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- PDB-6tmu: Crystal structure of the chaperonin gp146 from the bacteriophage ... -

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Basic information

Entry
Database: PDB / ID: 6tmu
TitleCrystal structure of the chaperonin gp146 from the bacteriophage EL 2 (Pseudomonas aeruginosa) in presence of ATP-BeFx, crystal form II
ComponentsPutative GroEL-like chaperonine protein
KeywordsCHAPERONE / molecular chaperone / ATPase / chaperonin
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding / identical protein binding
Similarity search - Function
Chaperonin Cpn60/GroEL / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / : / Putative GroEL-like chaperonine protein
Similarity search - Component
Biological speciesPseudomonas phage EL (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.54 Å
AuthorsBracher, A. / Paul, S.S. / Wang, H. / Wischnewski, N. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: PLoS One / Year: 2020
Title: Structure and conformational cycle of a bacteriophage-encoded chaperonin.
Authors: Andreas Bracher / Simanta S Paul / Huping Wang / Nadine Wischnewski / F Ulrich Hartl / Manajit Hayer-Hartl /
Abstract: Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key ...Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionarily distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionarily more ancient chaperonin prior to acquisition of the encapsulation mechanism.
History
DepositionDec 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative GroEL-like chaperonine protein
B: Putative GroEL-like chaperonine protein
C: Putative GroEL-like chaperonine protein
D: Putative GroEL-like chaperonine protein
E: Putative GroEL-like chaperonine protein
F: Putative GroEL-like chaperonine protein
G: Putative GroEL-like chaperonine protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,89122
Polymers432,3277
Non-polymers3,56415
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25770 Å2
ΔGint-189 kcal/mol
Surface area160350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.516, 151.461, 261.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 551
2010B2 - 551
1020A2 - 551
2020C2 - 551
1030A2 - 551
2030D2 - 551
1040A2 - 549
2040E2 - 549
1050A2 - 550
2050F2 - 550
1060A2 - 551
2060G2 - 551
1070B2 - 551
2070C2 - 551
1080B2 - 551
2080D2 - 551
1090B2 - 550
2090E2 - 550
10100B2 - 549
20100F2 - 549
10110B2 - 551
20110G2 - 551
10120C2 - 551
20120D2 - 551
10130C2 - 549
20130E2 - 549
10140C2 - 550
20140F2 - 550
10150C2 - 551
20150G2 - 551
10160D2 - 550
20160E2 - 550
10170D2 - 549
20170F2 - 549
10180D2 - 551
20180G2 - 551
10190E2 - 550
20190F2 - 550
10200E2 - 550
20200G2 - 550
10210F2 - 549
20210G2 - 549

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

#1: Protein
Putative GroEL-like chaperonine protein


Mass: 61760.941 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage EL (virus) / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2Z0T5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 8 % PEG-6000, 0.15 M NaCl and 0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 3.54→49.47 Å / Num. obs: 70880 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.056 / Rrim(I) all: 0.125 / Net I/σ(I): 7.9 / Num. measured all: 348403
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.54-3.624.91.1192192945160.4650.5571.2551.399.9
16.98-49.473.70.05625716920.9940.0320.06522.394.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.551
Highest resolutionLowest resolution
Rotation49.41 Å6.64 Å

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Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018data reduction
Aimless0.5.28data scaling
MOLREP11.4.06phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EMD-6492

Resolution: 3.54→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 94.355 / SU ML: 0.618 / SU R Cruickshank DPI: 0.6819 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.655
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 3576 5.1 %RANDOM
Rwork0.2504 ---
obs0.2516 67159 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 343.38 Å2 / Biso mean: 170.101 Å2 / Biso min: 82.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--1.36 Å2-0 Å2
3----1.74 Å2
Refinement stepCycle: final / Resolution: 3.54→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29093 0 213 0 29306
Biso mean--151.22 --
Num. residues----3828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01929766
X-RAY DIFFRACTIONr_bond_other_d0.0030.0228177
X-RAY DIFFRACTIONr_angle_refined_deg0.9671.96940472
X-RAY DIFFRACTIONr_angle_other_deg0.865364540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05453816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55924.4571308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.241154931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.92215196
X-RAY DIFFRACTIONr_chiral_restr0.0510.24794
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0233955
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026612
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A313590.07
12B313590.07
21A322410.05
22C322410.05
31A315980.06
32D315980.06
41A323060.06
42E323060.06
51A316960.06
52F316960.06
61A318320.05
62G318320.05
71B315790.06
72C315790.06
81B320180.05
82D320180.05
91B314990.07
92E314990.07
101B317120.06
102F317120.06
111B315130.07
112G315130.07
121C319440.05
122D319440.05
131C323100.04
132E323100.04
141C319430.05
142F319430.05
151C319200.05
152G319200.05
161D317620.06
162E317620.06
171D320160.05
172F320160.05
181D316760.06
182G316760.06
191E318710.06
192F318710.06
201E317820.05
202G317820.05
211F317630.06
212G317630.06
LS refinement shellResolution: 3.54→3.631 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 249 -
Rwork0.353 4882 -
all-5131 -
obs--99.88 %
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)
12.6089-0.5154-0.92624.1506-1.23892.5041-0.0125-0.1342-0.13360.38020.12550.56270.1166-0.3616-0.1130.0952-0.00010.11550.34010.04960.2661-37.4878-124.1328-46.6319
22.5699-2.13330.61544.2264-4.07456.90970.172-0.0932-0.4124-0.2169-0.23490.887-0.4003-0.28220.06290.55810.1883-0.04040.9526-0.05551.4062-62.4018-110.6645-54.7375
33.8194-0.84250.52757.060.33221.04930.36910.61840.2497-1.7879-0.2320.02370.09870.3603-0.13711.2414-0.0431-0.15091.42570.15291.5283-69.7422-131.1965-73.7985
43.0807-0.2262-0.55464.7257-0.70531.9673-0.1328-0.3298-0.43020.13050.1660.39690.5935-0.1935-0.03320.25370.00920.06210.4358-0.01180.2355-16.8259-154.3266-66.6102
57.8958-3.87850.48464.835-1.05423.9636-0.3952-0.1313-0.13320.15890.12210.70950.1768-0.23490.27310.4186-0.29490.01550.77310.08370.7562-48.6478-157.3596-67.278
60.35630.1785-0.24160.1317-0.04273.5211-0.29730.65650.1873-0.31930.13810.1142-0.6606-0.39540.15931.6312-0.0943-0.30132.1137-0.19661.4031-48.1679-159.9826-97.5818
71.9680.37-0.36484.7227-0.55781.42130.05860.2351-0.4328-0.3019-0.1912-0.10060.06850.11260.13260.07510.00840.02340.357-0.06720.118911.5378-150.0672-95.7959
88.35440.94880.05144.9259-1.1110.4155-0.23810.11060.0048-0.03920.51630.8757-0.1278-0.4652-0.27820.79730.0223-0.10091.0683-0.00160.7224-12.0609-166.7798-102.8134
