1S72

REFINED CRYSTAL STRUCTURE OF THE HALOARCULA MARISMORTUI LARGE RIBOSOMAL SUBUNIT AT 2.4 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Roles of Ribosomal Proteins in the Structure, Assembly and Evolution of the Large Ribosomal Subunit

Klein, D.J.Moore, P.B.Steitz, T.A.

(2004) J Mol Biol 340: 141-177

  • DOI: 10.1016/j.jmb.2004.03.076
  • Primary Citation of Related Structures:  
    1S72

  • PubMed Abstract: 
  • The structures of ribosomal proteins and their interactions with RNA have been examined in the refined crystal structure of the Haloarcula marismortui large ribosomal subunit. The protein structures fall into six groups based on their topology. The 50S subunit proteins function primarily to stabilize inter-domain interactions that are necessary to maintain the subunit's structural integrity ...

    The structures of ribosomal proteins and their interactions with RNA have been examined in the refined crystal structure of the Haloarcula marismortui large ribosomal subunit. The protein structures fall into six groups based on their topology. The 50S subunit proteins function primarily to stabilize inter-domain interactions that are necessary to maintain the subunit's structural integrity. An extraordinary variety of protein-RNA interactions is observed. Electrostatic interactions between numerous arginine and lysine residues, particularly those in tail extensions, and the phosphate groups of the RNA backbone mediate many protein-RNA contacts. Base recognition occurs via both the minor groove and widened major groove of RNA helices, as well as through hydrophobic binding pockets that capture bulged nucleotides and through insertion of amino acid residues into hydrophobic crevices in the RNA. Primary binding sites on contiguous RNA are identified for 20 of the 50S ribosomal proteins, which along with few large protein-protein interfaces, suggest the order of assembly for some proteins and that the protein extensions fold cooperatively with RNA. The structure supports the hypothesis of co-transcriptional assembly, centered around L24 in domain I. Finally, comparing the structures and locations of the 50S ribosomal proteins from H.marismortui and D.radiodurans revealed striking examples of molecular mimicry. These comparisons illustrate that identical RNA structures can be stabilized by unrelated proteins.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2PC [auth A]240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3PD [auth B]338Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4EE [auth C]246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5PF [auth D]177Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6PG [auth E]178Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeH [auth F]120Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Acidic ribosomal protein P0 homologI [auth G]348Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10eJ [auth H]171Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11PK [auth I]162Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13PL [auth J]145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14PM [auth K]132Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 14
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50S ribosomal protein L15PN [auth L]165Haloarcula marismortuiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15eO [auth M]194Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18PP [auth N]187Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18eQ [auth O]116Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19ER [auth P]149Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21eS [auth Q]96Haloarcula marismortuiMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22PT [auth R]155Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23PU [auth S]85Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24PV [auth T]120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24EW [auth U]66Haloarcula marismortuiMutation(s): 0 
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Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29PX [auth V]71Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30PY [auth W]154Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31eZ [auth X]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32EAA [auth Y]241Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37AeBA [auth Z]73Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37eCA [auth 1]57Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L39eDA [auth 2]50Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L44EEA [auth 3]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 0]2922Haloarcula marismortui
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth 9]122Haloarcula marismortui
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

