3D Electron Microscopy (3D-EM) Data Navigator [English / [日本語]]
Top Gallery List Statistics Shape search Viewer
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-5oom

This page is a legacy version and will be discarded in future. The new page is here.

Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA

by single particle reconstruction, at 3.03 A resolution

Movie

Orientation:

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-3843, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5oom
TitleStructure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA
DescriptorRibosomal protein 63,mitochondrial
Peptidyl-tRNA hydrolase ICT1,mitochondrial
Growth arrest and DNA damage-inducible proteins-interacting protein 1
Unknown protein or protein extension
Mitochondrial assembly of ribosomal large subunit protein 1
and more 3 items
KeywordsRIBOSOME, Ribosome, mitochondria, biogenesis, translation, electron cryomicroscopy
AuthorsBrown, A., Rathore, S., Kimanius, D., Aibara, S., Bia, X.C., Rorbach, J., Amunts, A., Ramakrishnan, V.
DateDeposition: 2017-08-08, Release: 2017-09-13
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-3843, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-3843

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - primary
ArticleNat. Struct. Mol. Biol., Year 2017
TitleStructures of the human mitochondrial ribosome in native states of assembly.
AuthorsAlan Brown, Sorbhi Rathore, Dari Kimanius, Shintaro Aibara, Xiao-Chen Bai, Joanna Rorbach, Alexey Amunts, V Ramakrishnan
MRC Laboratory of Molecular Biology, Cambridge, UK.
Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
LinksPubMed: 28892042, DOI: 10.1038/nsmb.3464
Components
ID 1 : 16S ribosomal RNA
Description16S ribosomal RNA
Typepolyribonucleotide
Formula weight500019.594 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 1559
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksGenBank: 1025814679, Sequence view
ID 2 : mitochondrial tRNAVal
Descriptionmitochondrial tRNAVal
Typepolyribonucleotide
Formula weight22022.131 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 69
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksGenBank: 1215733170, Sequence view
ID 3 : MRP-L2,Mitochondrial large ribosomal subunit protein uL2m
Description39S ribosomal protein L2, mitochondrial
Typepolypeptide(L)
Formula weight33355.941 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 305
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q5T653, Sequence view
ID 4 : MRP-L3,Mitochondrial large ribosomal subunit protein uL3m
Description39S ribosomal protein L3, mitochondrial
Typepolypeptide(L)
Formula weight38689.562 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 348
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: P09001, Sequence view
ID 5 : MRP-L4,Mitochondrial large ribosomal subunit protein uL4m
Description39S ribosomal protein L4, mitochondrial
Typepolypeptide(L)
Formula weight34970.195 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 311
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BYD3, Sequence view
ID 6 : MRP-L9,Mitochondrial large ribosomal subunit protein bL9m
Description39S ribosomal protein L9, mitochondrial
Typepolypeptide(L)
Formula weight30296.355 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 267
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BYD2, Sequence view
ID 7 : MRP-L10,39S ribosomal protein L8,mitochondrial,MRP-L8,Mitochondrial large ribosomal subunit protein uL10m
Description39S ribosomal protein L10, mitochondrial
Typepolypeptide(L)
Formula weight29322.529 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 261
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q7Z7H8, Sequence view
ID 8 : MRP-L11,Mitochondrial large ribosomal subunit protein uL11m
Description39S ribosomal protein L11, mitochondrial
Typepolypeptide(L)
Formula weight20716.227 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 192
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9Y3B7, Sequence view
ID 9 : MRP-L13,Mitochondrial large ribosomal subunit protein uL13m
Description39S ribosomal protein L13, mitochondrial
Typepolypeptide(L)
Formula weight20722.988 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 178
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BYD1, Sequence view
ID 10 : MRP-L14,39S ribosomal protein L32,mitochondrial,MRP-L32,Mitochondrial large ribosomal subunit protein uL14m
