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Database: PDB / ID: 5ool
TitleStructure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA
Components
  • (39S ribosomal protein ...) x 47
  • 16S ribosomal RNA
  • Acyl carrier protein, mitochondrial
  • Growth arrest and DNA damage-inducible proteins-interacting protein 1
  • MIEF1 upstream open reading frame protein
  • Mitochondrial assembly of ribosomal large subunit protein 1
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Ribosomal protein 63, mitochondrialRibosome
  • Unknown protein or protein extension
  • mitochondrial tRNAVal
KeywordsRIBOSOME / Ribosome / mitochondria / biogenesis / translation / electron cryomicroscopy
Function / homologyRibosomal silencing factor during starvation / Ribosomal protein S10 domain superfamily / Phosphatidylethanolamine-binding protein, eukaryotic / Ribosomal protein L36 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Thioredoxin-like superfamily / Ribosomal protein L17 superfamily / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L22/L17 superfamily ...Ribosomal silencing factor during starvation / Ribosomal protein S10 domain superfamily / Phosphatidylethanolamine-binding protein, eukaryotic / Ribosomal protein L36 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Thioredoxin-like superfamily / Ribosomal protein L17 superfamily / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L22/L17 superfamily / PEBP-like superfamily / ACP-like superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L14 superfamily / L28p-like / Ribosomal protein S18 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / MRP-L47 superfamily, mitochondrial / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L20, C-terminal / 39S ribosomal protein L52, mitochondrial / Ribosomal protein L16p/L10e / Ribosomal protein L9, N-terminal / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Ribosomal protein L50, mitochondria / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L55, mitochondrial / Ribosomal protein L27/L41, mitochondrial / Ribosomal protein L28/L40, mitochondrial / Ribosomal protein L35, mitochondrial / Ribosomal protein S32, mitochondrial / Ribosomal protein L51, mitochondrial / Ribosomal protein L53, mitochondrial / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L11, C-terminal / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L11, N-terminal / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal protein L46 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein S10 domain / Mitochondrial ribosomal protein L48 / Ribosomal protein L15 / NTF2-like domain superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L23 / Ribosomal protein L10e/L16 / Mitochondrial ribosome protein 63 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L27 / Mitochondrial ribosomal protein L28 / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial 28S ribosomal protein S32 / Mitochondrial ribosomal subunit / Ribosomal subunit 39S / 39S ribosomal protein L53/MRP-L53 / 39S mitochondrial ribosomal protein L46 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Phosphopantetheine attachment site. / Ribosomal protein L3 signature. / Ribosomal protein L13 signature. / Ribosomal protein L24 signature. / Carrier protein (CP) domain profile. / Double stranded RNA-binding domain (dsRBD) profile. / Glyoxylate metabolism and glycine degradation / Mitochondrial translation initiation / Mitochondrial translation elongation / Mitochondrial translation termination / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Complex 1 protein (LYR family) / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L3 / Ribosomal protein L4/L1 family / Ribosomal protein L11, RNA binding domain / Ribosomal protein L30p/L7e / Ribosomal protein S10p/S20e / Ribosomal protein L36 / Ribosomal protein L20