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AJ [auth 3], LI [auth O], UI [auth U], XI [auth Z], YI [auth 1]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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KE [auth 0], LE [auth 0]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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BJ [auth 3] , CI [auth J] , DI [auth J] , EI [auth J] , GH [auth 0] , HH [auth 0] , HI [auth L] , IH [auth 0] , 
BJ [auth 3], CI [auth J], DI [auth J], EI [auth J], GH [auth 0], HH [auth 0], HI [auth L], IH [auth 0], JH [auth 0], JI [auth M], KH [auth 0], KI [auth N], LH [auth 0], MH [auth 0], MI [auth O], NH [auth 0], OH [auth 0], PH [auth 0], QI [auth R], VH [auth A], WI [auth Y], XH [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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AB [auth 0] , AC [auth 0] , AD [auth 0] , AE [auth 0] , BB [auth 0] , BC [auth 0] , BD [auth 0] , BE [auth 0] , 
AB [auth 0], AC [auth 0], AD [auth 0], AE [auth 0], BB [auth 0], BC [auth 0], BD [auth 0], BE [auth 0], CB [auth 0], CC [auth 0], CD [auth 0], CE [auth 0], DB [auth 0], DC [auth 0], DD [auth 0], DE [auth 0], EB [auth 0], EC [auth 0], ED [auth 0], EE [auth 0], FA [auth 0], FB [auth 0], FC [auth 0], FD [auth 0], FE [auth 0], FI [auth K], GA [auth 0], GB [auth 0], GC [auth 0], GD [auth 0], GE [auth 0], HA [auth 0], HB [auth 0], HC [auth 0], HD [auth 0], HE [auth 0], IA [auth 0], IB [auth 0], IC [auth 0], ID [auth 0], IE [auth 0], JA [auth 0], JB [auth 0], JC [auth 0], JD [auth 0], JE [auth 0], KA [auth 0], KB [auth 0], KC [auth 0], KD [auth 0], LA [auth 0], LB [auth 0], LC [auth 0], LD [auth 0], MA [auth 0], MB [auth 0], MC [auth 0], MD [auth 0], NA [auth 0], NB [auth 0], NC [auth 0], ND [auth 0], OA [auth 0], OB [auth 0], OC [auth 0], OD [auth 0], PA [auth 0], PB [auth 0], PC [auth 0], PD [auth 0], QA [auth 0], QB [auth 0], QC [auth 0], QD [auth 0], QH [auth 9], RA [auth 0], RB [auth 0], RC [auth 0], RD [auth 0], SA [auth 0], SB [auth 0], SC [auth 0], SD [auth 0], SI [auth T], TA [auth 0], TB [auth 0], TC [auth 0], TD [auth 0], TH [auth A], UA [auth 0], UB [auth 0], UC [auth 0], UD [auth 0], VA [auth 0], VB [auth 0], VC [auth 0], VD [auth 0], VI [auth Y], WA [auth 0], WB [auth 0], WC [auth 0], WD [auth 0], WH [auth B], XA [auth 0], XB [auth 0], XC [auth 0], XD [auth 0], YA [auth 0], YB [auth 0], YC [auth 0], YD [auth 0], ZA [auth 0], ZB [auth 0], ZC [auth 0], ZD [auth 0], ZI [auth 3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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AF [auth 0] , AG [auth 0] , AH [auth 0] , AI [auth H] , BF [auth 0] , BG [auth 0] , BH [auth 0] , BI [auth J] , 
AF [auth 0], AG [auth 0], AH [auth 0], AI [auth H], BF [auth 0], BG [auth 0], BH [auth 0], BI [auth J], CF [auth 0], CG [auth 0], CH [auth 0], DF [auth 0], DG [auth 0], DH [auth 0], EF [auth 0], EG [auth 0], EH [auth 0], FF [auth 0], FG [auth 0], FH [auth 0], GF [auth 0], GG [auth 0], GI [auth L], HF [auth 0], HG [auth 0], IF [auth 0], IG [auth 0], II [auth M], JF [auth 0], JG [auth 0], KF [auth 0], KG [auth 0], LF [auth 0], LG [auth 0], ME [auth 0], MF [auth 0], MG [auth 0], NE [auth 0], NF [auth 0], NG [auth 0], NI [auth Q], OE [auth 0], OF [auth 0], OG [auth 0], OI [auth R], PE [auth 0], PF [auth 0], PG [auth 0], PI [auth R], QE [auth 0], QF [auth 0], QG [auth 0], RE [auth 0], RF [auth 0], RG [auth 0], RH [auth 9], RI [auth S], SE [auth 0], SF [auth 0], SG [auth 0], SH [auth 9], TE [auth 0], TF [auth 0], TG [auth 0], TI [auth T], UE [auth 0], UF [auth 0], UG [auth 0], UH [auth A], VE [auth 0], VF [auth 0], VG [auth 0], WE [auth 0], WF [auth 0], WG [auth 0], XE [auth 0], XF [auth 0], XG [auth 0], YE [auth 0], YF [auth 0], YG [auth 0], YH [auth C], ZE [auth 0], ZF [auth 0], ZG [auth 0], ZH [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • 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
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance