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- PDB-5uyz: Structure of Human T-complex protein 1 subunit epsilon (CCT5) mut... -

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Basic information

Entry
Database: PDB / ID: 5uyz
TitleStructure of Human T-complex protein 1 subunit epsilon (CCT5) mutant His147Arg
ComponentsT-complex protein 1 subunit epsilon
KeywordsPROTEIN BINDING / chaperonin Hexadecameric complex ATP-dependent CCT5 gene
Function / homology
Function and homology information


positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / BBSome-mediated cargo-targeting to cilium / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / beta-tubulin binding ...positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / BBSome-mediated cargo-targeting to cilium / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein folding / protein folding chaperone / positive regulation of telomere maintenance via telomerase / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / mRNA 5'-UTR binding / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / unfolded protein binding / protein folding / cell body / microtubule / protein stabilization / centrosome / ATP hydrolysis activity / extracellular exosome / ATP binding / cytosol
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / T-complex protein 1, epsilon subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / T-complex protein 1, epsilon subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / T-complex protein 1 subunit epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsPereira, J.H. / McAndrew, R.P. / Sergeeva, O.A. / Ralston, C.Y. / King, J.A. / Adams, P.D.
CitationJournal: Sci Rep / Year: 2017
Title: Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy.
Authors: Pereira, J.H. / McAndrew, R.P. / Sergeeva, O.A. / Ralston, C.Y. / King, J.A. / Adams, P.D.
History
DepositionFeb 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-complex protein 1 subunit epsilon
B: T-complex protein 1 subunit epsilon
C: T-complex protein 1 subunit epsilon
D: T-complex protein 1 subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,85811
Polymers239,0764
Non-polymers1,7827
Water00
1
A: T-complex protein 1 subunit epsilon
B: T-complex protein 1 subunit epsilon
C: T-complex protein 1 subunit epsilon
D: T-complex protein 1 subunit epsilon
hetero molecules

A: T-complex protein 1 subunit epsilon
B: T-complex protein 1 subunit epsilon
C: T-complex protein 1 subunit epsilon
D: T-complex protein 1 subunit epsilon
hetero molecules

A: T-complex protein 1 subunit epsilon
B: T-complex protein 1 subunit epsilon
C: T-complex protein 1 subunit epsilon
D: T-complex protein 1 subunit epsilon
hetero molecules

A: T-complex protein 1 subunit epsilon
B: T-complex protein 1 subunit epsilon
C: T-complex protein 1 subunit epsilon
D: T-complex protein 1 subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)963,43144
Polymers956,30416
Non-polymers7,12728
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area89410 Å2
ΔGint-486 kcal/mol
Surface area321760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.570, 205.570, 163.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 59769.004 Da / Num. of mol.: 4 / Mutation: H147R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT5, CCTE, KIAA0098 / Production host: Escherichia coli (E. coli) / References: UniProt: P48643
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 3.61 Å3/Da / Density % sol: 65.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 MSodium acetate, 0.04 M citric acid, 0.06 M Bis-Tris propane pH 6.4, and 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→67 Å / Num. obs: 41130 / % possible obs: 100 % / Redundancy: 14.7 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2650: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UYX

5uyx


Resolution: 3.6→66.417 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.16
RfactorNum. reflection% reflection
Rfree0.3241 2067 5.03 %
Rwork0.2748 --
obs0.2773 41121 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→66.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14851 0 111 0 14962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415131
X-RAY DIFFRACTIONf_angle_d0.89620408
X-RAY DIFFRACTIONf_dihedral_angle_d20.3125824
X-RAY DIFFRACTIONf_chiral_restr0.0482414
X-RAY DIFFRACTIONf_plane_restr0.0042619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.68380.38041070.34912571X-RAY DIFFRACTION100
3.6838-3.77590.37691420.34812550X-RAY DIFFRACTION100
3.7759-3.8780.33551370.33662578X-RAY DIFFRACTION100
3.878-3.99210.39321370.33262556X-RAY DIFFRACTION100
3.9921-4.12090.38831500.32212542X-RAY DIFFRACTION100
4.1209-4.26820.31531280.29832581X-RAY DIFFRACTION100
4.2682-4.43910.31051430.27992582X-RAY DIFFRACTION100
4.4391-4.6410.31381190.28022590X-RAY DIFFRACTION100
4.641-4.88570.28951300.25512600X-RAY DIFFRACTION100
4.8857-5.19160.33671430.27582588X-RAY DIFFRACTION100
5.1916-5.59230.37551420.30672619X-RAY DIFFRACTION100
5.5923-6.15470.3461570.30242578X-RAY DIFFRACTION100
6.1547-7.04450.30691400.27432645X-RAY DIFFRACTION100
7.0445-8.87190.24461520.22272654X-RAY DIFFRACTION100
8.8719-66.42840.33281400.22932820X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 65.8448 Å / Origin y: -26.1058 Å / Origin z: 61.0646 Å
111213212223313233
T0.2863 Å2-0.0944 Å2-0.0446 Å2-0.3655 Å20.0992 Å2--0.3541 Å2
L0.174 °20.0765 °2-0.081 °2-0.1583 °2-0.0387 °2--0.1358 °2
S0.043 Å °0.0006 Å °0.0581 Å °0.0207 Å °0.0633 Å °-0.0142 Å °0.053 Å °-0.1773 Å °0.001 Å °
Refinement TLS groupSelection details: all

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