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.06 Å resolution
AuthorsBrown, A. / Rathore, S. / Kimanius, D. / Aibara, S. / Bai, X.C. / Rorbach, J. / Amunts, A. / Ramakrishnan, V.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structures of the human mitochondrial ribosome in native states of assembly.
Authors: Alan Brown / Sorbhi Rathore / Dari Kimanius / Shintaro Aibara / Xiao-Chen Bai / Joanna Rorbach / Alexey Amunts / V Ramakrishnan
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 8, 2017 / Release: Sep 13, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 13, 2017Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Oct 18, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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  • EMDB-3842
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 16S ribosomal RNA
B: mitochondrial tRNAVal
D: 39S ribosomal protein L2, mitochondrial
E: 39S ribosomal protein L3, mitochondrial
F: 39S ribosomal protein L4, mitochondrial
H: 39S ribosomal protein L9, mitochondrial
I: 39S ribosomal protein L10, mitochondrial
J: 39S ribosomal protein L11, mitochondrial
K: 39S ribosomal protein L13, mitochondrial
L: 39S ribosomal protein L14, mitochondrial
M: 39S ribosomal protein L15, mitochondrial
N: 39S ribosomal protein L16, mitochondrial
O: 39S ribosomal protein L17, mitochondrial
P: 39S ribosomal protein L18, mitochondrial
Q: 39S ribosomal protein L19, mitochondrial
R: 39S ribosomal protein L20, mitochondrial
S: 39S ribosomal protein L21, mitochondrial
T: 39S ribosomal protein L22, mitochondrial
U: 39S ribosomal protein L23, mitochondrial
V: 39S ribosomal protein L24, mitochondrial
W: 39S ribosomal protein L27, mitochondrial
X: 39S ribosomal protein L28, mitochondrial
Y: 39S ribosomal protein L47, mitochondrial
Z: 39S ribosomal protein L30, mitochondrial
0: 39S ribosomal protein L32, mitochondrial
1: 39S ribosomal protein L33, mitochondrial
2: 39S ribosomal protein L34, mitochondrial
3: 39S ribosomal protein L35, mitochondrial
4: 39S ribosomal protein L36, mitochondrial
5: 39S ribosomal protein L37, mitochondrial
6: 39S ribosomal protein L38, mitochondrial
7: 39S ribosomal protein L39, mitochondrial
8: 39S ribosomal protein L40, mitochondrial
9: 39S ribosomal protein L41, mitochondrial
a: 39S ribosomal protein L42, mitochondrial
b: 39S ribosomal protein L43, mitochondrial
c: 39S ribosomal protein L44, mitochondrial
d: 39S ribosomal protein L45, mitochondrial
e: 39S ribosomal protein L46, mitochondrial
f: 39S ribosomal protein L48, mitochondrial
g: 39S ribosomal protein L49, mitochondrial
h: 39S ribosomal protein L50, mitochondrial
i: 39S ribosomal protein L51, mitochondrial
j: 39S ribosomal protein L52, mitochondrial
k: 39S ribosomal protein L53, mitochondrial
l: 39S ribosomal protein L54, mitochondrial
m: 39S ribosomal protein L55, mitochondrial
o: Ribosomal protein 63, mitochondrial
p: Peptidyl-tRNA hydrolase ICT1, mitochondrial
q: Growth arrest and DNA damage-inducible proteins-interacting protein 1
r: 39S ribosomal protein S18a, mitochondrial
s: 39S ribosomal protein S30, mitochondrial
t: Unknown protein or protein extension
u: Mitochondrial assembly of ribosomal large subunit protein 1
v: MIEF1 upstream open reading frame protein
w: Acyl carrier protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,797,381152
Polyers1,794,59056
Non-polymers2,79196
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)341640
ΔGint (kcal/M)-3020
Surface area (Å2)500180
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 16S ribosomal RNA /


