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- PDB-7v9r: Crystal Structure of the heptameric EcHsp60 -

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Basic information

Entry
Database: PDB / ID: 7v9r
TitleCrystal Structure of the heptameric EcHsp60
Components60 kDa chaperonin
KeywordsCHAPERONE / mtHsp60 / Heptamer / Single-ring
Function / homology
Function and homology information


chaperonin ATPase / ATP-dependent protein folding chaperone / protein refolding / mitochondrial matrix / 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: 3.5 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 26, 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
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin


Theoretical massNumber of molelcules
Total (without water)430,6307
Polymers430,6307
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Negative stain TEM analysis confirmed the seven subunits formed a ring structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17860 Å2
ΔGint-95 kcal/mol
Surface area152790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.055, 140.967, 240.339
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: 61518.617 Da / Num. of mol.: 7 / Mutation: M330V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epinephelus coioides (orange-spotted grouper)
Gene: HSP60 / Plasmid: pET-EcHsp60_T / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: A0A097BVP4, chaperonin ATPase

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.75 / Details: 50 Mm Tris-HCl, 500 mM MgCl2, 10.5% (w/v) PEG1000

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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: Jun 21, 2020
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→29.79 Å / Num. obs: 51897 / % possible obs: 85.47 % / Redundancy: 4.2 % / Biso Wilson estimate: 115.75 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.03 / Rrim(I) all: 0.067 / Net I/σ(I): 14.09
Reflection shellResolution: 3.5→3.625 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 3.11 / Num. unique obs: 4277 / CC1/2: 0.799 / CC star: 0.942 / Rpim(I) all: 0.2743 / Rrim(I) all: 0.54 / % possible all: 71.64

