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- PDB-7v98: Crystal Structure of the Dimeric EcHsp60 -

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Basic information

Entry
Database: PDB / ID: 7v98
TitleCrystal Structure of the Dimeric EcHsp60
Components60 kDa chaperonin
KeywordsCHAPERONE / Hsp60 / Homodimer / Inactive form
Function / homology
Function and homology information


chaperonin ATPase / ATP-dependent protein folding chaperone / protein refolding / ATP binding
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / 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
60 kDa heat shock protein, mitochondrial
Similarity search - Component
Biological speciesEpinephelus coioides (orange-spotted grouper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLai, M.C. / Lin, S.M.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2636-B-006 -012 - Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2636-B-006 -012 - Taiwan
CitationJournal: Life Sci Alliance / Year: 2023
Title: Crystal structures of dimeric and heptameric mtHsp60 reveal the mechanism of chaperonin inactivation.
Authors: Lai, M.C. / Cheng, H.Y. / Lew, S.H. / Chen, Y.A. / Yu, C.H. / Lin, H.Y. / Lin, S.M.
History
DepositionAug 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 60 kDa chaperonin
B: 60 kDa chaperonin


Theoretical massNumber of molelcules
Total (without water)124,7232
Polymers124,7232
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The retention time is closed to 120 kDa., SAXS, The Rg is 35.86
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-33 kcal/mol
Surface area37010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.287, 95.378, 128.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 60 kDa chaperonin / 60 kDa heat shock protein / mitochondrial / Chaperonin 60 / Heat shock protein 60


Mass: 62361.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epinephelus coioides (orange-spotted grouper)
Gene: HSP60 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: A0A097BVP4, chaperonin ATPase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 400 mM KNaC4H4O6, 21 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 42352 / % possible obs: 91.47 % / Redundancy: 5.6 % / Biso Wilson estimate: 49.35 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Net I/σ(I): 13.69
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 3936 / CC1/2: 0.722 / CC star: 0.916 / Rpim(I) all: 0.404 / Rrim(I) all: 0.904 / % possible all: 86.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASER1.19.2_4158phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MRD

