1KQS

The Haloarcula marismortui 50S Complexed with a Pretranslocational Intermediate in Protein Synthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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This is version 2.0 of the entry. See complete history


Literature

A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits.

Schmeing, T.M.Seila, A.C.Hansen, J.L.Freeborn, B.Soukup, J.K.Scaringe, S.A.Strobel, S.A.Moore, P.B.Steitz, T.A.

(2002) Nat Struct Biol 9: 225-230

  • DOI: https://doi.org/10.1038/nsb758
  • Primary Citation of Related Structures:  
    1KQS

  • PubMed Abstract: 

    The large ribosomal subunit catalyzes peptide bond formation during protein synthesis. Its peptidyl transferase activity has often been studied using a 'fragment assay' that depends on high concentrations of methanol or ethanol. Here we describe a version of this assay that does not require alcohol and use it to show, both crystallographically and biochemically, that crystals of the large ribosomal subunits from Haloarcula marismortui are enzymatically active. Addition of these crystals to solutions containing substrates results in formation of products, which ceases when crystals are removed. When substrates are diffused into large subunit crystals, the subsequent structure shows that products have formed. The CC-puromycin-peptide product is found bound to the A-site and the deacylated CCA is bound to the P-site, with its 3prime prime or minute OH near N3 A2486 (Escherichia coli A2451). Thus, this structure represents a state that occurs after peptide bond formation but before the hybrid state of protein synthesis.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2E [auth A]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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3F [auth B]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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L4G [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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L5H [auth D]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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L6I [auth E]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: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L7AEJ [auth F]119Haloarcula marismortuiMutation(s): 0 
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Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10K [auth G]348Haloarcula marismortuiMutation(s): 0 
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Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10EL [auth H]167Haloarcula marismortuiMutation(s): 0 
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Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L13M [auth I]145Haloarcula marismortuiMutation(s): 0 
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Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L14N [auth J]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: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15O [auth K]164Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15EP [auth L]194Haloarcula marismortuiMutation(s): 0 
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Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18Q [auth M]186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18ER [auth N]115Haloarcula marismortuiMutation(s): 0 
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Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L19ES [auth O]148Haloarcula marismortuiMutation(s): 0 
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Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L21ET [auth P]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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L22U [auth Q]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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L23V [auth R]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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24W [auth S]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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24EX [auth T]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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L29Y [auth U]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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L30Z [auth V]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: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L31EAA [auth W]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: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L32EBA [auth X]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: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37AeCA [auth Y]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: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37EDA [auth Z]56Haloarcula marismortuiMutation(s): 0 
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Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L39EEA [auth 1]48Haloarcula marismortuiMutation(s): 0 
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Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L44EFA [auth 2]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 RRNAA [auth 0]2,922Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S RRNAB [auth 9]122Haloarcula marismortui
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Entity ID: 3
MoleculeChains LengthOrganismImage
CCAC [auth 3]3N/A
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Entity ID: 4
MoleculeChains LengthOrganismImage
CC-Pmn-pcbD [auth 4]2N/A
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PPU
Query on PPU

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WH [auth 4]PUROMYCIN-5'-MONOPHOSPHATE
C22 H30 N7 O8 P
NYICMZBLMICLBS-NVWDDTSBSA-N
BTN
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ZH [auth 4]BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
PHA
Query on PHA

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XH [auth 4]PHENYLALANINAL
C9 H11 N O
CQIUZHAQYHXKRY-VIFPVBQESA-N
ACA
Query on ACA

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YH [auth 4]6-AMINOHEXANOIC ACID
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
CD
Query on CD

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DJ [auth Y],
EJ [auth Z],
GJ [auth 2],
QI [auth N],
ZI [auth T]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

