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- PDB-5mb9: Crystal structure of the eukaryotic ribosome associated complex (... -

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Basic information

Entry
Database: PDB / ID: 5mb9
TitleCrystal structure of the eukaryotic ribosome associated complex (RAC), a unique Hsp70/Hsp40 pair
Components
  • Putative heat shock protein
  • Putative ribosome associated protein
KeywordsCHAPERONE / Hsp70 / Hsp40
Function / homology
Function and homology information


'de novo' cotranslational protein folding / regulation of translational fidelity / Hsp70 protein binding / ATP-dependent protein folding chaperone / ribosome binding / ATP binding / cytoplasm
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Heat shock protein 70 family ...Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Putative ribosome associated protein / Putative heat shock protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGumiero, A. / Weyer, F.A. / Valentin Gese, G. / Lapouge, K. / Sinning, I.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex.
Authors: Weyer, F.A. / Gumiero, A. / Gese, G.V. / Lapouge, K. / Sinning, I.
History
DepositionNov 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative heat shock protein
B: Putative heat shock protein
C: Putative ribosome associated protein
D: Putative ribosome associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,9579
Polymers137,8024
Non-polymers1,1555
Water1448
1
A: Putative heat shock protein
D: Putative ribosome associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4324
Polymers68,9012
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-41 kcal/mol
Surface area25280 Å2
MethodPISA
2
B: Putative heat shock protein
C: Putative ribosome associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5245
Polymers68,9012
Non-polymers6243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-39 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.918, 179.359, 155.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 12 or resseq 14:30 or (resid...
21(chain B and (resseq 12 or resseq 14:30 or (resid...
12(chain F and resseq 700:701)
22(chain E and resseq 700:701)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 12 or resseq 14:30 or (resid...A12
121(chain A and (resseq 12 or resseq 14:30 or (resid...A14 - 30
131(chain A and (resseq 12 or resseq 14:30 or (resid...A31
141(chain A and (resseq 12 or resseq 14:30 or (resid...A11 - 566
151(chain A and (resseq 12 or resseq 14:30 or (resid...A11 - 566
161(chain A and (resseq 12 or resseq 14:30 or (resid...A11 - 566
171(chain A and (resseq 12 or resseq 14:30 or (resid...A11 - 566
181(chain A and (resseq 12 or resseq 14:30 or (resid...A11 - 566
211(chain B and (resseq 12 or resseq 14:30 or (resid...B12
221(chain B and (resseq 12 or resseq 14:30 or (resid...B14 - 30
231(chain B and (resseq 12 or resseq 14:30 or (resid...B31
241(chain B and (resseq 12 or resseq 14:30 or (resid...B12 - 566
251(chain B and (resseq 12 or resseq 14:30 or (resid...B12 - 566
261(chain B and (resseq 12 or resseq 14:30 or (resid...B12 - 566
271(chain B and (resseq 12 or resseq 14:30 or (resid...B12 - 566
281(chain B and (resseq 12 or resseq 14:30 or (resid...B12 - 566
112(chain F and resseq 700:701)F700 - 701
212(chain E and resseq 700:701)E700 - 701

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Putative heat shock protein /


Mass: 63838.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0008010 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0RZX9
#2: Protein/peptide Putative ribosome associated protein


Mass: 5062.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0006310 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0RYD6

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Non-polymers , 4 types, 13 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 26% PEG 3350 and 0.2 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9733 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9733 Å / Relative weight: 1
ReflectionResolution: 3.2→47.973 Å / Num. obs: 21953 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 96.41 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.2-3.425.61.2690.6031100
9.05-47.974.50.0420.998199.3

