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- PDB-3j6b: Structure of the yeast mitochondrial large ribosomal subunit -

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Basic information

Entry
Database: PDB / ID: 3j6b
TitleStructure of the yeast mitochondrial large ribosomal subunit
Components
  • (54S ribosomal protein ...) x 37
  • 21S ribosomal RNA
  • E-site tRNA
  • Mitochondrial homologous recombination protein 1
  • mitochondrial ribosomal protein YNL122C
KeywordsRIBOSOME / mitochondrial ribosome / large subunit / protein-RNA complex
Function / homology
Function and homology information


positive regulation of mitochondrial DNA replication / DNA strand exchange activity / mitochondrial genome maintenance / ribonuclease III activity / mitochondrial large ribosomal subunit / mitochondrial translation / RNA processing / cell redox homeostasis / rRNA processing / large ribosomal subunit rRNA binding ...positive regulation of mitochondrial DNA replication / DNA strand exchange activity / mitochondrial genome maintenance / ribonuclease III activity / mitochondrial large ribosomal subunit / mitochondrial translation / RNA processing / cell redox homeostasis / rRNA processing / large ribosomal subunit rRNA binding / double-stranded RNA binding / single-stranded DNA binding / ribosome biogenesis / large ribosomal subunit / cellular response to oxidative stress / cytosolic large ribosomal subunit / transferase activity / DNA recombination / mitochondrial inner membrane / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
54S ribosomal protein L8, C-terminal / Ribosomal L27 protein, C-terminal / Ribosomal L27 protein C-terminal domain / 54S ribosomal protein L8 C-terminal domain / : / Mitochondrial ribosomal protein subunit L20 / Ribosomal protein L31p, N-terminal / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 ...54S ribosomal protein L8, C-terminal / Ribosomal L27 protein, C-terminal / Ribosomal L27 protein C-terminal domain / 54S ribosomal protein L8 C-terminal domain / : / Mitochondrial ribosomal protein subunit L20 / Ribosomal protein L31p, N-terminal / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L3, double-stranded RNA binding domain / Transcriptional regulation of mitochondrial recombination / Mitochondrial ribosomal protein mL59 / 54S ribosomal protein L28, mitochondrial / Ribosomal protein L31, mitochondrial / 54S ribosomal protein L36, yeast / Mitochondrial ribosomal protein L31 / Ribonuclease-III-like / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Ribonuclease III / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / ACP-like superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein mL60 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL58 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein mL60 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL58 / Large ribosomal subunit protein mL59 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL6m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL5m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein mL57 / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein bL31m / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL67 / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL13m
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAmunts, A. / Brown, A. / Bai, X.C. / Llacer, J.L. / Hussain, T. / Emsley, P. / Long, F. / Murshudov, G. / Scheres, S.H.W. / Ramakrishnan, V.
CitationJournal: Science / Year: 2014
Title: Structure of the yeast mitochondrial large ribosomal subunit.
Authors: Alexey Amunts / Alan Brown / Xiao-Chen Bai / Jose L Llácer / Tanweer Hussain / Paul Emsley / Fei Long / Garib Murshudov / Sjors H W Scheres / V Ramakrishnan /
Abstract: Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single- ...Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle cryo-electron microscopy. The resolution of 3.2 angstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site, and a putative membrane docking site.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Other
SupersessionDec 10, 2014ID: 1VW3, 1VW4
Revision 1.2Dec 10, 2014Group: Other
Revision 1.3Dec 17, 2014Group: Other
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 21S ribosomal RNA
B: 54S ribosomal protein RML2, mitochondrial
C: 54S ribosomal protein L9, mitochondrial
D: 54S ribosomal protein YmL6, mitochondrial
E: 54S ribosomal protein L7, mitochondrial
F: 54S ribosomal protein L6, mitochondrial
G: 54S ribosomal protein L50, mitochondrial
H: 54S ribosomal protein L23, mitochondrial
I: 54S ribosomal protein L38, mitochondrial
J: 54S ribosomal protein L10, mitochondrial
K: 54S ribosomal protein L16, mitochondrial
L: 54S ribosomal protein L8, mitochondrial
M: 54S ribosomal protein IMG1, mitochondrial
N: 54S ribosomal protein L49, mitochondrial
O: 54S ribosomal protein L22, mitochondrial
P: 54S ribosomal protein L41, mitochondrial
Q: 54S ribosomal protein L40, mitochondrial
R: 54S ribosomal protein L2, mitochondrial
S: 54S ribosomal protein L24, mitochondrial
T: 54S ribosomal protein L4, mitochondrial
U: 54S ribosomal protein L33, mitochondrial
V: 54S ribosomal protein L36, mitochondrial
W: 54S ribosomal protein L32, mitochondrial
X: 54S ribosomal protein L39, mitochondrial
Y: 54S ribosomal protein L34, mitochondrial
Z: mitochondrial ribosomal protein YNL122C
0: 54S ribosomal protein RTC6, mitochondrial
1: 54S ribosomal protein L35, mitochondrial
2: 54S ribosomal protein L28, mitochondrial
3: 54S ribosomal protein L27, mitochondrial
4: 54S ribosomal protein L51, mitochondrial
5: 54S ribosomal protein L3, mitochondrial
6: 54S ribosomal protein L17, mitochondrial
7: 54S ribosomal protein IMG2, mitochondrial
8: 54S ribosomal protein L13, mitochondrial
9: 54S ribosomal protein L15, mitochondrial
a: 54S ribosomal protein L20, mitochondrial
b: 54S ribosomal protein L25, mitochondrial
c: 54S ribosomal protein L31, mitochondrial
d: Mitochondrial homologous recombination protein 1
e: E-site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,040,158154
Polymers2,037,33141
Non-polymers2,827113
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules Ae