Description39S ribosomal protein L14, mitochondrial
Typepolypeptide(L)
Formula weight15973.702 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 145
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q6P1L8, Sequence view
ID 11 : MRP-L15,Mitochondrial large ribosomal subunit protein uL15m
Description39S ribosomal protein L15, mitochondrial
Typepolypeptide(L)
Formula weight33473.820 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 296
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9P015, Sequence view
ID 12 : MRP-L16,Mitochondrial large ribosomal subunit protein uL16m
Description39S ribosomal protein L16, mitochondrial
Typepolypeptide(L)
Formula weight28496.285 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 251
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9NX20, Sequence view
ID 13 : MRP-L17,LYST-interacting protein 2,Mitochondrial large ribosomal subunit protein bL17m
Description39S ribosomal protein L17, mitochondrial
Typepolypeptide(L)
Formula weight20083.266 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 175
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9NRX2, Sequence view
ID 14 : MRP-L18,Mitochondrial large ribosomal subunit protein uL18m
Description39S ribosomal protein L18, mitochondrial
Typepolypeptide(L)
Formula weight20607.570 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 180
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9H0U6, Sequence view
ID 15 : MRP-L19,39S ribosomal protein L15,mitochondrial,MRP-L15,Mitochondrial large ribosomal subunit protein bL19m
Description39S ribosomal protein L19, mitochondrial
Typepolypeptide(L)
Formula weight33584.996 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 292
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: P49406, Sequence view
ID 16 : MRP-L20,Mitochondrial large ribosomal subunit protein bL20m
Description39S ribosomal protein L20, mitochondrial
Typepolypeptide(L)
Formula weight17479.654 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 149
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BYC9, Sequence view
ID 17 : MRP-L21,Mitochondrial large ribosomal subunit protein bL21m
Description39S ribosomal protein L21, mitochondrial
Typepolypeptide(L)
Formula weight22847.682 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 205
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q7Z2W9, Sequence view
ID 18 : MRP-L22,39S ribosomal protein L25,mitochondrial,MRP-L25,Mitochondrial large ribosomal subunit protein uL22m
Description39S ribosomal protein L22, mitochondrial
Typepolypeptide(L)
Formula weight23683.732 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 206
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9NWU5, Sequence view
ID 19 : MRP-L23,L23 mitochondrial-related protein,Mitochondrial large ribosomal subunit protein uL23m,Ribosomal protein L23-like
Description39S ribosomal protein L23, mitochondrial
Typepolypeptide(L)
Formula weight17807.189 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 153
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q16540, Sequence view
ID 20 : MRP-L24,Mitochondrial large ribosomal subunit protein uL24m
Description39S ribosomal protein L24, mitochondrial
Typepolypeptide(L)
Formula weight24953.875 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 216
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q96A35, Sequence view
ID 21 : MRP-L27,Mitochondrial large ribosomal subunit protein bL27m
Description39S ribosomal protein L27, mitochondrial
Typepolypeptide(L)
Formula weight16102.859 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 148
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9P0M9, Sequence view
ID 22 : MRP-L28,Melanoma antigen p15,Melanoma-associated antigen recognized by T-lymphocytes,Mitochondrial large ribosomal subunit protein bL28m
Description39S ribosomal protein L28, mitochondrial
Typepolypeptide(L)
Formula weight30202.867 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 256
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q13084, Sequence view
ID 23 : MRP-L47,Mitochondrial large ribosomal subunit protein uL29m,Nasopharyngeal carcinoma metastasis-related protein 1
Description39S ribosomal protein L47, mitochondrial
Typepolypeptide(L)
Formula weight29508.535 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 250
