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- PDB-3cjh: Tim8-Tim13 complex -

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Basic information

Entry
Database: PDB / ID: 3cjh
TitleTim8-Tim13 complex
Components
  • Mitochondrial import inner membrane translocase subunit TIM13
  • Mitochondrial import inner membrane translocase subunit TIM8
KeywordsPROTEIN TRANSPORT / cyclic heterohexamer / Chaperone / Inner membrane / Membrane / Metal-binding / Mitochondrion / Translocation / Transport
Function / homology
Function and homology information


mitochondrial intermembrane space protein transporter complex / protein transporter activity / protein insertion into mitochondrial inner membrane / mitochondrial intermembrane space / mitochondrial inner membrane / mitochondrion / metal ion binding
Similarity search - Function
Mitochondrial import inner membrane translocase subunit tim13 like domains / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial import inner membrane translocase subunit TIM13 / Mitochondrial import inner membrane translocase subunit TIM8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSawaya, M.R. / Schmid, E. / Beverly, K.N. / Koehler, C.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Tim8-Tim13 complex has multiple substrate binding sites and binds cooperatively to Tim23
Authors: Beverly, K.N. / Sawaya, M.R. / Schmid, E. / Koehler, C.M.
History
DepositionMar 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial import inner membrane translocase subunit TIM13
B: Mitochondrial import inner membrane translocase subunit TIM8
C: Mitochondrial import inner membrane translocase subunit TIM13
D: Mitochondrial import inner membrane translocase subunit TIM8
E: Mitochondrial import inner membrane translocase subunit TIM13
F: Mitochondrial import inner membrane translocase subunit TIM8
G: Mitochondrial import inner membrane translocase subunit TIM13
H: Mitochondrial import inner membrane translocase subunit TIM8
I: Mitochondrial import inner membrane translocase subunit TIM13
J: Mitochondrial import inner membrane translocase subunit TIM8
K: Mitochondrial import inner membrane translocase subunit TIM13
L: Mitochondrial import inner membrane translocase subunit TIM8


Theoretical massNumber of molelcules
Total (without water)86,55212
Polymers86,55212
Non-polymers00
Water73941
1
A: Mitochondrial import inner membrane translocase subunit TIM13
B: Mitochondrial import inner membrane translocase subunit TIM8
C: Mitochondrial import inner membrane translocase subunit TIM13
D: Mitochondrial import inner membrane translocase subunit TIM8
E: Mitochondrial import inner membrane translocase subunit TIM13
F: Mitochondrial import inner membrane translocase subunit TIM8


Theoretical massNumber of molelcules
Total (without water)43,2766
Polymers43,2766
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-82.2 kcal/mol
Surface area17580 Å2
MethodPISA
2
G: Mitochondrial import inner membrane translocase subunit TIM13
H: Mitochondrial import inner membrane translocase subunit TIM8
I: Mitochondrial import inner membrane translocase subunit TIM13
J: Mitochondrial import inner membrane translocase subunit TIM8
K: Mitochondrial import inner membrane translocase subunit TIM13
L: Mitochondrial import inner membrane translocase subunit TIM8


Theoretical massNumber of molelcules
Total (without water)43,2766
Polymers43,2766
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-82.3 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.655, 56.303, 59.837
Angle α, β, γ (deg.)89.18, 89.65, 60.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71A
81C
91E
101G
111I
121K
131A
141C
151E
161G
171I
181K
191A
201C
211E
221G
231I
241K
12B
22D
32F
42H
52J
62L
72B
82D
92F
102H
112J
122L
132B
142D
152F
162H
172J
182L
192B
202D
212F
222H
232J
242L
13A
23C
33E
43G
53I
63K
14B
24D
34F
44H
54J
64L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEULEULEU1AA49 - 628 - 21
211LEULEULEULEU1CC49 - 628 - 21
311LEULEULEULEU1EE49 - 628 - 21
411LEULEULEULEU1GG49 - 628 - 21
511LEULEULEULEU1II49 - 628 - 21
611LEULEULEULEU1KK49 - 628 - 21
721ALAALATYRTYR1AA72 - 8131 - 40
821ALAALATYRTYR1CC72 - 8131 - 40
921ALAALATYRTYR1EE72 - 8131 - 40
1021ALAALATYRTYR1GG72 - 8131 - 40
1121ALAALATYRTYR1II72 - 8131 - 40
1221ALAALATYRTYR1KK72 - 8131 - 40
1331ARGARGSERSER1AA83 - 9442 - 53
1431ARGARGSERSER1CC83 - 9442 - 53
1531ARGARGSERSER1EE83 - 9442 - 53
1631ARGARGSERSER1GG83 - 9442 - 53
1731ARGARGSERSER1II83 - 9442 - 53
1831ARGARGSERSER1KK83 - 9442 - 53
1941METMETMETMET3AA8241
2041METMETMETMET3CC8241
2141METMETMETMET3EE8241
2241METMETMETMET3GG8241
2341METMETMETMET3II8241
2441METMETMETMET3KK8241
112SERSERHISHIS1BB36 - 3813 - 15
212SERSERHISHIS1DD36 - 3813 - 15
312SERSERHISHIS1FF36 - 3813 - 15
412SERSERHISHIS1HH36 - 3813 - 15
512SERSERHISHIS1JJ36 - 3813 - 15
612SERSERHISHIS1LL36 - 3813 - 15
722GLUGLULEULEU1BB61 - 8338 - 60
822GLUGLULEULEU1DD61 - 8338 - 60
922GLUGLULEULEU1FF61 - 8338 - 60
1022GLUGLULEULEU1HH61 - 8338 - 60
1122GLUGLULEULEU1JJ61 - 8338 - 60
1222GLUGLULEULEU1LL61 - 8338 - 60
1332PHEPHECYSCYS1BB40 - 4817 - 25
1432PHEPHECYSCYS1DD40 - 4817 - 25
1532PHEPHECYSCYS1FF40 - 4817 - 25
1632PHEPHECYSCYS1HH40 - 4817 - 25
1732PHEPHECYSCYS1JJ40 - 4817 - 25
1832PHEPHECYSCYS1LL40 - 4817 - 25
1942GLNGLNGLNGLN3BB3916
2042GLNGLNGLNGLN3DD3916
2142GLNGLNGLNGLN3FF3916
2242GLNGLNGLNGLN3HH3916
2342GLNGLNGLNGLN3JJ3916
2442GLNGLNGLNGLN3LL3916
113ALAALAGLUGLU6AA46 - 485 - 7
213ALAALAGLUGLU6CC46 - 485 - 7
313ALAALAGLUGLU6EE46 - 485 - 7
413ALAALAGLUGLU6GG46 - 485 - 7
513ALAALAGLUGLU6II46 - 485 - 7
613ALAALAGLUGLU6KK46 - 485 - 7
114LYSLYSMETMET5BB30 - 357 - 12
214LYSLYSMETMET5DD30 - 357 - 12
314LYSLYSMETMET5FF30 - 357 - 12
414LYSLYSMETMET5HH30 - 357 - 12
514LYSLYSMETMET5JJ30 - 357 - 12
614LYSLYSMETMET5LL30 - 357 - 12

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Mitochondrial import inner membrane translocase subunit TIM13


Mass: 7083.026 Da / Num. of mol.: 6 / Fragment: residues 42-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIM13 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: P53299
#2: Protein
Mitochondrial import inner membrane translocase subunit TIM8


