1M90

Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Structural insights into peptide bond formation.

Hansen, J.L.Schmeing, T.M.Moore, P.B.Steitz, T.A.

(2002) Proc Natl Acad Sci U S A 99: 11670-11675

  • DOI: https://doi.org/10.1073/pnas.172404099
  • Primary Citation of Related Structures:  
    1M90, 1Q7Y, 1Q81, 1Q82, 1Q86

  • PubMed Abstract: 

    The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2D [auth C]239Haloarcula 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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3E [auth D]337Haloarcula 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L4F [auth E]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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L5G [auth F]176Haloarcula 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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L6H [auth G]177Haloarcula 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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L7AEI [auth H]119Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10J [auth I]348Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10EK [auth J]167Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L13L [auth K]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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L14M [auth L]132Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15N [auth M]164Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15EO [auth N]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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18P [auth O]186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18EQ [auth P]115Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L19ER [auth Q]148Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L21ES [auth R]95Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L22T [auth S]154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L23U [auth T]84Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24V [auth U]119Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24EW [auth V]66Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L29X [auth W]70Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L30Y [auth X]154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L31EZ [auth Y]91Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L32EAA [auth Z]240Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37AeBA [auth 1]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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37ECA [auth 2]56Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L39EDA [auth 3]48Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L44EEA [auth 4]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S RRNA2,922Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S RRNA122Haloarcula marismortui
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Entity ID: 3
MoleculeChains LengthOrganismImage
CCAC [auth 5]3N/A
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPS
Query on SPS

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WH [auth 5]SPARSOMYCIN
C13 H19 N3 O5 S2
XKLZIVIOZDNKEQ-CLQLPEFOSA-N
PHA
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YH [auth 5]PHENYLALANINAL
C9 H11 N O
CQIUZHAQYHXKRY-VIFPVBQESA-N
ACA
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ZH [auth 5]6-AMINOHEXANOIC ACID
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
CD
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DJ [auth 1],
EJ [auth 2],
GJ [auth 4],
QI [auth P],
ZI [auth V]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

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HH [auth A],
IH [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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BJ [auth Z]
CI [auth C]
DI [auth D]
HI [auth K]
HJ [auth 4]
BJ [auth Z],
CI [auth C],
DI [auth D],
HI [auth K],
HJ [auth 4],
II [auth K],
JH [auth A],
JI [auth K],
KH [auth A],
LH [auth A],
MH [auth A],
MI [auth M],
NH [auth A],
OH [auth A],
OI [auth N],
PH [auth A],
PI [auth O],
QH [auth A],
RH [auth A],
RI [auth P],
SH [auth A],
VI [auth S]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AI [auth C]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AI [auth C],
AJ [auth Z],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CJ [auth 1],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FJ [auth 4],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KI [auth L],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TH [auth B],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XH [auth 5],
XI [auth U],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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AF [auth A]
AG [auth A]
AH [auth A]
BF [auth A]
BG [auth A]
AF [auth A],
AG [auth A],
AH [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth C],
CF [auth A],
CG [auth A],
CH [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
EI [auth E],
FF [auth A],
FG [auth A],
FH [auth A],
FI [auth J],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth K],
HF [auth A],
HG [auth A],
IF [auth A],
IG [auth A],
JF [auth A],
JG [auth A],
KF [auth A],
KG [auth A],
LF [auth A],
LG [auth A],
LI [auth M],
ME [auth A],
MF [auth A],
MG [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NI [auth N],
OE [auth A],
OF [auth A],
OG [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
SI [auth R],
TE [auth A],
TF [auth A],
TG [auth A],
TI [auth S],
UE [auth A],
UF [auth A],
UG [auth A],
UH [auth B],
UI [auth S],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth B],
WE [auth A],
WF [auth A],
WG [auth A],
WI [auth T],
XE [auth A],
XF [auth A],
XG [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YI [auth U],
ZE [auth A],
ZF [auth A],
ZG [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.661α = 90
b = 299.773β = 90
c = 573.684γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description