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- PDB-2guz: Structure of the Tim14-Tim16 complex of the mitochondrial protein... -

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Basic information

Entry
Database: PDB / ID: 2guz
TitleStructure of the Tim14-Tim16 complex of the mitochondrial protein import motor
Components
  • Mitochondrial import inner membrane translocase subunit TIM14
  • Mitochondrial import inner membrane translocase subunit TIM16
KeywordsCHAPERONE / PROTEIN TRANSPORT / DnaJ-fold
Function / homology
Function and homology information


PAM complex, Tim23 associated import motor / TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / ATPase activator activity / mitochondrial inner membrane / membrane => GO:0016020 / protein domain specific binding / mitochondrion
Similarity search - Function
Mitochondrial import inner membrane translocase subunit Tim16 / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Mitochondrial import inner membrane translocase subunit TIM16 / Mitochondrial import inner membrane translocase subunit TIM14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMokranjac, D. / Bourenkov, G. / Hell, K. / Neupert, W. / Groll, M.
CitationJournal: Embo J. / Year: 2006
Title: Structure and function of Tim14 and Tim16, the J and J-like components of the mitochondrial protein import motor.
Authors: Mokranjac, D. / Bourenkov, G. / Hell, K. / Neupert, W. / Groll, M.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial import inner membrane translocase subunit TIM14
B: Mitochondrial import inner membrane translocase subunit TIM16
C: Mitochondrial import inner membrane translocase subunit TIM14
D: Mitochondrial import inner membrane translocase subunit TIM16
E: Mitochondrial import inner membrane translocase subunit TIM14
F: Mitochondrial import inner membrane translocase subunit TIM16
G: Mitochondrial import inner membrane translocase subunit TIM14
H: Mitochondrial import inner membrane translocase subunit TIM16
I: Mitochondrial import inner membrane translocase subunit TIM14
J: Mitochondrial import inner membrane translocase subunit TIM16
K: Mitochondrial import inner membrane translocase subunit TIM14
L: Mitochondrial import inner membrane translocase subunit TIM16
M: Mitochondrial import inner membrane translocase subunit TIM14
N: Mitochondrial import inner membrane translocase subunit TIM16
O: Mitochondrial import inner membrane translocase subunit TIM14
P: Mitochondrial import inner membrane translocase subunit TIM16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,70220
Polymers125,94516
Non-polymers7564
Water16,592921
1
A: Mitochondrial import inner membrane translocase subunit TIM14
B: Mitochondrial import inner membrane translocase subunit TIM16


Theoretical massNumber of molelcules
Total (without water)15,7432
Polymers15,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-12 kcal/mol
Surface area7940 Å2
MethodPISA
2
C: Mitochondrial import inner membrane translocase subunit TIM14
D: Mitochondrial import inner membrane translocase subunit TIM16


Theoretical massNumber of molelcules
Total (without water)15,7432
Polymers15,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-11 kcal/mol
Surface area7930 Å2
MethodPISA
3
E: Mitochondrial import inner membrane translocase subunit TIM14
F: Mitochondrial import inner membrane translocase subunit TIM16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1214
Polymers15,7432
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-8 kcal/mol
Surface area7940 Å2
MethodPISA
4
G: Mitochondrial import inner membrane translocase subunit TIM14
H: Mitochondrial import inner membrane translocase subunit TIM16


Theoretical massNumber of molelcules
Total (without water)15,7432
Polymers15,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-11 kcal/mol
Surface area8110 Å2
MethodPISA
5
I: Mitochondrial import inner membrane translocase subunit TIM14
J: Mitochondrial import inner membrane translocase subunit TIM16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9323
Polymers15,7432
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area8010 Å2
MethodPISA
6
K: Mitochondrial import inner membrane translocase subunit TIM14
L: Mitochondrial import inner membrane translocase subunit TIM16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9323
Polymers15,7432
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-9 kcal/mol
Surface area7980 Å2
MethodPISA
7
M: Mitochondrial import inner membrane translocase subunit TIM14
N: Mitochondrial import inner membrane translocase subunit TIM16


Theoretical massNumber of molelcules
Total (without water)15,7432
Polymers15,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-11 kcal/mol
Surface area8270 Å2
MethodPISA
8
O: Mitochondrial import inner membrane translocase subunit TIM14
P: Mitochondrial import inner membrane translocase subunit TIM16


Theoretical massNumber of molelcules
Total (without water)15,7432
Polymers15,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.591, 114.441, 162.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Mitochondrial import inner membrane translocase subunit TIM14 / Presequence translocated-associated motor subunit PAM18


Mass: 7982.391 Da / Num. of mol.: 8 / Fragment: J-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAM18, TIM14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07914
#2: Protein
Mitochondrial import inner membrane translocase subunit TIM16 / Presequence translocated-associated motor subunit PAM16


Mass: 7760.792 Da / Num. of mol.: 8 / Fragment: J-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAM16, TIM16 / Production host: Escherichia coli (E. coli) / References: UniProt: P42949
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 921 / 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: 4.11 Å3/Da / Density % sol: 70.08 %
Description: The K2OsCl6-soak changed the space group from P212121 to P43212 with unit cell dimensions of a=b=114.1, c=163.1 (eight subunits in the asymmetric unit cell). Seven Os4+ positions in the ...Description: The K2OsCl6-soak changed the space group from P212121 to P43212 with unit cell dimensions of a=b=114.1, c=163.1 (eight subunits in the asymmetric unit cell). Seven Os4+ positions in the asymmetric unit cell were localized by combining direct and difference Patterson search methods using ShelXD. The improved electron density allowed identifying four Tim14 and four Tim16 subunits, according to their amino acid sequence. Next, we transferred and expanded the coordinates to the high resolution native data set, applying the parameters of the space group P212121.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.65M sodium citrate, protein concentration 400mg/ml, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW611.05
SYNCHROTRONMPG/DESY, HAMBURG BW621.1402, 1.1407, 1.05
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDMay 30, 2005
MAR CCD 165 mm2CCDMay 30, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
21.14021
31.14071
ReflectionResolution: 2→99 Å / Num. all: 137971 / Num. obs: 137971 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.088
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.484 / Num. unique all: 5382

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.989 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.138 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25257 6848 5 %RANDOM
Rwork0.20542 ---
all0.21 135755 --
obs0.20778 128907 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.85 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8846 0 52 921 9819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0228865
X-RAY DIFFRACTIONr_bond_other_d0.0020.028101
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.98211841
X-RAY DIFFRACTIONr_angle_other_deg0.893318994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.98451086
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37325.227419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.764151787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.491548
X-RAY DIFFRACTIONr_chiral_restr0.1110.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021695
X-RAY DIFFRACTIONr_nbd_refined0.2290.22298
X-RAY DIFFRACTIONr_nbd_other0.1930.28512
X-RAY DIFFRACTIONr_nbtor_refined0.1920.24397
X-RAY DIFFRACTIONr_nbtor_other0.0940.25136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2768
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.236
X-RAY DIFFRACTIONr_mcbond_it5.26466942
X-RAY DIFFRACTIONr_mcbond_other1.83462271
X-RAY DIFFRACTIONr_mcangle_it5.64288612
X-RAY DIFFRACTIONr_scbond_it6.86883993
X-RAY DIFFRACTIONr_scangle_it8.345123222
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 473 -
Rwork0.274 9254 -
obs--96.18 %

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