5OOM

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: Particle
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 5OOM

Classification: RIBOSOME

Total Structure Weight: 1784460.88


Macromolecule Entities
Molecule Chains Length Organism Details
39S ribosomal protein L2, mitochondrial D 305 Homo sapiens Gene Name(s): MRPL2 Gene View CGI-22
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L3, mitochondrial E 348 Homo sapiens Gene Name(s): MRPL3 Gene View MRL3 RPML3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L4, mitochondrial F 311 Homo sapiens Gene Name(s): MRPL4 Gene View CDABP0091 CGI-28
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L9, mitochondrial H 267 Homo sapiens Gene Name(s): MRPL9 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L10, mitochondrial I 261 Homo sapiens Gene Name(s): MRPL10 Gene View MRPL8 RPML8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L11, mitochondrial J 192 Homo sapiens Gene Name(s): MRPL11 Gene View CGI-113
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L13, mitochondrial K 178 Homo sapiens Gene Name(s): MRPL13 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L14, mitochondrial L 145 Homo sapiens Gene Name(s): MRPL14 Gene View MRPL32 Gene View RPML32
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L15, mitochondrial M 296 Homo sapiens Gene Name(s): MRPL15 Gene View HSPC145
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L16, mitochondrial N 251 Homo sapiens Gene Name(s): MRPL16 Gene View PNAS-111
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L17, mitochondrial O 175 Homo sapiens Gene Name(s): MRPL17 Gene View LIP2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L18, mitochondrial P 180 Homo sapiens Gene Name(s): MRPL18 Gene View HSPC071
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L19, mitochondrial Q 292 Homo sapiens Gene Name(s): MRPL19 Gene View KIAA0104 MRPL15 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L20, mitochondrial R 149 Homo sapiens Gene Name(s): MRPL20 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L21, mitochondrial S 205 Homo sapiens Gene Name(s): MRPL21 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L22, mitochondrial T 206 Homo sapiens Gene Name(s): MRPL22 Gene View MRPL25 RPML25 HSPC158
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L23, mitochondrial U 153 Homo sapiens Gene Name(s): MRPL23 Gene View L23MRP RPL23L
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L24, mitochondrial V 216 Homo sapiens Gene Name(s): MRPL24 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L27, mitochondrial W 148 Homo sapiens Gene Name(s): MRPL27 Gene View HSPC250
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L28, mitochondrial X 256 Homo sapiens Gene Name(s): MRPL28 Gene View MAAT1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L47, mitochondrial Y 250 Homo sapiens Gene Name(s): MRPL47 Gene View NCM1 CGI-204
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L30, mitochondrial Z 161 Homo sapiens Gene Name(s): MRPL30 Gene View MRPL28 Gene View RPML28 HSPC249
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L32, mitochondrial 0 188 Homo sapiens Gene Name(s): MRPL32 Gene View HSPC283
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L33, mitochondrial 1 65 Homo sapiens Gene Name(s): MRPL33 Gene View C2orf1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L34, mitochondrial 2 92 Homo sapiens Gene Name(s): MRPL34 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L35, mitochondrial 3 188 Homo sapiens Gene Name(s): MRPL35 Gene View BM-007
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L37, mitochondrial 5 423 Homo sapiens Gene Name(s): MRPL37 Gene View MRPL2 Gene View RPML2 HSPC235
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L38, mitochondrial 6 380 Homo sapiens Gene Name(s): MRPL38 Gene View HSPC262
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L39, mitochondrial 7 338 Homo sapiens Gene Name(s): MRPL39 Gene View C21orf92 MRPL5 RPML5 MSTP003 PRED22
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L40, mitochondrial 8 206 Homo sapiens Gene Name(s): MRPL40 Gene View NLVCF URIM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L41, mitochondrial 9 137 Homo sapiens Gene Name(s): MRPL41 Gene View BMRP MRPL27 Gene View RPML27 PIG3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L42, mitochondrial a 142 Homo sapiens Gene Name(s): MRPL42 Gene View MRPL31 MRPS32 RPML31 HSPC204 PTD007
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L43, mitochondrial b 215 Homo sapiens Gene Name(s): MRPL43 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L44, mitochondrial c 332 Homo sapiens EC#: 3.1.26 IUBMB
Gene Name(s): MRPL44 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L45, mitochondrial d 306 Homo sapiens Gene Name(s): MRPL45 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L46, mitochondrial e 279 Homo sapiens Gene Name(s): MRPL46 Gene View C15orf4 LIECG2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L48, mitochondrial f 212 Homo sapiens Gene Name(s): MRPL48 Gene View CGI-118 HSPC290
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L49, mitochondrial g 166 Homo sapiens Gene Name(s): MRPL49 Gene View C11orf4 NOF1 OK/SW-cl.67
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L50, mitochondrial h 158 Homo sapiens Gene Name(s): MRPL50 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L51, mitochondrial i 128 Homo sapiens Gene Name(s): MRPL51 Gene View MRP64 CDA09 HSPC241
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L52, mitochondrial j 123 Homo sapiens Gene Name(s): MRPL52 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L53, mitochondrial k 112 Homo sapiens Gene Name(s): MRPL53 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L54, mitochondrial l 138 Homo sapiens Gene Name(s): MRPL54 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein L55, mitochondrial m 128 Homo sapiens Gene Name(s): MRPL55 Gene View UNQ5835/PRO19675
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ribosomal protein 63, mitochondrial o 102 Homo sapiens Gene Name(s): MRPL57 Gene View MRP63
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Peptidyl-tRNA hydrolase ICT1, mitochondrial p 206 Homo sapiens EC#: 3.1.1.29 IUBMB
Gene Name(s): ICT1 DS1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Growth arrest and DNA damage-inducible proteins-interacting protein 1 q 222 Homo sapiens Gene Name(s): GADD45GIP1 Gene View MRPL59 PLINP1 PRG6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein S18a, mitochondrial r 196 Homo sapiens Gene Name(s): MRPS18A Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
39S ribosomal protein S30, mitochondrial s 439 Homo sapiens Gene Name(s): MRPS30 Gene View PDCD9 BM-047
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Unknown protein or protein extension t 28 Homo sapiens
Mitochondrial assembly of ribosomal large subunit protein 1 u 234 Homo sapiens Gene Name(s): MALSU1 Gene View C7orf30
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
MIEF1 upstream open reading frame protein v 70 Homo sapiens Gene Name(s): MIEF1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Acyl carrier protein, mitochondrial w 156 Homo sapiens Gene Name(s): NDUFAB1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA A 1559 Homo sapiens
mitochondrial tRNAVal B 69 Homo sapiens

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PNS
Query on PNS

v 4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

0, I ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, W, g MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
t L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-08-08
  • Released Date: 2017-09-13
  • Deposition author(s): Brown, A., Rathore, S., Kimanius, D., Aibara, S., Bia, X.C., Rorbach, J., Amunts, A., Ramakrishnan, V.

Revision History

  • 2017-09-20
    Type: Database references