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GNI AND 1DKZ

4gni

1dkz


Resolution: 3.2→47.973 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.31
RfactorNum. reflection% reflection
Rfree0.2849 1127 5.14 %
Rwork0.2273 --
obs0.2301 21927 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 290.31 Å2 / Biso mean: 110.0131 Å2 / Biso min: 41.08 Å2
Refinement stepCycle: final / Resolution: 3.2→47.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8107 0 70 8 8185
Biso mean--73.71 74.73 -
Num. residues----1060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038304
X-RAY DIFFRACTIONf_angle_d0.70311284
X-RAY DIFFRACTIONf_chiral_restr0.0481347
X-RAY DIFFRACTIONf_plane_restr0.0041451
X-RAY DIFFRACTIONf_dihedral_angle_d13.6855060
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4006X-RAY DIFFRACTION13.905TORSIONAL
12B4006X-RAY DIFFRACTION13.905TORSIONAL
21C26X-RAY DIFFRACTION13.905TORSIONAL
22D26X-RAY DIFFRACTION13.905TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.34570.3921210.320926032724100
3.3457-3.5220.3581350.299825602695100
3.522-3.74260.33931540.263525802734100
3.7426-4.03140.31871300.256425762706100
4.0314-4.43690.2781360.21192579271599
4.4369-5.07830.27831480.20562563271199
5.0783-6.39570.25921470.23512616276399
6.3957-47.97830.25071560.19312723287999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.76760.296-0.26350.7495-0.04290.1165-0.49770.2582-0.8928-0.26580.59930.14150.77960.0422-0.09141.05010.03030.37830.7648-0.17591.2135-5.5979-22.462320.2131
23.8111.6339-1.18763.09950.37492.3707-0.79861.12660.0259-1.27040.7062-0.1371-0.1916-0.25730.06811.2514-0.1440.17610.90070.00550.5753-10.6613-5.405313.2983
33.88552.8426-0.2332.5494-0.0352.702-0.1803-0.2029-0.2466-0.55180.0394-0.1147-0.1203-0.05380.12730.7380.22250.01670.4030.05440.6088-16.5626-10.851334.5482
42.86551.5709-1.17061.5135-0.11062.2491-0.0161-0.0156-0.6736-0.8268-0.1001-0.4472-0.0914-0.08290.07391.11020.0430.10510.72950.00481.063-31.9943-38.804333.1201
51.4382-1.06610.17795.4553-4.45175.11360.18190.5499-0.9015-0.4526-0.09071.20491.7640.027-0.70381.1682-0.11610.10130.8687-0.08661.3187-33.0303-54.02937.5277
61.76420.45590.06542.8491-0.67663.66870.1642-0.15230.05350.0635-0.0103-0.19270.01360.3045-0.14770.30740.0718-0.01760.6667-0.19170.4896-50.71215.355419.348
71.7978-0.2381.46312.83050.94431.8031-0.54711.22470.5033-0.45720.1507-0.2442-0.78820.75640.37171.3713-0.48120.13021.6137-0.04221.3342-35.43946.99945.638
80.51570.21621.43990.10720.54884.22750.23240.2646-1.873-0.167-0.3621-0.88381.39410.66890.15841.9017-0.13970.35551.85810.19371.0499-33.325943.6517-7.5512
95.66240.41861.37697.1609-1.00574.3936-0.23370.13650.583-1.72111.3742-0.5642-1.07531.5825-1.0741.169-0.35790.01911.3349-0.12110.9931-45.564636.2942.6425
103.0781-0.8816-1.58927.0087-2.16622.1838-0.8422-0.74131.0419-0.74990.84610.4221-0.0473-0.4062-0.21380.9344-0.13040.06411.27050.16141.1516-55.257446.17764.7032
112.6103-0.5889-3.07922.56670.36843.6811-1.63440.23930.42680.8343-0.15-0.36521.1195-0.76651.06122.1768-0.4189-0.46060.6696-0.27461.8193-40.8098-49.428429.5109
127.4758-3.1019-0.09832.15520.97093.16620.14330.1521-1.1489-1.11630.5125-0.233-0.62960.5695-0.49791.6007-0.34760.16130.9702-0.13940.8714-29.8062-31.540322.1256
135.38642.45091.34964.18910.26390.37830.2841.6886-1.0438-0.39590.537-0.61450.29410.2011-0.54862.0613-0.12680.7931.5164-0.58931.8701-21.1547-41.237417.4376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 38 )A11 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 175 )A39 - 175
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 401 )A176 - 401
4X-RAY DIFFRACTION4chain 'A' and (resid 402 through 531 )A402 - 531
5X-RAY DIFFRACTION5chain 'A' and (resid 532 through 566 )A532 - 566
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 401 )B12 - 401
7X-RAY DIFFRACTION7chain 'B' and (resid 402 through 566 )B402 - 566
8X-RAY DIFFRACTION8chain 'C' and (resid 29 through 33 )C29 - 33
9X-RAY DIFFRACTION9chain 'C' and (resid 34 through 43 )C34 - 43
10X-RAY DIFFRACTION10chain 'C' and (resid 44 through 57 )C44 - 57
11X-RAY DIFFRACTION11chain 'D' and (resid 22 through 33 )D22 - 33
12X-RAY DIFFRACTION12chain 'D' and (resid 34 through 43 )D34 - 43
13X-RAY DIFFRACTION13chain 'D' and (resid 44 through 56 )D44 - 56

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