[English] 日本語
Yorodumi
- PDB-3uq3: TPR2AB-domain:pHSP90-complex of yeast Sti1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uq3
TitleTPR2AB-domain:pHSP90-complex of yeast Sti1
Components
  • Heat shock protein STI1Heat shock response
  • Heat shock protein
KeywordsCHAPERONE / Hsp90 / peptide binding
Function / homology
Function and homology information


RND1 GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ATPase inhibitor activity / protein targeting to mitochondrion / Hsp70 protein binding / Hsp90 protein binding / protein localization / protein folding / mRNA binding / cytoplasm
Similarity search - Function
STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. ...STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein STI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchmid, A.B. / Lagleder, S. / Graewert, M.A. / Roehl, A. / Hagn, F. / Wandinger, S.K. / Cox, M.B. / Demmer, O. / Richter, K. / Groll, M. ...Schmid, A.B. / Lagleder, S. / Graewert, M.A. / Roehl, A. / Hagn, F. / Wandinger, S.K. / Cox, M.B. / Demmer, O. / Richter, K. / Groll, M. / Kessler, H. / Buchner, J.
CitationJournal: Embo J. / Year: 2012
Title: The architecture of functional modules in the Hsp90 co-chaperone Sti1/Hop.
Authors: Schmid, A.B. / Lagleder, S. / Grawert, M.A. / Rohl, A. / Hagn, F. / Wandinger, S.K. / Cox, M.B. / Demmer, O. / Richter, K. / Groll, M. / Kessler, H. / Buchner, J.
History
DepositionNov 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock protein STI1
B: Heat shock protein
C: Heat shock protein


Theoretical massNumber of molelcules
Total (without water)30,5883
Polymers30,5883
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-3 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.191, 62.897, 66.842
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe AU contains one biological assembly

-
Components

#1: Protein Heat shock protein STI1 / Heat shock response


Mass: 29344.836 Da / Num. of mol.: 1 / Fragment: TPR repeats 4-9, residues 262-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: STI1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Codon Plus / References: UniProt: P15705
#2: Protein/peptide Heat shock protein /


Mass: 621.657 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in yeast - C-terminus of HSP90.
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.2 M TMAO, 0.1 M Tris, 20% PEG 2000 MME, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 14, 2011
RadiationMonochromator: graphite monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 18105 / Num. obs: 17924 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.26
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.2 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PROTEUM2data collection
PHASERphasing
REFMAC5.5.0109refinement
PROTEUM2data reduction
PROTEUM2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ELR

1elr


Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 29.877 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27854 545 5 %RANDOM
Rwork0.21719 ---
obs0.22027 17480 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.607 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å21.2 Å2
2---2.25 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 0 52 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022165
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.9592908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7295263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90524.779113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22615403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0471515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021657
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9151.51325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60822102
X-RAY DIFFRACTIONr_scbond_it3.2423842
X-RAY DIFFRACTIONr_scangle_it5.1384.5808
X-RAY DIFFRACTIONr_rigid_bond_restr1.28132165
X-RAY DIFFRACTIONr_sphericity_free45.899515
X-RAY DIFFRACTIONr_sphericity_bonded7.63352169
LS refinement shellResolution: 2.6→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 37 -
Rwork0.286 683 -
obs--97.17 %
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)
110.1030.4675-4.5943.7267-0.609311.15430.03860.06190.2843-0.3794-0.23190.1227-0.2658-0.38780.19330.07750.0721-0.01560.09770.02070.07432.38692.0981-8.1321
24.4818-1.3185-1.74395.8117-0.86363.4462-0.0442-0.22240.06420.31350.0427-0.20050.0833-0.3060.00160.0301-0.0172-0.01720.09570.02060.06375.88090.09670.6519
39.0358-4.0987-0.29783.20934.396413.80020.2490.06640.8835-0.2437-0.0948-0.5679-0.4581-0.1498-0.15410.04540.03860.02860.14580.1440.539417.5816-2.9638-9.9595
44.6799-0.4734-6.23766.6111-1.43949.5272-0.1114-0.4170.15590.73990.0927-0.2801-0.09090.37450.01870.12610.0664-0.06120.2190.01450.185212.6261-8.03136.0967
52.0819-2.61930.9324.59540.37132.2512-0.1266-0.2494-0.04370.57350.2485-0.05110.4023-0.2058-0.12190.140.0078-0.050.13650.04420.098411.8267-13.2517-0.5181
66.5025-1.2967-0.11696.0495-0.70884.0547-0.0167-0.08390.072-0.1405-0.1705-0.51590.30040.51370.18720.04020.0559-0.02770.0845-0.01840.193520.4227-16.4387-3.8289
79.1498-2.3519-3.1160.85761.10255.9647-0.14290.4998-0.3275-0.1154-0.1774-0.1140.9554-0.08950.32030.47720.0920.10510.1153-0.01560.340218.7883-24.2123-9.2837
85.6761-3.6539-1.74189.36362.03893.67570.0953-0.19770.2254-0.1420.1167-0.5032-0.38880.4111-0.2120.17450.0328-0.00290.15560.02440.122545.1834-27.4346-16.2747
98.61264.2623-3.600421.01844.19825.5084-0.1653-0.43390.20670.02640.3947-1.2914-0.24630.7877-0.22930.20690.0788-0.1160.2639-0.00980.263452.6238-44.1916-13.4876
103.4428-2.17731.3646.58541.1771.5998-0.0162-0.15210.0930.178-0.12460.20660.0697-0.02840.14070.03840.02330.0180.0889-0.00780.01943.5814-38.8512-18.6672
114.73150.16760.30245.74470.24711.6997-0.15830.01620.1138-0.59380.26040.36780.2599-0.3142-0.10210.1916-0.0423-0.02180.15170.01030.113839.8793-46.3054-27.3068
125.44140.5836-1.79698.6108-1.96295.8684-0.05520.4670.0236-0.57860.1414-0.0038-0.041-0.1596-0.08620.2422-0.08210.01290.1523-0.06860.107943.6422-51.0123-37.4063
1332.93944.0491-3.21428.2937-7.79075.9741-0.10260.7893-1.1415-0.662-0.23010.42170.3566-1.09960.33260.4412-0.076-0.03140.3967-0.07350.214543.1059-61.9242-36.0795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A258 - 283
2X-RAY DIFFRACTION2A284 - 304
3X-RAY DIFFRACTION3A305 - 312
4X-RAY DIFFRACTION4A313 - 332
5X-RAY DIFFRACTION5A333 - 343
6X-RAY DIFFRACTION6A344 - 366
7X-RAY DIFFRACTION7A367 - 384
8X-RAY DIFFRACTION8A385 - 401
9X-RAY DIFFRACTION9A402 - 414
10X-RAY DIFFRACTION10A415 - 443
11X-RAY DIFFRACTION11A444 - 477
12X-RAY DIFFRACTION12A478 - 509
13X-RAY DIFFRACTION13A510 - 515

+
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