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9HD33, Sequence view
ID 24 : MRP-L30,39S ribosomal protein L28,mitochondrial,MRP-L28,Mitochondrial large ribosomal subunit protein uL30m
Description39S ribosomal protein L30, mitochondrial
Typepolypeptide(L)
Formula weight18582.812 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 161
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q8TCC3, Sequence view
ID 25 : MRP-L32,Mitochondrial large ribosomal subunit protein bL32m
Description39S ribosomal protein L32, mitochondrial
Typepolypeptide(L)
Formula weight21437.799 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 188
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BYC8, Sequence view
ID 26 : MRP-L33,Mitochondrial large ribosomal subunit protein bL33m
Description39S ribosomal protein L33, mitochondrial
Typepolypeptide(L)
Formula weight7635.204 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 65
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: O75394, Sequence view
ID 27 : MRP-L34,Mitochondrial large ribosomal subunit protein bL34m
Description39S ribosomal protein L34, mitochondrial
Typepolypeptide(L)
Formula weight10183.913 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 92
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BQ48, Sequence view
ID 28 : MRP-L35,Mitochondrial large ribosomal subunit protein bL35m
Description39S ribosomal protein L35, mitochondrial
Typepolypeptide(L)
Formula weight21558.488 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 188
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9NZE8, Sequence view
ID 29 : MRP-L37,39S ribosomal protein L2,mitochondrial,MRP-L2,Mitochondrial large ribosomal subunit protein mL37
Description39S ribosomal protein L37, mitochondrial
Typepolypeptide(L)
Formula weight48183.344 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 423
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BZE1, Sequence view
ID 30 : MRP-L38,Mitochondrial large ribosomal subunit protein mL38
Description39S ribosomal protein L38, mitochondrial
Typepolypeptide(L)
Formula weight44659.430 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 380
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q96DV4, Sequence view
ID 31 : MRP-L39,39S ribosomal protein L5,mitochondrial,MRP-L5,Mitochondrial large ribosomal subunit protein mL39
Description39S ribosomal protein L39, mitochondrial
Typepolypeptide(L)
Formula weight38764.785 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 338
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9NYK5, Sequence view
ID 32 : MRP-L40,Mitochondrial large ribosomal subunit protein mL40,Nuclear localization signal-containing protein deleted in velocardiofacial syndrome,Up-regulated in metastasis
Description39S ribosomal protein L40, mitochondrial
Typepolypeptide(L)
Formula weight24534.422 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 206
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9NQ50, Sequence view
ID 33 : MRP-L41,39S ribosomal protein L27 homolog,Bcl-2-interacting mitochondrial ribosomal protein L41,Cell proliferation-inducing gene 3 protein,MRP-L27 homolog,Mitochondrial large ribosomal subunit protein mL41
Description39S ribosomal protein L41, mitochondrial
Typepolypeptide(L)
Formula weight15404.708 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 137
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q8IXM3, Sequence view
ID 34 : MRP-L42,39S ribosomal protein L31,mitochondrial,MRP-L31,Mitochondrial large ribosomal subunit protein mL42
Description39S ribosomal protein L42, mitochondrial
Typepolypeptide(L)
Formula weight16691.176 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 142
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9Y6G3, Sequence view
ID 35 : MRP-L43,Mitochondrial large ribosomal subunit protein mL43,Mitochondrial ribosomal protein bMRP36a
Description39S ribosomal protein L43, mitochondrial
Typepolypeptide(L)
Formula weight23457.789 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 215
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q8N983, Sequence view
ID 36 : MRP-L44,Mitochondrial large ribosomal subunit protein mL44
Description39S ribosomal protein L44, mitochondrial
Typepolypeptide(L)
Formula weight37583.312 Da
Number of molecules1
ID36
Ec3.1.26.-
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 332
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9H9J2, Sequence view
