7L20

Cryo-EM structure of the human 39S mitoribosomal subunit in complex with RRFmt and EF-G2mt.

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2020-12-15 Released: 2021-05-12 
  • Deposition Author(s): Agrawal, E., Koripella, R.
  • Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of Mammalian mitochondrial ribosome complex with mtEFG2 and mtRRF

Koripella, R.K.Deep, A.Agrawal, E.K.Keshavan, P.Banavali, N.K.Agrawal, R.K.

To be published.

Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialC [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialD [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialE [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialF [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialG [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialH [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialI [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialJ [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialK [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialL [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 13
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39S ribosomal protein L27, mitochondrialM [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialN [auth X]256Homo sapiensMutation(s): 3 
Gene Names: MRPL28MAAT1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialO [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialP [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialQ [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialR [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialS [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialT [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialU [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialV [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialW [auth b]155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialX [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialY [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialZ [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNAAA [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialBA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialCA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1DA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialEA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialFA [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialGA [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 34
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39S ribosomal protein L16, mitochondrialHA [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18, isoform CRA_bIA [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18hCG_34030
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialJA [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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Entity ID: 37
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39S ribosomal protein L24, mitochondrialKA [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 38
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39S ribosomal protein L3, mitochondrialLA [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialMA [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 40
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39S ribosomal protein L38, mitochondrialNA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 41
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39S ribosomal protein L39, mitochondrialOA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 42
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39S ribosomal protein L41, mitochondrialPA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 43
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39S ribosomal protein L42, mitochondrialQA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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Entity ID: 44
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39S ribosomal protein L44, mitochondrialRA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 45
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39S ribosomal protein L45, mitochondrialSA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialTA [auth f]194Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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Entity ID: 47
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39S ribosomal protein L50, mitochondrialUA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 48
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39S ribosomal protein L53, mitochondrialVA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialWA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialXA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialYA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialZA [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
39 S P-site fingerAB [auth u]65Homo sapiensMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L12, mitochondrialBB [auth TA], CB [auth TB], DB [auth TC]198Homo sapiensMutation(s): 0 
Gene Names: MRPL12MRPL7RPML12
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-recycling factor, mitochondrialEB [auth z]204Homo sapiensMutation(s): 0 
Gene Names: MRRF
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PHAROS:  Q96E11
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-releasing factor 2, mitochondrialFB [auth w]696Homo sapiensMutation(s): 0 
Gene Names: GFM2EFG2MSTP027
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNA mitochondrialA1559Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
tRNAvalB73Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
GF [auth w]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BF [auth 0], CF [auth 4], EF [auth r]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A] , AD [auth A] , AE [auth A] , AF [auth W] , BC [auth A] , BD [auth A] , BE [auth A] , CC [auth A] , 
AC [auth A],  AD [auth A],  AE [auth A],  AF [auth W],  BC [auth A],  BD [auth A],  BE [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth g],  EC [auth A],  ED [auth A],  EE [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth E],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth w],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  WE [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XE [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  YE [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZE [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesR01 GM61576

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release