Mass: 7342.226 Da / Num. of mol.: 6 / Fragment: residues 24-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIM8 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: P57744
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.63 %
Crystal growTemperature: 298 K / pH: 8
Details: 10 mM Tris, pH 8.0, 10 mM NaCl, 3% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2003
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→90 Å / Num. obs: 19026 / % possible obs: 96 % / Redundancy: 3.3 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.378 / % possible all: 94.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.3 Å48.4 Å
Translation4.3 Å48.4 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.94 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.835 / SU B: 32.852 / SU ML: 0.338 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELLIPSOIDAL TRUNCATION AND ANISOTROPIC SCALE FACTORS HAVE BEEN APPLIED TO THE STRUCTURE FACTORS AND USED IN REFINEMENT. THE ELLIPSOID HAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELLIPSOIDAL TRUNCATION AND ANISOTROPIC SCALE FACTORS HAVE BEEN APPLIED TO THE STRUCTURE FACTORS AND USED IN REFINEMENT. THE ELLIPSOID HAS PRINCIPLE AXES OF 2.5, 2.5, AND 3.1 ANGSTROMS NEAR A*, B*, AND C*, RESPECTIVELY. THE SUBMITTED STRUCTURE FACTOR ARCHIVE CONTAINS THE TRUNCATED/SCALE STRUCTURE FACTORS AND THE ORIGINAL, UNMODIFIED INTENSITIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.28884 777 5.3 %RANDOM
Rwork0.24448 ---
obs0.24691 14640 75.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-1.09 Å2-0.02 Å2
2--0.92 Å21.36 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 0 41 5279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225316
X-RAY DIFFRACTIONr_bond_other_d0.0020.023578
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9347115
X-RAY DIFFRACTIONr_angle_other_deg1.20538781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4925647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88525.649262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.899151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7911530
X-RAY DIFFRACTIONr_chiral_restr0.0770.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02995
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_it1.9523281
X-RAY DIFFRACTIONr_mcbond_other0.26221306
X-RAY DIFFRACTIONr_mcangle_it3.5335330
X-RAY DIFFRACTIONr_scbond_it2.57822035
X-RAY DIFFRACTIONr_scangle_it4.12931833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A499tight positional0.030.05
11C499tight positional0.030
11E499tight positional0.030
11G499tight positional0.030
11I499tight positional0.080
11K499tight positional0.030
22B487tight positional0.030.05
22D487tight positional0.020
22F487tight positional0.020
22H487tight positional0.030
22J487tight positional0.020
22L487tight positional0.030
44B36medium positional0.290.5
44D36medium positional0.180.01
44F36medium positional0.20
44H36medium positional0.160
44J36medium positional0.150
44L36medium positional0.190
11A8loose positional0.575
11C8loose positional0.250.62
11E8loose positional0.080.08
11G8loose positional0.230.01
11I8loose positional0.090
11K8loose positional0.070
22B9loose positional0.125
22D9loose positional0.590.56
22F9loose positional0.230.06
22H9loose positional0.120.01
22J9loose positional0.350
22L9loose positional0.20
33A31loose positional15
33C31loose positional1.560.16
33E31loose positional0.740.01
33G31loose positional0.960
33I31loose positional1.640
33K31loose positional0.720
44B56loose positional1.865
44D56loose positional0.890.09
44F56loose positional0.560
44H56loose positional0.780
44J56loose positional0.670
44L56loose positional0.610
11A499tight thermal0.070.5
11C499tight thermal0.070
11E499tight thermal0.070
11G499tight thermal0.060
11I499tight thermal0.070
11K499tight thermal0.070
22B487tight thermal0.070.5
22D487tight thermal0.060
22F487tight thermal0.060
22H487tight thermal0.070
22J487tight thermal0.060
22L487tight thermal0.060
44B36medium thermal0.312
44D36medium thermal0.270.06
44F36medium thermal0.290
44H36medium thermal0.220
44J36medium thermal0.240
44L36medium thermal0.310
11A8loose thermal0.0210
11C8loose thermal0.081.25
11E8loose thermal0.040.16
11G8loose thermal0.040.02
11I8loose thermal0.060
11K8loose thermal0.070
22B9loose thermal0.0310
22D9loose thermal0.051.11
22F9loose thermal0.040.12
22H9loose thermal0.020.01
22J9loose thermal0.030
22L9loose thermal0.030
33A31loose thermal1.710
33C31loose thermal1.470.32
33E31loose thermal1.590.01
33G31loose thermal1.840
33I31loose thermal0.710
33K31loose thermal0.590
44B56loose thermal0.2710
44D56loose thermal0.180.18
44F56loose thermal0.230
44H56loose thermal0.140
44J56loose thermal0.130
44L56loose thermal0.160
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 12 -
Rwork0.217 285 -
obs--20.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.51861.14840.32790.7588-0.01580.15890.044-0.1693-0.21980.1647-0.0329-0.11560.0162-0.0038-0.01110.1037-0.03430.01370.10730.0220.035541.221627.068838.7111
22.2222-0.9923-0.16520.757-0.06620.07470.01910.16540.177-0.1717-0.0289-0.1256-0.0084-0.0030.00980.11770.01620.00210.1160.02740.036841.24079.622111.2469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA46 - 975 - 56
2X-RAY DIFFRACTION1BB28 - 865 - 63
3X-RAY DIFFRACTION1CC46 - 975 - 56
4X-RAY DIFFRACTION1DD29 - 836 - 60
5X-RAY DIFFRACTION1EE46 - 975 - 56
6X-RAY DIFFRACTION1FF29 - 866 - 63
7X-RAY DIFFRACTION2GG46 - 975 - 56
8X-RAY DIFFRACTION2HH29 - 866 - 63
9X-RAY DIFFRACTION2II46 - 995 - 58
10X-RAY DIFFRACTION2JJ29 - 856 - 62
11X-RAY DIFFRACTION2KK46 - 975 - 56
12X-RAY DIFFRACTION2LL29 - 866 - 63

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