Mass: 500019.594 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 1025814679
#2: RNA chain mitochondrial tRNAVal


Mass: 22022.131 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 1215733170

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39S ribosomal protein ... , 47 types, 47 molecules DEFHIJKLMNOPQRSTUVWXYZ01234567...

#3: Protein/peptide 39S ribosomal protein L2, mitochondrial / Ribosome / MRP-L2 / Mitochondrial large ribosomal subunit protein uL2m


Mass: 33355.941 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T653
#4: Protein/peptide 39S ribosomal protein L3, mitochondrial / Ribosome / MRP-L3 / Mitochondrial large ribosomal subunit protein uL3m


Mass: 38689.562 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P09001
#5: Protein/peptide 39S ribosomal protein L4, mitochondrial / Ribosome / MRP-L4 / Mitochondrial large ribosomal subunit protein uL4m


Mass: 34970.195 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD3
#6: Protein/peptide 39S ribosomal protein L9, mitochondrial / Ribosome / MRP-L9 / Mitochondrial large ribosomal subunit protein bL9m


Mass: 30296.355 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD2
#7: Protein/peptide 39S ribosomal protein L10, mitochondrial / Ribosome / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / MRP-L8 / Mitochondrial large ribosomal subunit protein uL10m


Mass: 29322.529 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7H8
#8: Protein/peptide 39S ribosomal protein L11, mitochondrial / Ribosome / MRP-L11 / Mitochondrial large ribosomal subunit protein uL11m


Mass: 20716.227 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B7
#9: Protein/peptide 39S ribosomal protein L13, mitochondrial / Ribosome / MRP-L13 / Mitochondrial large ribosomal subunit protein uL13m


Mass: 20722.988 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD1
#10: Protein/peptide 39S ribosomal protein L14, mitochondrial / Ribosome / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / MRP-L32 / Mitochondrial large ribosomal subunit protein uL14m


Mass: 15973.702 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1L8
#11: Protein/peptide 39S ribosomal protein L15, mitochondrial / Ribosome / MRP-L15 / Mitochondrial large ribosomal subunit protein uL15m


Mass: 33473.820 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P015
#12: Protein/peptide 39S ribosomal protein L16, mitochondrial / Ribosome / MRP-L16 / Mitochondrial large ribosomal subunit protein uL16m


Mass: 28496.285 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX20
#13: Protein/peptide 39S ribosomal protein L17, mitochondrial / Ribosome / MRP-L17 / LYST-interacting protein 2 / Mitochondrial large ribosomal subunit protein bL17m


Mass: 20083.266 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX2
#14: Protein/peptide 39S ribosomal protein L18, mitochondrial / Ribosome / MRP-L18 / Mitochondrial large ribosomal subunit protein uL18m


Mass: 20607.570 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H0U6
#15: Protein/peptide 39S ribosomal protein L19, mitochondrial / Ribosome / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal subunit protein bL19m


Mass: 33584.996 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P49406
#16: Protein/peptide 39S ribosomal protein L20, mitochondrial / Ribosome / MRP-L20 / Mitochondrial large ribosomal subunit protein bL20m


Mass: 17479.654 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC9
#17: Protein/peptide 39S ribosomal protein L21, mitochondrial / Ribosome / MRP-L21 / Mitochondrial large ribosomal subunit protein bL21m


Mass: 22847.682 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z2W9
#18: Protein/peptide 39S ribosomal protein L22, mitochondrial / Ribosome / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / MRP-L25 / Mitochondrial large ribosomal subunit protein uL22m


Mass: 23683.732 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWU5
#19: Protein/peptide 39S ribosomal protein L23, mitochondrial / Ribosome / MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / Ribosomal protein L23-like


Mass: 17807.189 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16540
#20: Protein/peptide 39S ribosomal protein L24, mitochondrial / Ribosome / MRP-L24 / Mitochondrial large ribosomal subunit protein uL24m


Mass: 24953.875 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A35
#21: Protein/peptide 39S ribosomal protein L27, mitochondrial / Ribosome / MRP-L27 / Mitochondrial large ribosomal subunit protein bL27m


Mass: 16102.859 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0M9
#22: Protein/peptide 39S ribosomal protein L28, mitochondrial / Ribosome / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / Mitochondrial large ribosomal subunit protein bL28m


Mass: 30202.867 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#23: Protein/peptide 39S ribosomal protein L47, mitochondrial / Ribosome / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis-related protein 1


Mass: 29508.535 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HD33
#24: Protein/peptide 39S ribosomal protein L30, mitochondrial / Ribosome / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / MRP-L28 / Mitochondrial large ribosomal subunit protein uL30m


Mass: 18582.812 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TCC3
#25: Protein/peptide 39S ribosomal protein L32, mitochondrial / Ribosome / MRP-L32 / Mitochondrial large ribosomal subunit protein bL32m


Mass: 21437.799 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC8
#26: Protein/peptide 39S ribosomal protein L33, mitochondrial / Ribosome / MRP-L33 / Mitochondrial large ribosomal subunit protein bL33m


