uniprot):MRPL2
Chain IDs:C (auth: D)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q5T653 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL3
Gene (Uniprot):MRPL3
Chain IDs:D (auth: E)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P09001 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL4
Gene (Uniprot):MRPL4
Chain IDs:E (auth: F)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYD3 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL9
Gene (Uniprot):MRPL9
Chain IDs:F (auth: H)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYD2 Pfam ID:PF01281, PF22078

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL10
Gene (Uniprot):MRPL10
Chain IDs:G (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z7H8 Pfam ID:PF00466

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL11
Gene (Uniprot):MRPL11
Chain IDs:H (auth: J)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3B7 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL13
Gene (Uniprot):MRPL13
Chain IDs:I (auth: K)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYD1 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL14
Gene (Uniprot):MRPL14
Chain IDs:J (auth: L)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6P1L8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL15
Gene (Uniprot):MRPL15
Chain IDs:K (auth: M)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P015 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL16
Gene (Uniprot):MRPL16
Chain IDs:L (auth: N)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NX20 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL17
Gene (Uniprot):MRPL17
Chain IDs:M (auth: O)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NRX2 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL18
Chain IDs:N (auth: P)
Chain Length:179
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H0U6 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL19
Gene (Uniprot):MRPL19
Chain IDs:O (auth: Q)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P49406 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL20
Gene (Uniprot):MRPL20
Chain IDs:P (auth: R)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYC9 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL21
Gene (Uniprot):MRPL21
Chain IDs:Q (auth: S)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z2W9 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL22
Chain IDs:R (auth: T)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NWU5 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL23
Gene (Uniprot):MRPL23
Chain IDs:S (auth: U)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q16540 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL24
Gene (Uniprot):MRPL24
Chain IDs:T (auth: V)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96A35 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL27
Gene (Uniprot):MRPL27
Chain IDs:U (auth: W)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P0M9 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL28
Chain IDs:V (auth: X)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13084 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL29
Gene (Uniprot):MRPL47
Chain IDs:W (auth: Y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9HD33 Pfam ID:PF06984

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL30
Gene (Uniprot):MRPL30
Chain IDs:X (auth: Z)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8TCC3 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL42
Gene (Uniprot):MRPL42
Chain IDs:IA (auth: a)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y6G3 Pfam ID:PF10210

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL43
Gene (Uniprot):MRPL43
Chain IDs:JA (auth: b)
Chain Length:155
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8N983 Pfam ID:PF05047

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL44
Gene (Uniprot):MRPL44
Chain IDs:KA (auth: c)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H9J2 Pfam ID:PF22935, PF22892

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL45
Gene (Uniprot):MRPL45
Chain IDs:LA (auth: d)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BRJ2 Pfam ID:PF04280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL46
Gene (Uniprot):MRPL46
Chain IDs:MA (auth: e)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H2W6 Pfam ID:PF11788

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL48
Gene (Uniprot):MRPL48
Chain IDs:NA (auth: f)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96GC5 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL49
Gene (Uniprot):MRPL49
Chain IDs:OA (auth: g)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13405 Pfam ID:PF05046

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL50
Gene (Uniprot):MRPL50
Chain IDs:PA (auth: h)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8N5N7 Pfam ID:PF10501

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL51
Gene (Uniprot):MRPL51
Chain IDs:QA (auth: i)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q4U2R6 Pfam ID:PF10244

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL52
Chain IDs:RA (auth: j)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q86TS9 Pfam ID:PF18699

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL53
Gene (Uniprot):MRPL53
Chain IDs:SA (auth: k)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96EL3 Pfam ID:PF10780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL63
Gene (Uniprot):MRPL57
Chain IDs:TA (auth: o)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BQC6 Pfam ID:PF14978

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ICT1
Gene (Uniprot):MRPL58
Chain IDs:UA (auth: p)
Chain Length:179
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q14197 Pfam ID:PF00472 EC:3.1.1.29

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CRIF1
Gene (Uniprot):GADD45GIP1
Chain IDs:VA (auth: q)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8TAE8 Pfam ID:PF10147

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bS18a
Gene (Uniprot):MRPS18A
Chain IDs:WA (auth: r)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NVS2 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS30
Gene (Uniprot):MRPS30
Chain IDs:XA (auth: s)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NP92 Pfam ID:PF07147

Polymer Type:polypeptide(L)
Molecule:unknown protein
Chain IDs:YA (auth: t)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens

Primary Citation

Structure of the large ribosomal subunit from human mitochondria.

Brown, A, Amunts, A, Bai, X.C, Sugimoto, Y, Edwards, P.C, Murshudov, G, Scheres, S.H, Ramakrishnan, V.Show

Science 346 718 722 (2014)

PMID: 25278503 DOI: 10.1126/science.1258026

Abstact

Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. Using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. The structure unveils an adaptation of the exit tunnel for hydrophobic nascent peptides, extensive remodeling of the central protuberance, including recruitment of mitochondrial valine transfer RNA (tRNA(Val)) to play an integral structural role, and changes in the tRNA binding sites related to the unusual characteristics of mitochondrial tRNAs.

Legend

Protein

Chemical

Disease

Primary Citation of related structures