5XYM

Large subunit of Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.

Li, Z.Ge, X.Zhang, Y.Zheng, L.Sanyal, S.Gao, N.

(2018) Protein Cell 9: 384-388


Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmFMSMEG_5489MSMEI_5337
Find proteins for A0R3I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 2B [auth 1]54Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmG2MSMEG_6067MSMEI_5907
Find proteins for A0R551 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmHMSMEG_6946MSMEI_6752
Find proteins for A0R7K0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35D [auth 3]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmIMSMEG_3792MSMEI_3704
Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmJMSMEG_1520MSMEI_1484
Find proteins for A0QSL4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2H [auth C]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplBMSMEG_1439MSMEI_1403
Find proteins for A0QSD4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3I [auth D]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplCMSMEG_1436MSMEI_1400
Find proteins for A0QSD1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4J [auth E]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplDMSMEG_1437MSMEI_1401
Find proteins for A0QSD2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5K [auth F]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplEMSMEG_1467MSMEI_1431
Find proteins for A0QSG1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6L [auth G]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplFMSMEG_1470MSMEI_1434
Find proteins for A0QSG4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9M [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplIMSMEG_6894MSMEI_6710
Find proteins for A0R7F6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13N [auth J]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplMMSMEG_1556MSMEI_1519
Find proteins for A0QSP8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14O [auth K]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplNMSMEG_1465MSMEI_1429
Find proteins for A0QSF9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15P [auth L]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplOMSMEG_1474
Find proteins for A0QSG8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16Q [auth M]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplPMSMEG_1443MSMEI_1407
Find proteins for A0QSD8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17R [auth N]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplQMSMEG_1525MSMEI_1489
Find proteins for A0QSL9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18S [auth O]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplRMSMEG_1471
Find proteins for A0QSG5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19T [auth P]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplSMSMEG_2440MSMEI_2379
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20U [auth Q]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplTMSMEG_3791MSMEI_3703
Find proteins for A0QYU6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21V [auth R]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplUMSMEG_4625MSMEI_4508
Find proteins for A0R151 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22W [auth S]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplVMSMEG_1441MSMEI_1405
Find proteins for A0QSD6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23X [auth T]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplWMSMEG_1438MSMEI_1402
Find proteins for A0QSD3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24Y [auth U]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplXMSMEG_1466MSMEI_1430
Find proteins for A0QSG0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25Z [auth V]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplYctcMSMEG_5431
Find proteins for A0R3D2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27AA [auth W]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmAMSMEG_4624MSMEI_4507
Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28BA [auth X]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmBMSMEG_2400
Find proteins for A0QV03 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29CA [auth Y]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmCMSMEG_1444MSMEI_1408
Find proteins for A0QSD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30DA [auth Z]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmDMSMEG_1473MSMEI_1437
Find proteins for A0QSG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein bL37EA [auth a]24Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1916
Find proteins for A0QTP4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChainsLengthOrganismImage
23S RNAF [auth A]3164Mycolicibacterium smegmatis MC2 155
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Entity ID: 7
MoleculeChainsLengthOrganismImage
5S RNAG [auth B]118Mycolicibacterium smegmatis MC2 155
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , AF [auth A] , BB [auth A] , BC [auth A] , BD [auth A] , 
AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  AF [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  BF [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  CF [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  EF [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth A],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  GF [auth A],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth A],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  IF [auth A],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  JF [auth A],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  KF [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  LF [auth A],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  MF [auth A],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  NF [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  OF [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  PF [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  QF [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  RF [auth A],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  SF [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  TF [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth A],  UF [auth A],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth A],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  WE [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XE [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  YE [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZE [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references