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- PDB-4gni: Structure of the Ssz1 ATPase bound to ATP and Magnesium -

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Basic information

Entry
Database: PDB / ID: 4gni
TitleStructure of the Ssz1 ATPase bound to ATP and Magnesium
ComponentsPutative heat shock protein
KeywordsCHAPERONE / Hsp70-type ATPase / ATP binding protein / magnesium binding / co-translational chaperone / ribosome-associated complex / RAC
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / ATP binding
Similarity search - Function
: / Defensin A-like - #30 / Defensin A-like / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...: / Defensin A-like - #30 / Defensin A-like / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Putative heat shock protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsBange, G. / Sinning, I.
CitationJournal: 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.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative heat shock protein
B: Putative heat shock protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9686
Polymers88,9052
Non-polymers1,0634
Water14,988832
1
A: Putative heat shock protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9843
Polymers44,4531
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative heat shock protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9843
Polymers44,4531
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-6 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.630, 55.380, 98.790
Angle α, β, γ (deg.)90.00, 106.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative heat shock protein


Mass: 44452.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0008010 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta 2 / References: UniProt: G0RZX9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5; 20 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2010
RadiationMonochromator: horizontally diffracting Si (111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.796→36.07 Å / Num. obs: 78273 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 9
Reflection shellResolution: 1.796→1.89 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→36.066 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 1914 2.56 %RANDOM
Rwork0.201 ---
obs0.2021 74623 95.35 %-
all-0 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.219 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1323 Å2-0 Å25.5299 Å2
2---0.432 Å2-0 Å2
3---0.2997 Å2
Refinement stepCycle: LAST / Resolution: 1.796→36.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5887 0 64 832 6783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076047
X-RAY DIFFRACTIONf_angle_d1.1078221
X-RAY DIFFRACTIONf_dihedral_angle_d13.6162229
X-RAY DIFFRACTIONf_chiral_restr0.065961
X-RAY DIFFRACTIONf_plane_restr0.0041067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.796-1.86020.33571700.31266420X-RAY DIFFRACTION85
1.8602-1.93470.29381800.2646732X-RAY DIFFRACTION89
1.9347-2.02270.25611820.22766974X-RAY DIFFRACTION92
2.0227-2.12930.25761960.2097252X-RAY DIFFRACTION95
2.1293-2.26270.24911880.19577323X-RAY DIFFRACTION97
2.2627-2.43740.26172000.20457426X-RAY DIFFRACTION97
2.4374-2.68260.27091930.20747511X-RAY DIFFRACTION99
2.6826-3.07060.24721980.19867594X-RAY DIFFRACTION99
3.0706-3.86790.21132020.18247659X-RAY DIFFRACTION100
3.8679-36.07320.2172050.17697818X-RAY DIFFRACTION100

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