[English] 日本語
Yorodumi
- PDB-6hfo: Human Hsp90 co-chaperone TTC4 C-domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hfo
TitleHuman Hsp90 co-chaperone TTC4 C-domain
ComponentsTetratricopeptide repeat protein 4
KeywordsCHAPERONE / unique fold / wheel domain / Hsp90 co-chaperone
Function / homology
Function and homology information


Hsp70 protein binding / Hsp90 protein binding / protein folding / defense response to virus / innate immune response / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cns1/TTC4, wheel domain / Cns1/TTC4 Wheel domain / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Tetratricopeptide repeat protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035/A02 Germany
CitationJournal: Mol.Cell / Year: 2019
Title: The Co-chaperone Cns1 and the Recruiter Protein Hgh1 Link Hsp90 to Translation Elongation via Chaperoning Elongation Factor 2.
Authors: Schopf, F.H. / Huber, E.M. / Dodt, C. / Lopez, A. / Biebl, M.M. / Rutz, D.A. / Muhlhofer, M. / Richter, G. / Madl, T. / Sattler, M. / Groll, M. / Buchner, J.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tetratricopeptide repeat protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7172
Polymers19,6221
Non-polymers951
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-8 kcal/mol
Surface area8670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.680, 42.800, 43.090
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

-
Components

#1: Protein Tetratricopeptide repeat protein 4 / TPR repeat protein 4


Mass: 19622.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTC4, My044 / Production host: Escherichia coli (E. coli) / References: UniProt: O95801
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.4 M Na/K phosphate pH 8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→45 Å / Num. obs: 20421 / % possible obs: 97.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.8
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.9 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HFM

6hfm


Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.38 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18947 1019 5 %RANDOM
Rwork0.15876 ---
obs0.16031 19370 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20.17 Å2
2--0.23 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 5 80 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191307
X-RAY DIFFRACTIONr_bond_other_d0.0020.021209
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9711774
X-RAY DIFFRACTIONr_angle_other_deg0.87732800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.11923.07765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2515222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7911511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
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_it2.1663.641623
X-RAY DIFFRACTIONr_mcbond_other2.1623.632622
X-RAY DIFFRACTIONr_mcangle_it2.895.411776
X-RAY DIFFRACTIONr_mcangle_other2.8895.42777
X-RAY DIFFRACTIONr_scbond_it2.2854.053684
X-RAY DIFFRACTIONr_scbond_other2.2344.05681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4525.853988
X-RAY DIFFRACTIONr_long_range_B_refined3.48441.9671417
X-RAY DIFFRACTIONr_long_range_B_other3.4741.8771412
X-RAY DIFFRACTIONr_rigid_bond_restr0.79832516
X-RAY DIFFRACTIONr_sphericity_free25.835553
X-RAY DIFFRACTIONr_sphericity_bonded13.12352510
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 74 -
Rwork0.358 1423 -
obs--97.65 %
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)
10.16320.018-0.06550.0069-0.02720.1129-0.0044-0.0044-0.00380.0001-0.00030.0014-0.00790.00360.00470.03080.00060.00790.0458-0.00050.046212.4079-24.680947.4534
22.78892.0361.66232.59652.14911.77920.13920.2098-0.08410.0564-0.0268-0.14220.0449-0.0307-0.11240.01680.01150.00640.05030.00030.0409-5.4734-24.583932.5051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A220 - 237
3X-RAY DIFFRACTION2A246 - 258
2X-RAY DIFFRACTION1A265 - 580

+
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