93.1787-0.15791.05061.4392-0.07025.5486-0.04850.18070.2222-0.0921-0.12420.023-0.2668-0.17060.17281.0621-0.111-0.14781.3301-0.06041.3289-14.2563-157.9926-130.8661
102.95770.7806-1.05143.54560.77373.3218-0.07240.2878-0.4643-0.09240.0308-0.45320.38020.2490.04150.10850.0854-0.02140.3681-0.03960.137225.374-115.5201-114.1397
114.85472.5076-1.50256.7051-1.70382.25120.087-0.1998-1.11130.1028-0.0971-0.44940.418-0.17360.01010.3898-0.0133-0.11420.7853-0.18280.449813.9676-137.5624-134.5717
127.70820.21270.42771.99750.1940.6733-0.21080.43890.52290.05740.1916-0.1301-0.20430.1110.01920.2772-0.0479-0.03290.6977-0.04820.2627-4.7919-117.0464-147.0047
132.49020.6402-1.0543.81730.01012.90630.12740.24730.3414-0.47290.1178-0.0329-0.4077-0.0026-0.24520.13660.04230.05160.32910.02870.056915.5112-76.8884-106.0571
146.35981.6209-1.56464.81162.20454.42490.53731.1328-0.7138-0.213-0.51570.38110.065-0.2719-0.02160.780.1922-0.12431.0724-0.10350.354110.7781-86.6863-133.4788
154.296-1.5440.46776.20810.03385.3727-0.0143-0.6715-0.22980.44250.29070.9770.4654-0.6301-0.27631.19150.21220.0341.46030.23220.9923-14.9992-72.7157-137.8415
162.0669-1.5653-1.28294.15860.53784.67350.4037-0.03130.795-0.375-0.0597-0.1037-1.3540.1984-0.3440.48840.04020.15850.45510.04970.4787-12.6067-62.3803-79.1464
170.2368-0.1304-0.92332.14342.07946.60790.40490.35110.0521-0.41780.36970.0061-1.2601-0.2374-0.77471.51630.41030.21121.30380.22761.1118-17.0835-52.3537-109.2653
180.7033-0.73350.2341.8588-0.92510.5474-0.0651-0.2939-0.9695-0.9271-0.07150.42330.4505-0.15730.13671.90780.3756-0.03022.71490.03832.0798-46.3719-59.6967-109.8899
192.4092-0.9705-0.63274.5547-0.33372.60650.1238-0.07990.06630.2768-0.15080.2779-0.2724-0.27390.02690.05080.02020.03140.30520.00940.069-35.8038-83.9003-53.0257
201.1739-0.05510.23231.6639-0.43217.8999-0.17870.58220.4237-0.64430.1102-0.073-0.64560.27250.06850.51930.10170.00191.02130.10070.5549-50.2778-67.6181-73.2823
212.24820.59810.98262.14071.07066.1677-0.21140.566-0.463-0.3417-0.0956-0.08780.7012-0.34540.3070.63360.05680.13751.0409-0.12290.6073-72.1585-87.2327-81.5544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 130
2X-RAY DIFFRACTION1A425 - 551
3X-RAY DIFFRACTION2A131 - 189
4X-RAY DIFFRACTION2A388 - 424
5X-RAY DIFFRACTION3A190 - 387
6X-RAY DIFFRACTION4B2 - 130
7X-RAY DIFFRACTION4B425 - 551
8X-RAY DIFFRACTION5B131 - 189
9X-RAY DIFFRACTION5B388 - 424
10X-RAY DIFFRACTION6B190 - 387
11X-RAY DIFFRACTION7C2 - 130
12X-RAY DIFFRACTION7C425 - 551
13X-RAY DIFFRACTION8C131 - 189
14X-RAY DIFFRACTION8C388 - 424
15X-RAY DIFFRACTION9C190 - 387
16X-RAY DIFFRACTION10D2 - 130
17X-RAY DIFFRACTION10D425 - 551
18X-RAY DIFFRACTION11D131 - 189
19X-RAY DIFFRACTION11D388 - 424
20X-RAY DIFFRACTION12D190 - 387
21X-RAY DIFFRACTION13E2 - 130
22X-RAY DIFFRACTION13E425 - 550
23X-RAY DIFFRACTION14E131 - 189
24X-RAY DIFFRACTION14E388 - 424
25X-RAY DIFFRACTION15E190 - 387
26X-RAY DIFFRACTION16F2 - 130
27X-RAY DIFFRACTION16F425 - 550
28X-RAY DIFFRACTION17F131 - 189
29X-RAY DIFFRACTION17F388 - 424
30X-RAY DIFFRACTION18F190 - 387
31X-RAY DIFFRACTION19G2 - 130
32X-RAY DIFFRACTION19G425 - 551
33X-RAY DIFFRACTION20G131 - 189
34X-RAY DIFFRACTION20G388 - 424
35X-RAY DIFFRACTION21G190 - 387

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