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Processing

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

6mrd


Resolution: 3.5→29.79 Å / SU ML: 0.4053 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 1980 3.82 %
Rwork0.1837 49895 -
obs0.1855 51875 85.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.42 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26003 0 0 0 26003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001926219
X-RAY DIFFRACTIONf_angle_d0.453135597
X-RAY DIFFRACTIONf_chiral_restr0.03914481
X-RAY DIFFRACTIONf_plane_restr0.00314628
X-RAY DIFFRACTIONf_dihedral_angle_d10.49753780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.33711120.26432920X-RAY DIFFRACTION71.14
3.59-3.680.32241200.2482982X-RAY DIFFRACTION72.56
3.68-3.790.28421250.22523041X-RAY DIFFRACTION74.39
3.79-3.910.28571330.20633153X-RAY DIFFRACTION76.76
3.91-4.050.25411310.19413248X-RAY DIFFRACTION78.99
4.05-4.220.23261380.17873402X-RAY DIFFRACTION82.19
4.22-4.410.22651330.16863540X-RAY DIFFRACTION85.62
4.41-4.640.23751440.16843642X-RAY DIFFRACTION88.05
4.64-4.930.19311450.16243673X-RAY DIFFRACTION89.12
4.93-5.310.21361530.16773789X-RAY DIFFRACTION91.23
5.31-5.840.25081600.19813928X-RAY DIFFRACTION93.55
5.84-6.670.28021550.20674066X-RAY DIFFRACTION96.55
6.67-8.380.23041610.17764215X-RAY DIFFRACTION99.64
8.38-29.790.18191700.16984296X-RAY DIFFRACTION97.68
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)
15.623619600110.4606427264630.8984516735773.362208787-1.010124525621.33773928268-0.248622925420.352921889916-0.007533781293820.01695301857010.3050957168660.185542043007-0.4543573756490.169804134298-0.07151456981740.632638106663-0.04601563825950.01622642104260.6826854460080.01874893164140.440008602451-16.0327846102-62.8407677199-26.7942656733
20.8467802617841.32470509044-0.203197813626.5608610813-0.001199891113251.020651681170.197170571014-0.1353201871080.06164825256950.422155250271-0.176256811982-0.0224441658076-0.243138713499-0.157539346456-0.02415411816690.7614625234020.1024326822230.02307203395060.9563638232-0.04938723195130.689339137011-20.3406121482-46.1281967291-9.22408530824
35.872756969431.56361916777-1.865538657783.99362362587-4.170134887546.150400556150.1047466338211.39501638190.407346132091-1.03021079728-0.009474442756290.2218970197890.124397119927-0.0643316094385-0.1281595578520.94926892676-0.004428150071560.04722498427530.898853742007-0.06281950008480.692569602213-24.6936034461-23.0781334257-23.8812310628
42.06565161562-0.7675853427960.635861243080.9404826980610.817366140361.67606627270.102378420232-0.46983987831-0.1774065447050.386912202344-0.0207725017703-0.2400745735980.196127881226-0.0721452681977-0.08762903501760.997538154067-0.1334039840910.05808020727560.8888013747910.06108420265030.664365435566-22.3007029104-58.6787043519-10.2566821135
57.385751437720.559188754449-4.060690882711.96607578112-0.4701730899443.261856221630.05577512745340.5988719603510.1251182021750.1518434347440.0475921446441-0.0531706863204-0.234568252731-0.125345534029-0.06948884913760.8307585504350.0511206256845-0.2157292304730.573988754096-0.01493534737880.44261106264316.0402393664-62.9720511303-27.0630674385
62.139273512492.398819053240.2345061558083.684070581021.206832287221.110663148050.449991593711-0.07035039379110.374499030570.60328353194-0.2987636053280.1262409396910.0873192523527-0.161033537508-0.089846133730.8830832389030.121423113304-0.002012986200110.7303604211260.06931885275030.54089721850528.4877427274-53.6770879344-7.5772440891
74.58817725021-2.33562964410.7011182949581.73740095203-1.302857703376.188048158770.1381475129780.00705134229508-0.16428425686-0.143196739230.01450910059020.1500192688290.0511629096484-0.784854264949-0.09738051079810.930218221777-0.005113096247870.06076930060350.7788009394070.137924622990.9411100093716.689272984-25.8976479853-18.6948897111
83.778735720491.681709978740.03036947633661.771069761860.7127485639942.186041457380.1187945857950.140947580138-0.351859441791-0.1180636228020.0783137038438-0.222706981880.1049898370680.127376760677-0.2153198366090.7547024305120.0422307206888-0.1618307934530.6629873524620.02455631400960.48698802647325.3601683263-59.4895553247-12.0700151828
94.34178627817-0.531577286061-0.7228977414060.614927485086-2.326378689436.1916385354-0.04284620768390.04899001657870.08190388815720.155358382445-0.1083622989770.001530853343850.0717265721787-0.3306811834630.1436817201280.695074200202-0.00211776702187-0.0479043040140.528896635714-0.0809191069420.55829407801235.4377178211-63.1261740375-51.8892994684
100.9912343524912.02719874755-0.1663969587695.102356117170.009272282147670.2585810500830.1212579192330.07376288632860.1079648847080.0582976022323-0.2933896348670.0674644616605-0.2667588570970.3143210769660.1514212657670.8043188984150.04648286157730.002625647641171.059730973920.09264193622190.78063233240953.8315656049-46.0369989193-52.2754239926
119.73234188689-1.039486823721.514582364583.276353915932.80848727565.83394665405-0.188806350311-0.358336249342-0.3201669357380.1964746202960.01442876217740.316271099227-0.0525398698112-0.8408526588910.1227369535380.959035049815-0.01698604924990.0966107248970.7113187338290.1644665753080.60145888951641.259396784-23.7232887202-44.8566697242
121.990854203211.06072887959-0.3225332770071.21059754573-0.5540204444320.4848117844330.1872391801040.513599111687-0.23255242543-0.0857114908581-0.349361999473-0.3678660613530.03046903229020.2153889366820.1801669428950.8461920996130.18498358425-0.0927822582651.242137961220.0240056355130.88348697045653.068910188-59.4446622357-49.823563114
135.00487076396-2.097806391513.550196182.95182780472-0.9958419826536.41718773915-0.0995079180258-0.0657512250813-0.0749816845930.1132236884510.1106078862170.01140737155050.078233476717-0.5970578435670.0280556966770.6874266613580.05397872654060.1038454615670.612767030944-0.1212154721840.57522143860328.3508987768-62.9311430078-83.2527269117
