[English] 日本語
Yorodumi
- PDB-5mb9: Crystal structure of the eukaryotic ribosome associated complex (... -

+
Open data


ID or keywords:

Loading...

-
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 / nucleus / cytosol
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / : / Ribosome-associated complex head domain / Zuotin-like, zuotin homology domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily ...Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / : / Ribosome-associated complex head domain / Zuotin-like, zuotin homology 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 4 types, 13 molecules

#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: 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


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


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more