1W2B

Trigger Factor ribosome binding domain in complex with 50S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Trigger Factor in Complex with the Ribosome Forms a Molecular Cradle for Nascent Proteins

Ferbitz, L.Maier, T.Patzelt, H.Bukau, B.Deuerling, E.Ban, N.

(2004) Nature 431: 590

  • DOI: 10.1038/nature02899
  • Primary Citation of Related Structures:  
    1W26, 1W2B

  • PubMed Abstract: 
  • During protein biosynthesis, nascent polypeptide chains that emerge from the ribosomal exit tunnel encounter ribosome-associated chaperones, which assist their folding to the native state. Here we present a 2.7 A crystal structure of Escherichia coli trigger factor, the best-characterized chaperone of this type, together with the structure of its ribosome-binding domain in complex with the Haloarcula marismortui large ribosomal subunit ...

    During protein biosynthesis, nascent polypeptide chains that emerge from the ribosomal exit tunnel encounter ribosome-associated chaperones, which assist their folding to the native state. Here we present a 2.7 A crystal structure of Escherichia coli trigger factor, the best-characterized chaperone of this type, together with the structure of its ribosome-binding domain in complex with the Haloarcula marismortui large ribosomal subunit. Trigger factor adopts a unique conformation resembling a crouching dragon with separated domains forming the amino-terminal ribosome-binding 'tail', the peptidyl-prolyl isomerase 'head', the carboxy-terminal 'arms' and connecting regions building up the 'back'. From its attachment point on the ribosome, trigger factor projects the extended domains over the exit of the ribosomal tunnel, creating a protected folding space where nascent polypeptides may be shielded from proteases and aggregation. This study sheds new light on our understanding of co-translational protein folding, and suggests an unexpected mechanism of action for ribosome-associated chaperones.


    Organizational Affiliation

    Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg (ETH Zürich), HPK Gebäude, CH-8093 Zürich, Switzerland.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L39EB [auth 1]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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L44E LA, HLA, RIBOSOMAL PROTEIN L44EC [auth 2]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TRIGGER FACTORD [auth 5]144Escherichia coliMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2PF [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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3PG [auth B]337Haloarcula marismortuiMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4PH [auth C]246Haloarcula marismortuiMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5P HMAL5, HL13, RIBOSOMAL PROTEIN L5I [auth D]176Haloarcula marismortuiMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6PJ [auth E]177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L7AEK [auth F]119Haloarcula marismortuiMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10EL [auth G]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: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10EM [auth H]167Haloarcula marismortuiMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13PN [auth I]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: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14PO [auth J]132Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15PP [auth K]164Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15EQ [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: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18PR [auth M]186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 19
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50S RIBOSOMAL PROTEIN L18ES [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: 20
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50S RIBOSOMAL PROTEIN L19ET [auth O]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: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21EU [auth P]95Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22P HMAL22, HL23, RIBOSOMAL PROTEIN L22V [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: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23PW [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: 24
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24X [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: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24PY [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: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24EZ [auth U]70Haloarcula marismortuiMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30PAA [auth V]154Haloarcula marismortuiMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31EBA [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: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32ECA [auth X]240Haloarcula marismortuiMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L37AEDA [auth Y]73Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37EEA [auth Z]56Haloarcula marismortuiMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RRNAA [auth 0]2,922Haloarcula marismortui
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Entity ID: 5
MoleculeChainsLengthOrganismImage
5S RRNAE [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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BJ [auth Y],
CJ [auth Z],
LH [auth 2],
OI [auth N],
YI [auth T]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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