ID 37 : MRP-L45,Mitochondrial large ribosomal subunit protein mL45
Description39S ribosomal protein L45, mitochondrial
Typepolypeptide(L)
Formula weight35402.918 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 306
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BRJ2, Sequence view
ID 38 : MRP-L46,Mitochondrial large ribosomal subunit protein mL46,P2ECSL
Description39S ribosomal protein L46, mitochondrial
Typepolypeptide(L)
Formula weight31748.107 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 279
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9H2W6, Sequence view
ID 39 : MRP-L48,Mitochondrial large ribosomal subunit protein mL48
Description39S ribosomal protein L48, mitochondrial
Typepolypeptide(L)
Formula weight23970.814 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 212
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q96GC5, Sequence view
ID 40 : MRP-L49,Mitochondrial large ribosomal subunit protein mL49,Neighbor of FAU,NOF,Protein NOF1
Description39S ribosomal protein L49, mitochondrial
Typepolypeptide(L)
Formula weight19225.043 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 166
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q13405, Sequence view
ID 41 : MRP-L50,Mitochondrial large ribosomal subunit protein mL50
Description39S ribosomal protein L50, mitochondrial
Typepolypeptide(L)
Formula weight18349.943 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 158
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q8N5N7, Sequence view
ID 42 : MRP-L51,Mitochondrial large ribosomal subunit protein mL51,bMRP-64,bMRP64
Description39S ribosomal protein L51, mitochondrial
Typepolypeptide(L)
Formula weight15125.917 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 128
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q4U2R6, Sequence view
ID 43 : MRP-L52,Mitochondrial large ribosomal subunit protein mL52
Description39S ribosomal protein L52, mitochondrial
Typepolypeptide(L)
Formula weight13682.658 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 123
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q86TS9, Sequence view
ID 44 : MRP-L53,Mitochondrial large ribosomal subunit protein mL53
Description39S ribosomal protein L53, mitochondrial
Typepolypeptide(L)
Formula weight12125.859 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 112
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q96EL3, Sequence view
ID 45 : MRP-L54,Mitochondrial large ribosomal subunit protein mL54
Description39S ribosomal protein L54, mitochondrial
Typepolypeptide(L)
Formula weight15844.178 Da
Number of molecules1
ID45
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 138
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q6P161, Sequence view
ID 46 : MRP-L55,Mitochondrial large ribosomal subunit protein bL31m,Mitochondrial large ribosomal subunit protein mL55
Description39S ribosomal protein L55, mitochondrial
Typepolypeptide(L)
Formula weight15160.433 Da
Number of molecules1
ID46
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 128
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q7Z7F7, Sequence view
ID 47 : hMRP63,Mitochondrial large ribosomal subunit protein mL63,Mitochondrial ribosomal protein 63,Mitochondrial ribosomal protein L57
DescriptionRibosomal protein 63, mitochondrial
Typepolypeptide(L)
Formula weight12292.333 Da
Number of molecules1
ID47
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 102
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9BQC6, Sequence view
ID 48 : 39S ribosomal protein L58,mitochondrial,MRP-L58,Digestion substraction 1,DS-1,Immature colon carcinoma transcript 1 protein,Mitochondrial large ribosomal subunit protein mL62
DescriptionPeptidyl-tRNA hydrolase ICT1, mitochondrial
Typepolypeptide(L)
Formula weight23674.203 Da
Number of molecules1
ID48
Ec3.1.1.29
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 206
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q14197, Sequence view
ID 49 : 39S ribosomal protein L59,mitochondrial,MRP-L59,CKII beta-associating protein,CR6-interacting factor 1,CRIF1,Mitochondrial large ribosomal subunit protein mL64,Papillomavirus L2-interacting nuclear protein 1,PLINP-1,p53-responsive gene 6 protein
DescriptionGrowth arrest and DNA damage-inducible proteins-interacting protein 1
Typepolypeptide(L)
Formula weight25426.895 Da
Number of molecules1
ID49
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 222
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q8TAE8, Sequence view
ID 50 : S18mt-a,39S ribosomal protein S18-3,mitochondrial,MRP-S18-3,Mitochondrial large ribosomal subunit protein bS18a,Mitochondrial large ribosomal subunit protein mL66
Description39S ribosomal protein S18a, mitochondrial
Typepolypeptide(L)
Formula weight22224.078 Da
Number of molecules1
ID50
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 196
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9NVS2, Sequence view
ID 51 : S30mt,Mitochondrial large ribosomal subunit protein mL65,Mitochondrial large ribosomal subunit protein mS30,Programmed cell death protein 9
Description39S ribosomal protein S30, mitochondrial
Typepolypeptide(L)
Formula weight50429.578 Da
Number of molecules1
ID51
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 439
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q9NP92, Sequence view
ID 52 : Unknown protein or protein extension
DescriptionUnknown protein or protein extension
Typepolypeptide(L)
Formula weight2400.951 Da
Number of molecules1
ID52
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 28
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksSequence view
ID 53 : Mitochondrial assembly of ribosomal large subunit protein 1
DescriptionMitochondrial assembly of ribosomal large subunit protein 1
Typepolypeptide(L)
Formula weight26203.076 Da
Number of molecules1
ID53
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 234
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q96EH3, Sequence view
ID 54 : MIEF1 upstream open reading frame protein
DescriptionMIEF1 upstream open reading frame protein
Typepolypeptide(L)
Formula weight8460.787 Da
Number of molecules1
ID54
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 70
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: L0R8F8, Sequence view
ID 55 : ACP,CI-SDAP,NADH-ubiquinone oxidoreductase 9.6 kDa subunit
DescriptionAcyl carrier protein, mitochondrial
Typepolypeptide(L)
Formula weight17434.273 Da
Number of molecules1
ID55
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 156
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: O14561, Sequence view
ID 56 : MAGNESIUM ION
DescriptionMAGNESIUM ION
Typenon-polymer
Formula weight24.305 Da
Number of molecules49
ID56
SourceMethod: Obtained synthetically
ID 57 : ZINC ION
DescriptionZINC ION
Typenon-polymer
Formula weight65.409 Da
Number of molecules2
ID57
SourceMethod: Obtained synthetically
ID 58 : 4'-PHOSPHOPANTETHEINE
Description4'-PHOSPHOPANTETHEINE
Typenon-polymer
Formula weight358.348 Da
Number of molecules1
ID58
SourceMethod: Obtained synthetically
Sample
Entity assembly
Entity id list1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55
NameMitochondrial ribosome large subunit with assembly factor
SourceNATURAL
TypeORGANELLE OR CELLULAR COMPONENT
Buffer
Specimen id1
Details2 mM Synercid (Santa Cruz Biotechnology, Inc) was added to reduce preferential orientation.
PH7.45
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
Grid materialCOPPER
Grid mesh size400
Grid typeQuantifoil R2/2
Vitrification
Specimen id1
Chamber temperature277
Cryogen nameETHANE
DetailsSample incubated for 30 s prior to freezing.
Humidity100
InstrumentFEI VITROBOT MARK IV
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TITAN KRIOS
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 130841 X
Specimen holder
Specimen holderModel: FEI TITAN KRIOS AUTOGRID HOLDER
Image scans
Image recording id1
Frames per image25
Used frames per image1-25
Processing
Single particle entity
Image processing id1
Point symmetryC1
3D reconstruction
Image processing id1
Number of particles379869
Resolution3.03 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
3D fitting
Temperature factor85
Refinement ProtocolOTHER
Refinement SpaceREAL
Target criteriaCross-correlation coefficient
3D fitting list
3D Fitting ID1
PDB entry ID3J9M
Refine
Refine idELECTRON MICROSCOPY
Software
Ordinal1
Classificationrefinement
NamePHENIX
Version1.11.1-2575_1479:
Download
PDB format
Allpdb5oom.ent.gz
pdb5oom.ent (uncompressed file)
Header onlypdb5oom.ent.gz
mmCIF format
mmCIF5oom.cif.gz
XML format
All5oom.xml.gz
No-atom5oom-noatom.xml.gz
Ext-atom5oom-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 6.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 7.1 MB