Journal: Nat Struct Mol Biol / Year: 2013 Title: Structural characterization of a eukaryotic chaperone--the ribosome-associated complex. Authors: Christoph Leidig / Gert Bange / Jürgen Kopp / Stefan Amlacher / Ajay Aravind / Stephan Wickles / Gregor Witte / Ed Hurt / Roland Beckmann / Irmgard Sinning / Abstract: Ribosome-associated chaperones act in early folding events during protein synthesis. Structural information is available for prokaryotic chaperones (such as trigger factor), but structural ...Ribosome-associated chaperones act in early folding events during protein synthesis. Structural information is available for prokaryotic chaperones (such as trigger factor), but structural understanding of these processes in eukaryotes lags far behind. Here we present structural analyses of the eukaryotic ribosome-associated complex (RAC) from Saccharomyces cerevisiae and Chaetomium thermophilum, consisting of heat-shock protein 70 (Hsp70) Ssz1 and the Hsp40 Zuo1. RAC is an elongated complex that crouches over the ribosomal tunnel exit and seems to be stabilized in a distinct conformation by expansion segment ES27. A unique α-helical domain in Zuo1 mediates ribosome interaction of RAC near the ribosomal proteins L22e and L31e and ribosomal RNA helix H59. The crystal structure of the Ssz1 ATPase domain bound to ATP-Mg²⁺ explains its catalytic inactivity and suggests that Ssz1 may act before the RAC-associated chaperone Ssb. Our study offers insights into the interplay between RAC, the ER membrane-integrated Hsp40-type protein ERj1 and the signal-recognition particle.
Resolution: 1.3→1.37 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 5.6 / Num. unique all: 3170 / % possible all: 100
-
Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
ACORN
phasing
PHENIX
(phenix.refine: 1.7.1_743)
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: AB INITIO PHASING / Resolution: 1.3→27.263 Å / SU ML: 0.34 / σ(F): 1.39 / Phase error: 15.12 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.188
1121
5.05 %
RANDOM
Rwork
0.1514
-
-
-
obs
0.1532
22198
99.52 %
-
all
-
0
-
-
Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.105 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-4.405 Å2
0 Å2
0 Å2
2-
-
0.9749 Å2
-0 Å2
3-
-
-
3.4301 Å2
Refinement step
Cycle: LAST / Resolution: 1.3→27.263 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
686
0
0
182
868
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
699
X-RAY DIFFRACTION
f_angle_d
0.887
945
X-RAY DIFFRACTION
f_dihedral_angle_d
10.439
262
X-RAY DIFFRACTION
f_chiral_restr
0.06
117
X-RAY DIFFRACTION
f_plane_restr
0.003
121
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.3-1.3592
0.2784
142
0.2338
2561
X-RAY DIFFRACTION
100
1.3592-1.4308
0.2072
151
0.1552
2599
X-RAY DIFFRACTION
100
1.4308-1.5205
0.1452
148
0.117
2602
X-RAY DIFFRACTION
100
1.5205-1.6378
0.1621
139
0.1139
2594
X-RAY DIFFRACTION
100
1.6378-1.8026
0.1684
139
0.1245
2630
X-RAY DIFFRACTION
100
1.8026-2.0634
0.2002
127
0.1374
2672
X-RAY DIFFRACTION
100
2.0634-2.5994
0.1741
137
0.1464
2684
X-RAY DIFFRACTION
100
2.5994-27.2693
0.2005
138
0.1713
2735
X-RAY DIFFRACTION
97
+
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