Mass: 7635.204 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75394
#27: Protein/peptide 39S ribosomal protein L34, mitochondrial / Ribosome / MRP-L34 / Mitochondrial large ribosomal subunit protein bL34m


Mass: 10183.913 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQ48
#28: Protein/peptide 39S ribosomal protein L35, mitochondrial / Ribosome / MRP-L35 / Mitochondrial large ribosomal subunit protein bL35m


Mass: 21558.488 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZE8
#29: Protein/peptide 39S ribosomal protein L36, mitochondrial / Ribosome / MRP-L36 / BRCA1-interacting protein 1 / Mitochondrial large ribosomal subunit protein bL36m


Mass: 11809.301 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J6
#30: Protein/peptide 39S ribosomal protein L37, mitochondrial / Ribosome / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit protein mL37


Mass: 48183.344 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE1
#31: Protein/peptide 39S ribosomal protein L38, mitochondrial / Ribosome / MRP-L38 / Mitochondrial large ribosomal subunit protein mL38


Mass: 44659.430 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DV4
#32: Protein/peptide 39S ribosomal protein L39, mitochondrial / Ribosome / MRP-L39 / 39S ribosomal protein L5 / mitochondrial / MRP-L5 / Mitochondrial large ribosomal subunit protein mL39


Mass: 38764.785 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYK5
#33: Protein/peptide 39S ribosomal protein L40, mitochondrial / Ribosome / MRP-L40 / Mitochondrial large ribosomal subunit protein mL40 / Nuclear localization signal-containing protein deleted in velocardiofacial syndrome / Up-regulated in metastasis


Mass: 24534.422 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NQ50
#34: Protein/peptide 39S ribosomal protein L41, mitochondrial / Ribosome / 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


Mass: 15404.708 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IXM3
#35: Protein/peptide 39S ribosomal protein L42, mitochondrial / Ribosome / MRP-L42 / 39S ribosomal protein L31 / mitochondrial / MRP-L31 / Mitochondrial large ribosomal subunit protein mL42


Mass: 16691.176 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6G3
#36: Protein/peptide 39S ribosomal protein L43, mitochondrial / Ribosome / MRP-L43 / Mitochondrial large ribosomal subunit protein mL43 / Mitochondrial ribosomal protein bMRP36a


Mass: 23457.789 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983
#37: Protein/peptide 39S ribosomal protein L44, mitochondrial / Ribosome / MRP-L44 / Mitochondrial large ribosomal subunit protein mL44


Mass: 37583.312 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: Q9H9J2, Endoribonucleases Producing 5'-Phosphomonoesters
#38: Protein/peptide 39S ribosomal protein L45, mitochondrial / Ribosome / MRP-L45 / Mitochondrial large ribosomal subunit protein mL45


Mass: 35402.918 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRJ2
#39: Protein/peptide 39S ribosomal protein L46, mitochondrial / Ribosome / MRP-L46 / Mitochondrial large ribosomal subunit protein mL46 / P2ECSL


Mass: 31748.107 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H2W6
#40: Protein/peptide 39S ribosomal protein L48, mitochondrial / Ribosome / MRP-L48 / Mitochondrial large ribosomal subunit protein mL48


Mass: 23970.814 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96GC5
#41: Protein/peptide 39S ribosomal protein L49, mitochondrial / Ribosome / MRP-L49 / Mitochondrial large ribosomal subunit protein mL49 / Neighbor of FAU / NOF / Protein NOF1


Mass: 19225.043 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13405
#42: Protein/peptide 39S ribosomal protein L50, mitochondrial / Ribosome / MRP-L50 / Mitochondrial large ribosomal subunit protein mL50


Mass: 18349.943 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N5N7
#43: Protein/peptide 39S ribosomal protein L51, mitochondrial / Ribosome / MRP-L51 / Mitochondrial large ribosomal subunit protein mL51 / bMRP-64 / bMRP64


Mass: 15125.917 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q4U2R6
#44: Protein/peptide 39S ribosomal protein L52, mitochondrial / Ribosome / MRP-L52 / Mitochondrial large ribosomal subunit protein mL52