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AF [auth 0],
AI [auth B],
DI [auth I],
EI [auth I],
FI [auth I],
AF [auth 0],
AI [auth B],
DI [auth I],
EI [auth I],
FI [auth I],
HI [auth J],
II [auth K],
KI [auth K],
MH [auth 2],
MI [auth L],
NI [auth M],
PI [auth N],
RI [auth P],
TI [auth Q],
UE [auth 0],
VE [auth 0],
WE [auth 0],
WH [auth A],
XE [auth 0],
YE [auth 0],
ZE [auth 0],
ZI [auth X]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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AB [auth 0],
AC [auth 0],
AG [auth 0],
AJ [auth X],
BB [auth 0],
AB [auth 0],
AC [auth 0],
AG [auth 0],
AJ [auth X],
BB [auth 0],
BC [auth 0],
BG [auth 0],
CB [auth 0],
CC [auth 0],
CG [auth 0],
DB [auth 0],
DC [auth 0],
DG [auth 0],
EB [auth 0],
EC [auth 0],
EG [auth 0],
FA [auth 0],
FB [auth 0],
FC [auth 0],
FF [auth 0],
FG [auth 0],
GA [auth 0],
GB [auth 0],
GC [auth 0],
GF [auth 0],
GG [auth 0],
GI [auth J],
HA [auth 0],
HB [auth 0],
HC [auth 0],
HF [auth 0],
HG [auth 0],
IA [auth 0],
IB [auth 0],
IC [auth 0],
IF [auth 0],
IG [auth 0],
JA [auth 0],
JB [auth 0],
JC [auth 0],
JF [auth 0],
JG [auth 0],
KA [auth 0],
KB [auth 0],
KC [auth 0],
KF [auth 0],
KG [auth 0],
LA [auth 0],
LB [auth 0],
LC [auth 0],
LF [auth 0],
LG [auth 0],
MA [auth 0],
MB [auth 0],
MC [auth 0],
MF [auth 0],
MG [auth 0],
NA [auth 0],
NB [auth 0],
NC [auth 0],
NF [auth 0],
NG [auth 0],
NH [auth 2],
OA [auth 0],
OB [auth 0],
OF [auth 0],
OG [auth 0],
OH [auth 9],
PA [auth 0],
PB [auth 0],
PF [auth 0],
PG [auth 0],
QA [auth 0],
QB [auth 0],
QF [auth 0],
QG [auth 0],
QH [auth 9],
RA [auth 0],
RB [auth 0],
RF [auth 0],
RG [auth 0],
SA [auth 0],
SB [auth 0],
SF [auth 0],
SG [auth 0],
SH [auth A],
TA [auth 0],
TB [auth 0],
TF [auth 0],
TG [auth 0],
TH [auth A],
UA [auth 0],
UB [auth 0],
UF [auth 0],
UG [auth 0],
VA [auth 0],
VB [auth 0],
VF [auth 0],
VG [auth 0],
VH [auth A],
WA [auth 0],
WB [auth 0],
WF [auth 0],
WG [auth 0],
XA [auth 0],
XB [auth 0],
XF [auth 0],
XH [auth B],
XI [auth S],
YA [auth 0],
YB [auth 0],
YF [auth 0],
YH [auth B],
ZA [auth 0],
ZB [auth 0],
ZF [auth 0],
ZH [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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AD [auth 0],
AE [auth 0],
AH [auth 0],
BD [auth 0],
BE [auth 0],
AD [auth 0],
AE [auth 0],
AH [auth 0],
BD [auth 0],
BE [auth 0],
BF [auth 0],
BH [auth 0],
BI [auth C],
CD [auth 0],
CE [auth 0],
CF [auth 0],
CH [auth 0],
CI [auth I],
DD [auth 0],
DE [auth 0],
DF [auth 0],
DH [auth 0],
ED [auth 0],
EE [auth 0],
EF [auth 0],
EH [auth 0],
FD [auth 0],
FE [auth 0],
FH [auth 0],
GD [auth 0],
GE [auth 0],
GH [auth 0],
HD [auth 0],
HE [auth 0],
HH [auth 0],
ID [auth 0],
IE [auth 0],
IH [auth 0],
JD [auth 0],
JE [auth 0],
JH [auth 0],
JI [auth K],
KD [auth 0],
KE [auth 0],
KH [auth 0],
LD [auth 0],
LE [auth 0],
LI [auth L],
MD [auth 0],
ME [auth 0],
ND [auth 0],
NE [auth 0],
OD [auth 0],
OE [auth 0],
PD [auth 0],
PE [auth 0],
PH [auth 9],
QC [auth 0],
QD [auth 0],
QE [auth 0],
QI [auth P],
RC [auth 0],
RD [auth 0],
RE [auth 0],
RH [auth 9],
SC [auth 0],
SD [auth 0],
SE [auth 0],
SI [auth Q],
TC [auth 0],
TD [auth 0],
TE [auth 0],
UC [auth 0],
UD [auth 0],
UH [auth A],
UI [auth Q],
VC [auth 0],
VD [auth 0],
VI [auth R],
WC [auth 0],
WD [auth 0],
WI [auth S],
XC [auth 0],
XD [auth 0],
XG [auth 0],
YC [auth 0],
YD [auth 0],
YG [auth 0],
ZC [auth 0],
ZD [auth 0],
ZG [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.746α = 90
b = 298.871β = 90
c = 574.173γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Derived calculations