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ME [auth 0],
NE [auth 0]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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BJ [auth X]
CI [auth A]
DI [auth B]
HI [auth I]
HJ [auth 2]
BJ [auth X],
CI [auth A],
DI [auth B],
HI [auth I],
HJ [auth 2],
II [auth I],
JH [auth 0],
JI [auth I],
KH [auth 0],
LH [auth 0],
MH [auth 0],
MI [auth K],
NH [auth 0],
OH [auth 0],
OI [auth L],
PH [auth 0],
PI [auth M],
QH [auth 0],
RH [auth 0],
RI [auth N],
SH [auth 0],
WI [auth Q]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AB [auth 0]
AC [auth 0]
AD [auth 0]
AE [auth 0]
AI [auth A]
AB [auth 0],
AC [auth 0],
AD [auth 0],
AE [auth 0],
AI [auth A],
AJ [auth X],
BB [auth 0],
BC [auth 0],
BD [auth 0],
BE [auth 0],
CB [auth 0],
CC [auth 0],
CD [auth 0],
CE [auth 0],
CJ [auth Y],
DB [auth 0],
DC [auth 0],
DD [auth 0],
DE [auth 0],
EB [auth 0],
EC [auth 0],
ED [auth 0],
EE [auth 0],
FB [auth 0],
FC [auth 0],
FD [auth 0],
FE [auth 0],
FJ [auth 2],
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],
KE [auth 0],
KI [auth J],
LA [auth 0],
LB [auth 0],
LC [auth 0],
LD [auth 0],
LE [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],
RA [auth 0],
RB [auth 0],
RC [auth 0],
RD [auth 0],
SA [auth 0],
SB [auth 0],
SC [auth 0],
SD [auth 0],
TA [auth 0],
TB [auth 0],
TC [auth 0],
TD [auth 0],
TH [auth 9],
UA [auth 0],
UB [auth 0],
UC [auth 0],
UD [auth 0],
VA [auth 0],
VB [auth 0],
VC [auth 0],
VD [auth 0],
WA [auth 0],
WB [auth 0],
WC [auth 0],
WD [auth 0],
XA [auth 0],
XB [auth 0],
XC [auth 0],
XD [auth 0],
YA [auth 0],
YB [auth 0],
YC [auth 0],
YD [auth 0],
YI [auth S],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0],
ZD [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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AF [auth 0]
AG [auth 0]
AH [auth 0]
BF [auth 0]
BG [auth 0]
AF [auth 0],
AG [auth 0],
AH [auth 0],
BF [auth 0],
BG [auth 0],
BH [auth 0],
BI [auth A],
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],
EI [auth C],
FF [auth 0],
FG [auth 0],
FH [auth 0],
FI [auth H],
GF [auth 0],
GG [auth 0],
GH [auth 0],
GI [auth I],
HF [auth 0],
HG [auth 0],
HH [auth 0],
IF [auth 0],
IG [auth 0],
IH [auth 0],
JF [auth 0],
JG [auth 0],
KF [auth 0],
KG [auth 0],
LF [auth 0],
LG [auth 0],
LI [auth K],
MF [auth 0],
MG [auth 0],
NF [auth 0],
NG [auth 0],
NI [auth L],
OE [auth 0],
OF [auth 0],
OG [auth 0],
PE [auth 0],
PF [auth 0],
PG [auth 0],
QE [auth 0],
QF [auth 0],
QG [auth 0],
RE [auth 0],
RF [auth 0],
RG [auth 0],
SE [auth 0],
SF [auth 0],
SG [auth 0],
SI [auth P],
TE [auth 0],
TF [auth 0],
TG [auth 0],
TI [auth Q],
UE [auth 0],
UF [auth 0],
UG [auth 0],
UH [auth 9],
UI [auth Q],
VE [auth 0],
VF [auth 0],
VG [auth 0],
VH [auth 9],
VI [auth Q],
WE [auth 0],
WF [auth 0],
WG [auth 0],
XE [auth 0],
XF [auth 0],
XG [auth 0],
XI [auth R],
YE [auth 0],
YF [auth 0],
YG [auth 0],
ZE [auth 0],
ZF [auth 0],
ZG [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.784α = 90
b = 300.349β = 90
c = 574.961γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
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: 2002-02-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations