4V9F

The re-refined crystal structure of the Haloarcula marismortui large ribosomal subunit at 2.4 Angstrom resolution: more complete structure of the L7/L12 and L1 stalk, L5 and LX proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Revisiting the Haloarcula marismortui 50S ribosomal subunit model.

Gabdulkhakov, A.Nikonov, S.Garber, M.

(2013) Acta Crystallogr D Biol Crystallogr 69: 997-1004

  • DOI: 10.1107/S0907444913004745
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of the large ribosomal subunit from the halophilic archaeon Haloarcula marismortui (Hma) is the only crystal structure of an archaeal ribosomal particle that has been determined to date. However, the first model of the Hma 50S ribosomal ...

    The structure of the large ribosomal subunit from the halophilic archaeon Haloarcula marismortui (Hma) is the only crystal structure of an archaeal ribosomal particle that has been determined to date. However, the first model of the Hma 50S ribosomal subunit contained some gaps: the structures of functionally important mobile lateral protuberances were not visualized. Subsequently, some parts of the P (L12) stalk base were visualized at 3.0 Å resolution [Kavran & Steitz (2007), J. Mol. Biol. 371, 1047-1059]: the RNA-binding domain of r-protein P0 (L10), the C-terminal domain of L11 and helices 43 and 44 of the 23 S rRNA. Here, the 2.4 Å resolution electron-density map of the Hma 50S ribosomal subunit was revisited and approximately two-thirds of the P0 protein, residues 1-58 of the N-terminal domains of two P1 protein molecules, residues 130-156 of L11, the full-length r-protein LX, nucleotides 2137-2149 and 2226-2237 of the 23S rRNA helix H76 forming the L1 stalk, nucleotides 2339-2343 of the 23S rRNA (contacting L5 protein) and loops 29-34 and 108-128 of protein L5 could be visualized. Thus, this paper provides a supplemented version of the Hma 50S ribosomal subunit model.


    Related Citations: 
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
      Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A.
      (2000) Science 289: 905

    Organizational Affiliation

    Institute of Protein Research, RAS, Pushchino, Moscow Region 142290, Russian Federation. azat@vega.protres.ru



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10eH177Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl10errnAC2357
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11PI162Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl11rrnAC1414
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13PJ145Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl13rrnAC0065
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14PK132Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl14rrnAC1602
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15PL165Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl15rrnAC1590
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15eM196Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl15errnAC2065
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18PN187Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl18rrnAC1593
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18eO116Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl18errnAC0064
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19eP149Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl19errnAC1594
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21eQ96Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl21errnAC0260
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22PR155Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl22rrnAC1606
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23PS85Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl23rrnAC1609
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24PT120Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl24rrnAC1601
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24eU67Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl24errnAC0104
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29PV71Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl29rrnAC1604
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30PW154Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl30rrnAC1591
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31eX92Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl31errnAC3113
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32eY241Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl32errnAC1595
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37AeZ92Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl37aerrnAC1669
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37e157Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl37errnAC0797.1
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2PA240Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl2rrnAC1608
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39e250Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl39errnAC3112
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44e392Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl44errnAC3514
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L124, 570Haloarcula marismortui ATCC 43049Mutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein LX656Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl18arpl20erplXrrnAC3115.1
Find proteins for P14125 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3PB338Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl3rrnAC1611
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4PC246Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl4rrnAC1610
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5PD177Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl5rrnAC1598
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6PE178Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl6rrnAC1596
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7AeF120Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl7aerrnAC0103
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10EG255Haloarcula marismortui ATCC 43049Mutation(s): 0 
Gene Names: rpl10rpl10erplP0rrnAC1417
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
23S Ribosomal RNA02910Haloarcula marismortui ATCC 43049

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Entity ID: 2
MoleculeChainsLengthOrganism
5S Ribosomal RNA9122Haloarcula marismortui ATCC 43049
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

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1, 3, O, U, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download CCD File 
0, W
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
0, O
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
0, 3, 9, A, B, F, G, J, L, M, N, O, R, Y
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
0, 3, 9, A, K, L, N, T, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
0, 9, A, C, H, J, L, M, Q, R, S
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.66α = 90
b = 299.67β = 90
c = 573.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-11-02 
  • Released Date: 2014-07-09 
  • Deposition Author(s): Gabdulkhakov, A.
  • This entry supersedes: 4HUB, 4I4M

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2017-06-28
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Database references, Derived calculations, Refinement description