#1: RNA chain 21S ribosomal RNA /


Mass: 1057805.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#41: RNA chain E-site tRNA


Mass: 6451.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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54S ribosomal protein ... , 37 types, 37 molecules BCDEFGHIJKLMNOPQRSTUVWXY012345...

#2: Protein 54S ribosomal protein RML2, mitochondrial / Ribosome / L2


Mass: 43870.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32611
#3: Protein 54S ribosomal protein L9, mitochondrial / Ribosome / YmL9


Mass: 29843.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P31334
#4: Protein 54S ribosomal protein YmL6, mitochondrial / Ribosome


Mass: 32014.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P51998
#5: Protein 54S ribosomal protein L7, mitochondrial / Ribosome / YmL5 / YmL7


Mass: 33152.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36519
#6: Protein 54S ribosomal protein L6, mitochondrial / Ribosome / YmL16


Mass: 23926.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32904
#7: Protein 54S ribosomal protein L50, mitochondrial / Ribosome


Mass: 16313.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53724
#8: Protein 54S ribosomal protein L23, mitochondrial / Ribosome / YmL23


Mass: 18499.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12487
#9: Protein 54S ribosomal protein L38, mitochondrial / Ribosome / YmL38 / 54S ribosomal protein L34 / mitochondrial / YmL34


Mass: 14929.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35996
#10: Protein 54S ribosomal protein L10, mitochondrial / Ribosome / YmL10/YmL18


Mass: 36414.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36520
#11: Protein 54S ribosomal protein L16, mitochondrial / Ribosome / YmL47


Mass: 26569.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38064
#12: Protein 54S ribosomal protein L8, mitochondrial / Ribosome / YmL8


Mass: 26989.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22353
#13: Protein 54S ribosomal protein IMG1, mitochondrial / Ribosome / Integrity of mitochondrial genome protein 1 / PetCR46


Mass: 19428.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25626
#14: Protein 54S ribosomal protein L49, mitochondrial / Ribosome / YmL49