6mrd


Resolution: 2.35→29.96 Å / SU ML: 0.3245 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2642 1964 4.64 %
Rwork0.2131 40339 -
obs0.2155 42303 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.9 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5715 0 0 81 5796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215763
X-RAY DIFFRACTIONf_angle_d0.43027792
X-RAY DIFFRACTIONf_chiral_restr0.0393962
X-RAY DIFFRACTIONf_plane_restr0.00341011
X-RAY DIFFRACTIONf_dihedral_angle_d13.0975810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.33181340.26332650X-RAY DIFFRACTION85.85
2.41-2.470.31151330.27342754X-RAY DIFFRACTION87.94
2.47-2.550.31321280.27092713X-RAY DIFFRACTION87.96
2.55-2.630.29351460.2592738X-RAY DIFFRACTION88.22
2.63-2.720.30341280.25992761X-RAY DIFFRACTION88.46
2.72-2.830.31971410.25452747X-RAY DIFFRACTION88.97
2.83-2.960.32951230.26762804X-RAY DIFFRACTION88.83
2.96-3.120.32431390.27362751X-RAY DIFFRACTION88.24
3.12-3.310.29961260.2472795X-RAY DIFFRACTION89.19
3.31-3.570.29871400.22812921X-RAY DIFFRACTION92.59
3.57-3.920.30241460.21153052X-RAY DIFFRACTION96.73
3.92-4.490.21931600.17323159X-RAY DIFFRACTION99.46
4.49-5.650.2261600.18023208X-RAY DIFFRACTION100
5.65-29.960.21731600.18483286X-RAY DIFFRACTION98.12
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)
14.39694507141-1.555306628191.767001242449.332485910981.593794118662.095780111310.08888003804520.1987193988290.28678301154-1.62922852067-0.434559163098-0.1719644665511.35810619986-0.6925030891470.3177375237750.577376502547-0.002709362821120.03294391029160.727788367911-0.1029504042440.6476521580321.00364980572.24833140971-23.813625836
28.21789551096-4.24752712761-7.564593184224.891330526365.339677667188.13421921487-0.644969424094-0.275683338142-0.5644949824550.3868091601810.2020992810650.4512301788040.6329411270730.3099954848920.3856528719310.4122869000890.0932712793175-0.1120423048750.6325457881310.1446528109640.4671167079723.34826571178-3.758175806363.75052910883
38.861768311963.115320127635.088704489049.298145397762.216727034057.89948148831-0.0973840007225-0.489705595448-0.2409856222870.4426766494810.228845965587-0.1219788641460.2860776122060.290391978791-0.1278676098750.3350710300480.07063016060550.1021516907010.4634252418840.03157837007710.40700802345-12.618089244210.733017945710.8136096693
44.029595850320.668329022519-2.114169727251.17697533462-0.8501860576892.625341076280.0272003338148-0.19770142023-0.1593782230630.171002696667-0.200161830512-0.07364733015990.1988648167270.1794321170240.1494340395520.3781774376180.00292222197945-0.01240487697380.3321169186470.04333814384030.370153162504-12.696934481418.2408123539-2.85557208992
52.4808666451.05486668353-0.5298521049363.21378832059-0.87116498553.51932047692-0.1042379997830.4014231585-0.293365883883-0.2083463309470.03816522740810.3020931514150.264232697814-0.4361620128750.06669286364010.3022930540450.0388213326870.003693781643610.434575168331-0.07227575633390.41586367849-23.260456391414.7705242173-15.5567122406
65.205770430141.044027159580.5799866529791.475167900770.3869705850335.83002415274-0.2250673261970.73905628359-1.09605399415-0.03650401436430.2448406672420.005408677671521.266466391140.393407575794-0.1813747333790.5420542635250.06243435570050.1421176601990.403879929663-0.0561369958410.706979510315-20.19010690592.82590389202-0.655529793838
74.07037829196-2.82504666338-1.616999493393.276859640553.510420321754.6849692417-0.125086813221-0.393158722776-0.00771271609706-0.2453059253110.333494828353-0.956069671679-0.250646570840.655005939725-0.1907056068480.459326440141-0.05293181988720.01514564244270.641975895240.02284060705770.487453973024-4.3808949911514.75307605587.02909160609
87.22769821631-1.25833100565-5.061480838153.282428873610.9174111089635.337410339330.0562216436975-1.277537076650.002042354568790.4681216675110.564680672182-0.3979985071070.2806263932041.09504289618-0.6372153987040.5489774932280.229303736198-0.1553693686310.940526126642-0.01868047225190.59455162375112.8158672994-5.575086312811.21128680142
93.980946025171.33132846226-1.096449024781.49569947306-0.8749692119970.523114649190.219202017175-1.179973912790.245535870885-0.230539088436-0.5852620560930.331447338718-0.799243868068-0.004381285486140.4740810779030.5756050737490.0448736543642-0.2384453918610.769825567868-0.08267527253740.81535504261220.60253653751.3891906165-4.74274669695
106.66116391702-7.173774246414.185613849997.96236439059-5.366863893223.037684514060.7820390370950.9580484946670.262814334223-0.991369850365-0.756020254562-0.3517019005040.3946190974170.630254553019-0.05790270754220.7114328167340.0689549407310.01766807569940.713036882448-0.01334475438180.54440050134319.719866253927.097162597-36.9298934924
110.8406231947231.35728103842-1.792951330413.06346443246-1.558938142825.94727867658-0.1545296462240.3129757169520.1578879719-0.518733976538-0.08162022820050.1011187196030.243226007679-0.1740976491520.1819378787820.3894290474060.004092107600840.005535258969060.4718954421670.09780410850750.4458275567372.1414400340635.6008557199-29.2781488339
122.790584989551.64680110614-1.292951044863.24968846833-1.117701727483.31098104026-0.05314643383560.01505224807270.5085951722360.0588511067472-0.06150147036290.0468359807329-0.5662517495330.05100155707950.1074188563850.3739495963980.0186954766593-0.06451050217720.3561849261480.08402248060.4136728039344.151380990145.9634964558-15.7301298151
135.285099307740.5826624948134.587433425842.060094519382.039284707936.56905435397-0.07446040427930.369400829723-0.271195107482-0.2859113177290.189742516483-0.1811836131740.1801630136970.637904731679-0.1094110470330.458313695763-0.001247116897140.04447809859020.514779892650.1739410869190.41652199121812.109323524238.5956447591-34.3003450183
141.93529844336-0.4581639154772.071948001386.28340213952-3.937222443926.475545662920.2229401346240.554554751397-0.229679124758-1.02051286316-0.09024154847790.04539613044390.9087523898330.177873557249-0.1177988957160.6669052663260.1691595807270.02971916012140.61061910185-0.08804960537870.55986387732426.983228462812.2237951595-31.6927464727
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 115 through 136 )AA115 - 1361 - 22
22chain 'A' and (resid 137 through 179 )AA137 - 17923 - 65
33chain 'A' and (resid 180 through 203 )AA180 - 20366 - 89
44chain 'A' and (resid 204 through 236 )AA204 - 23690 - 122
55chain 'A' and (resid 237 through 379 )AA237 - 379123 - 265
66chain 'A' and (resid 380 through 410 )AA380 - 410266 - 296
77chain 'A' and (resid 411 through 434 )AA411 - 434297 - 320
88chain 'A' and (resid 435 through 533 )AA435 - 533321 - 386
99chain 'B' and (resid 114 through 136 )BB114 - 1361 - 23
1010chain 'B' and (resid 137 through 203 )BB137 - 20324 - 90
1111chain 'B' and (resid 204 through 236 )BB204 - 23691 - 123
1212chain 'B' and (resid 237 through 378 )BB237 - 378124 - 265
1313chain 'B' and (resid 379 through 434 )BB379 - 434266 - 321
1414chain 'B' and (resid 435 through 533 )BB435 - 533322 - 386

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