141.30442041916-0.5292543243090.2847791835913.776940706131.26732065605-0.790824652682-0.2110455644340.1664001471270.124119659862-0.0146466597642-0.007953761505150.103340516277-0.1845933312910.396196812510.2978308128570.993380954870.0858158556143-0.05948405575651.11326774190.1493682628210.66857508375939.2981271228-33.775914958-89.4427541016
153.606558567610.51843144014-0.4179339799191.72488047694-1.531551538032.11526605307-0.09949983951390.822925264378-0.67894218857-0.595972831827-0.05151597353690.07813711967350.4755130555980.1632823281160.1657384688521.033158738090.2875700141490.01612492428161.16381765567-0.2306798655640.68646857461641.2046615952-59.9019156047-95.1784007951
165.867469869891.120556502071.311268018782.894685370151.163819557351.942292229640.1500421744010.124601458677-0.16442233375-0.2680502693920.0424099710566-0.256929361726-0.3536985997370.204908063773-0.1606071182790.8648790521810.129458117190.08402094294220.734097504834-0.02989388226160.476122223774-0.312747393277-62.8141679448-97.2961947977
170.483447069013-0.0970435684198-1.532813761233.457464862381.54910036790.500483267889-0.1250952969950.4023779825450.2545251992820.04759830216120.137898982163-0.2334283751150.1670990655690.0471756644461-0.02146314012380.968997128930.101978297554-0.08276511602490.9883387479530.03271207858520.665434387174-1.12095970717-39.4863286055-110.613078457
181.21753345152-0.285153141186-0.02666817472891.09330666478-0.2768200119991.723502584050.02289978903030.491635989878-0.0995902426169-0.0648420997251-0.0513352108445-0.08427324211290.106336901113-0.04487671013060.004416883088540.7491433436060.06187112885710.01678408214421.02650090457-0.1128722231770.7596883107081.09048075563-46.4316238851-112.297829673
198.67435362599-0.0412667779528-5.564413612411.42721672750.3150086566348.06459081398-0.0287415934992-0.0560239626598-0.348727894022-0.2134563597630.0516882306647-0.114962669893-0.0975218436890.195674884654-0.01988467940050.749821573213-0.0220390585634-0.08024082840.520186338992-0.07617347272140.53691902829-29.0203944967-62.909968444-83.2040224324
202.00145830522-1.30120542136-0.2975108799484.15212436357-0.7924547815370.02378617320460.2830055008030.3190752018050.275202392764-0.431758126849-0.13444420870.203619508218-0.08456353065550.0205573770760.08655116366140.789876071027-0.0224416720622-0.09527948134870.955206264388-0.1491471929040.513146458241-48.5776945203-49.583061103-93.4009014874
216.842083005551.432089728680.02796058825026.91906874622-0.2257416550124.396887537180.05282754508850.190574956082-0.246801275685-0.275655279662-0.156779569333-0.507834150248-0.1965753073560.7232182534420.1173133152410.8439379657270.004240667432090.01554986313930.9231601967640.0073073807110.580443107702-30.4685376202-24.8793699177-91.4823959185
222.17223776759-0.745690748702-0.848925754930.9405738623560.05782359375662.70529864105-0.1807398832450.26932300162-0.305928700051-0.1450911043110.2847459484320.2183393289440.203986904314-0.466620906181-0.035335085370.863178226357-0.140330673302-0.05697149012051.03581005724-0.1171502207950.656485311177-43.9269232252-59.6135370496-92.3623738902
236.052986016981.941723478061.202859496982.524944945031.0740497748.96058416151-0.2512688351240.469869931899-0.100241207865-0.311175920380.312435322089-0.157332956347-0.07397077942650.403299775524-0.03568194023480.5292093762240.00648395528601-0.03408464229390.498536351758-0.05197228596250.50017386859-35.9803980945-62.6178180147-51.7467424318
242.83218528317-0.606620101974-1.330489741095.775338155510.7529689579522.799721349580.143952638306-0.224909524880.2967348821110.75838859236-0.1177111753630.545486901006-0.393610777536-0.24323871291-0.03884561033540.7820703889270.0184539455387-0.07690540005860.867705251416-0.03464362781520.541997050913-52.5216743879-46.4460586325-44.4878119226
253.346643953282.280953604980.3847881239625.84221818633-2.605534816486.17196195573-0.7886263778381.07652092110.259466371265-0.3025598172150.447407520127-0.151562479874-0.006678365824010.8665741338220.3804660145450.89886718152-0.115503412822-0.002424895944140.982078475424-0.01734403009440.763368012139-44.4375145137-23.0946497493-56.6392232001
262.30412874443-0.896313031723-0.3833824865751.126252347460.4534258532351.30287522203-0.0874118698543-0.371559092645-0.209793260240.09626531902830.2650302795080.0430975476672-0.0287060443367-0.0574171888488-0.1566940527150.756047468046-0.1038836997350.03197775192540.849380028161-0.00450649966070.511464334057-52.8685492526-58.9556571251-46.6238578935
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 132 )AA26 - 1321 - 107
22chain 'A' and (resid 133 through 241 )AA133 - 241108 - 216
33chain 'A' and (resid 242 through 380 )AA242 - 380217 - 351
44chain 'A' and (resid 381 through 550 )AA381 - 550352 - 521
55chain 'B' and (resid 26 through 133 )BB26 - 1331 - 108
66chain 'B' and (resid 134 through 203 )BB134 - 203109 - 178
77chain 'B' and (resid 204 through 380 )BB204 - 380179 - 350
88chain 'B' and (resid 381 through 550 )BB381 - 550351 - 520
99chain 'C' and (resid 26 through 133 )CC26 - 1331 - 108
1010chain 'C' and (resid 134 through 241 )CC134 - 241109 - 216
1111chain 'C' and (resid 242 through 380 )CC242 - 380217 - 349
1212chain 'C' and (resid 381 through 550 )CC381 - 550350 - 516
1313chain 'D' and (resid 26 through 133 )DD26 - 1331 - 108
1414chain 'D' and (resid 134 through 379 )DD134 - 379109 - 348
1515chain 'D' and (resid 380 through 551 )DD380 - 551349 - 514
1616chain 'E' and (resid 26 through 133 )EE26 - 1331 - 108
1717chain 'E' and (resid 134 through 279 )EE134 - 279109 - 254
1818chain 'E' and (resid 280 through 550 )EE280 - 550255 - 517
1919chain 'F' and (resid 26 through 132 )FF26 - 1321 - 107
2020chain 'F' and (resid 133 through 219 )FF133 - 219108 - 194
2121chain 'F' and (resid 220 through 380 )FF220 - 380195 - 355
2222chain 'F' and (resid 381 through 550 )FF381 - 550356 - 522
2323chain 'G' and (resid 26 through 131 )GG26 - 1311 - 106
2424chain 'G' and (resid 132 through 241 )GG132 - 241107 - 216
2525chain 'G' and (resid 242 through 380 )GG242 - 380217 - 355
2626chain 'G' and (resid 381 through 550 )GG381 - 550356 - 525

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