Mass: 18420.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40858
#15: Protein 54S ribosomal protein L22, mitochondrial / Ribosome


Mass: 34957.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53881
#16: Protein 54S ribosomal protein L41, mitochondrial / Ribosome / YmL41


Mass: 30616.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32387
#17: Protein 54S ribosomal protein L40, mitochondrial / Ribosome / YmL40


Mass: 33808.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36534
#18: Protein 54S ribosomal protein L2, mitochondrial / Ribosome / YMR6 / YmL2


Mass: 43310.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12687
#19: Protein 54S ribosomal protein L24, mitochondrial / Ribosome / YmL14/YmL24


Mass: 30109.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36525
#20: Protein 54S ribosomal protein L4, mitochondrial / Ribosome / YmL4


Mass: 37019.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36517
#21: Protein 54S ribosomal protein L33, mitochondrial / Ribosome / YmL33


Mass: 9549.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20084
#22: Protein 54S ribosomal protein L36, mitochondrial / Ribosome / YmL36


Mass: 20125.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36531
#23: Protein 54S ribosomal protein L32, mitochondrial / Ribosome / YmL32


Mass: 21483.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25348
#24: Protein 54S ribosomal protein L39, mitochondrial / Ribosome / YmL39


Mass: 7992.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36533
#25: Protein 54S ribosomal protein L34, mitochondrial / Ribosome / L34mt


Mass: 12054.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04598
#27: Protein 54S ribosomal protein RTC6, mitochondrial / Ribosome / Restriction of telomere capping protein 6 / Translation associated element 4


Mass: 10718.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O14464
#28: Protein 54S ribosomal protein L35, mitochondrial / Ribosome / YmL35


Mass: 42886.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06678
#29: Protein 54S ribosomal protein L28, mitochondrial / Ribosome / YmL28


Mass: 17373.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36527
#30: Protein 54S ribosomal protein L27, mitochondrial / Ribosome / YmL27


Mass: 16521.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36526
#31: Protein 54S ribosomal protein L51, mitochondrial / Ribosome


Mass: 16153.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06090
#32: Protein 54S ribosomal protein L3, mitochondrial / Ribosome / YmL3


Mass: 44058.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36516
#33: Protein 54S ribosomal protein L17, mitochondrial / Ribosome / YmL17/YmL30


Mass: 32261.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36528
#34: Protein 54S ribosomal protein IMG2, mitochondrial / Ribosome / Integrity of mitochondrial genome protein 2


Mass: 16406.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25642
#35: Protein 54S ribosomal protein L13, mitochondrial / Ribosome / YmL13


Mass: 30317.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02204
#36: Protein 54S ribosomal protein L15, mitochondrial / Ribosome / YmL15


Mass: 28148.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36523
#37: Protein 54S ribosomal protein L20, mitochondrial / Ribosome / YmL20


Mass: 22431.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22354
#38: Protein 54S ribosomal protein L25, mitochondrial / Ribosome / YmL25


Mass: 18626.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23369
#39: Protein 54S ribosomal protein L31, mitochondrial / Ribosome / YmL31


Mass: 15555.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14063

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Protein , 2 types, 2 molecules Zd

#26: Protein mitochondrial ribosomal protein YNL122C


Mass: 13276.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53921
#40: Protein Mitochondrial homologous recombination protein 1 / Cross-linked transcription component 1


Mass: 26937.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06630

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Non-polymers , 3 types, 113 molecules