Mass: 13682.658 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q86TS9
#45: Protein/peptide 39S ribosomal protein L53, mitochondrial / Ribosome / MRP-L53 / Mitochondrial large ribosomal subunit protein mL53


Mass: 12125.859 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL3
#46: Protein/peptide 39S ribosomal protein L54, mitochondrial / Ribosome / MRP-L54 / Mitochondrial large ribosomal subunit protein mL54


Mass: 15844.178 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P161
#47: Protein/peptide 39S ribosomal protein L55, mitochondrial / Ribosome / MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal subunit protein mL55


Mass: 15160.433 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7F7
#51: Protein/peptide 39S ribosomal protein S18a, mitochondrial / Ribosome / S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / Mitochondrial large ribosomal subunit protein bS18a / Mitochondrial large ribosomal subunit protein mL66


Mass: 22224.078 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NVS2
#52: Protein/peptide 39S ribosomal protein S30, mitochondrial / Ribosome / S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ribosomal subunit protein mS30 / Programmed cell death protein 9


Mass: 50429.578 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NP92

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Protein/peptide , 7 types, 7 molecules opqtuvw

#48: Protein/peptide Ribosomal protein 63, mitochondrial / Ribosome / hMRP63 / Mitochondrial large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / Mitochondrial ribosomal protein L57


Mass: 12292.333 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6
#49: Protein/peptide Peptidyl-tRNA hydrolase ICT1, mitochondrial / 39S ribosomal protein L58 / mitochondrial / MRP-L58 / Digestion substraction 1 / DS-1 / Immature colon carcinoma transcript 1 protein / Mitochondrial large ribosomal subunit protein mL62


Mass: 23674.203 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, aminoacyl-tRNA hydrolase
#50: Protein/peptide Growth arrest and DNA damage-inducible proteins-interacting protein 1 / 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


Mass: 25426.895 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8
#53: Protein/peptide Unknown protein or protein extension


Mass: 2400.951 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#54: Protein/peptide Mitochondrial assembly of ribosomal large subunit protein 1


Mass: 26203.076 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3
#55: Protein/peptide MIEF1 upstream open reading frame protein


Mass: 8460.787 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8
#56: Protein/peptide Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 17434.273 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O14561

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Non-polymers , 3 types, 96 molecules

#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 92 / Formula: Mg / Magnesium
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn / Zinc
#59: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Formula: C11H23N2O7PS / Phosphopantetheine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial ribosome large subunit with assembly factor
Type: ORGANELLE OR CELLULAR COMPONENT
Entity ID: 1, 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, 56
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionDetails: 2 mM Synercid (Santa Cruz Biotechnology, Inc) was added to reduce preferential orientation.
pH: 7.45
Buffer component
IDConc.NameFormulaBuffer ID
120 mMHEPES-KOH1
2100 mMPotassium chlorideKCl1
320 mMMagnesium acetateMgOAc1
42 mMDithiothreitol1
SpecimenDetails: Sample concentration = 100 nM / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: Sample incubated for 30 s prior to freezing.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 130841 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 1.56 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 25 / Used frames/image: 1-25

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Processing

SoftwareName: PHENIX / Version: 1.11.1-2575_1479: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION2.0particle selection
2EPUimage acquisition
4Gctf0.5CTF correction
7UCSF Chimera1.11model fitting
8Coot0.8.8model fitting
10PHENIX1.11.1model refinementPhenix.real_space_refine
11RELION2.0initial Euler assignment
12RELION2.0final Euler assignment
13RELION2.0classification
14RELION2.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 134685 / Symmetry type: POINT
Atomic model buildingOverall b value: 85 / Ref protocol: OTHER / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 3J9M
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010104307
ELECTRON MICROSCOPYf_angle_d1.024148152
ELECTRON MICROSCOPYf_dihedral_angle_d14.91959934
ELECTRON MICROSCOPYf_chiral_restr0.05717400
ELECTRON MICROSCOPYf_plane_restr0.00713469

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