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


Mass: 24.305 Da / Num. of mol.: 110 / Source method: obtained synthetically / Formula: Mg
#43: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#44: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast Mitochondrial Large Ribosomal Subunit / Type: RIBOSOME
Molecular weightValue: 1.9 MDa / Experimental value: NO
Buffer solutionName: 20 mM HEPES-KOH, pH 7.5, 100 mM potassium chloride, 20 mM magnesium acetate, 2 mM DTT
pH: 7.5
Details: 20 mM HEPES-KOH, pH 7.5, 100 mM potassium chloride, 20 mM magnesium acetate, 2 mM DTT
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon grids (Quantifoil R2/2) with home-made continuous carbon film
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temp: 90 K / Humidity: 100 %
Details: Blot 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK II)
Method: Blot 2.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 25, 2013
Details: Objective lens astigmatism was corrected at 59,000 times magnification
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 4700 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 85 K / Temperature (max): 90 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1030
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0067 2014/01/21 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47124 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å
Details: A newly developed statistical movie processing approach was used to compensate for beam-induced movement.
Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
RefinementResolution: 3.2→262.64 Å / Cor.coef. Fo:Fc: 0.938 / SU B: 16.551 / SU ML: 0.26 / Average fsc overall: 0.8808 / Average fsc work: 0.8808 / ESU R: 0.372
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.2485 955316 -
all0.249 --
Rfree--0 %
obs--100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 94.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.458 Å2-0.762 Å20.079 Å2
2---0.616 Å20.216 Å2
3---0.158 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.015121015
ELECTRON MICROSCOPYr_bond_other_d0.0020.0279796
ELECTRON MICROSCOPYr_ext_dist_refined_d0.5790.07156648
ELECTRON MICROSCOPYr_angle_refined_deg0.9991.574174274
ELECTRON MICROSCOPYr_angle_other_deg1.0953187243
ELECTRON MICROSCOPYr_dihedral_angle_1_deg18.5356.3387656
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.522.7842295
ELECTRON MICROSCOPYr_dihedral_angle_3_deg19.492159868
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.80815460
ELECTRON MICROSCOPYr_chiral_restr0.2380.20619375
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0291779
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0226185
ELECTRON MICROSCOPYr_nbd_refined0.1830.222881
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1950.285963
ELECTRON MICROSCOPYr_nbtor_refined0.2150.248552
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0740.244744
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1840.21959
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0690.236
ELECTRON MICROSCOPYr_metal_ion_refined0.0970.24
ELECTRON MICROSCOPYr_paralell_plane_angle_deg4.0021.21856
ELECTRON MICROSCOPYr_mcbond_it2.44710.19326772
ELECTRON MICROSCOPYr_mcbond_other2.44710.19326771
ELECTRON MICROSCOPYr_mcangle_it4.27815.28233332
ELECTRON MICROSCOPYr_mcangle_other4.27815.28233333
ELECTRON MICROSCOPYr_scbond_it2.289.54694243
ELECTRON MICROSCOPYr_scbond_other2.289.54694244
ELECTRON MICROSCOPYr_scangle_it3.91614.295140942
ELECTRON MICROSCOPYr_scangle_other3.91614.295140943
ELECTRON MICROSCOPYr_lrange_it9.48198.474380176
ELECTRON MICROSCOPYr_lrange_other9.48198.474380177
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: 0 / Total num. of bins used: 20 / % reflection obs: 100 % / WRfactor Rwork: 0

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work
3.2-3.2830.459707830.459707830.707
3.283-3.3730.396688720.396688720.76
3.373-3.4710.363669840.363669840.796
3.471-3.5780.334649170.334649170.831
3.578-3.6950.312631780.312631780.86
3.695-3.8250.29608550.29608550.884
3.825-3.9690.271589470.271589470.903
3.969-4.1310.257565730.257565730.912
4.131-4.3150.245543010.245543010.923
4.315-4.5250.235519580.235519580.933
4.525-4.770.223492410.223492410.94
4.77-5.0590.216466460.216466460.943
5.059-5.4080.207439210.207439210.948
5.408-5.8410.207408540.207408540.948
5.841-6.3990.215375430.215375430.944
6.399-7.1530.212339130.212339130.946
7.153-8.2590.207299090.207299090.949
8.259-10.1130.197253110.197253110.953
10.113-14.2910.179195370.179195370.961
14.291-262.640.186107410.186107410.978

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