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- PDB-3a3c: Crystal structure of TIM40/MIA40 fusing MBP, C296S and C298S mutant -

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Basic information

Entry
Database: PDB / ID: 3a3c
TitleCrystal structure of TIM40/MIA40 fusing MBP, C296S and C298S mutant
ComponentsMaltose-binding periplasmic protein, LINKER, Mitochondrial intermembrane space import and assembly protein 40
KeywordsPROTEIN TRANSPORT / Mitochondrion / inner membrane space / membrane / disulfide bond transfer / alpha helices / Sugar transport / Transport / Mitochondrion inner membrane / Phosphoprotein / Signal-anchor / Transit peptide / Translocation / Transmembrane
Function / homology
Function and homology information


thiol oxidase activity / : / protein import into mitochondrial intermembrane space / protein disulfide isomerase activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / protein-disulfide reductase activity / carbohydrate transmembrane transporter activity / maltose binding ...thiol oxidase activity / : / protein import into mitochondrial intermembrane space / protein disulfide isomerase activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / protein-disulfide reductase activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / protein folding / outer membrane-bounded periplasmic space / periplasmic space / mitochondrial inner membrane / oxidoreductase activity / DNA damage response / mitochondrion / membrane
Similarity search - Function
Helix Hairpins - #2900 / Mitochondrial intermembrane space import and assembly protein 40 / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein ...Helix Hairpins - #2900 / Mitochondrial intermembrane space import and assembly protein 40 / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Helix Hairpins / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Mitochondrial intermembrane space import and assembly protein 40
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKawano, S. / Naoe, M. / Momose, T. / Watanabe, N. / Endo, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis of yeast Tim40/Mia40 as an oxidative translocator in the mitochondrial intermembrane space.
Authors: Kawano, S. / Yamano, K. / Naoe, M. / Momose, T. / Terao, K. / Nishikawa, S. / Watanabe, N. / Endo, T.
History
DepositionJun 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, LINKER, Mitochondrial intermembrane space import and assembly protein 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0562
Polymers49,7141
Non-polymers3421
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.527, 101.837, 109.613
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 Maltose-binding periplasmic protein, LINKER, Mitochondrial intermembrane space import and assembly protein 40 / MMBP / Maltodextrin-binding protein / Mitochondrial import inner membrane translocase TIM40


Mass: 49713.805 Da / Num. of mol.: 1 / Mutation: C296S, C298S
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF MMBP (UNP RESIDUES 29-392), LINKER (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE TIM40 (UNP RESIDUES 284-353)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: MIA40, TIM40, YKL195W / Plasmid: PMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: P0AEX9, UniProt: P36046
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FUSION PROTEIN OF MMBP (UNP RESIDUES 29-392), LINKER (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT ...THE FUSION PROTEIN OF MMBP (UNP RESIDUES 29-392), LINKER (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE TIM40 (UNP RESIDUES 284-353)

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM K-acetate, 200 mM NH4-acetate, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 16430 / Num. obs: 15266 / % possible obs: 91.3 % / Redundancy: 12.1 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.138
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 9.5 / Num. unique all: 1519 / Rsym value: 0.626 / % possible all: 91.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZXT

2zxt


Resolution: 2.5→30.88 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 177067.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.316 746 4.9 %RANDOM
Rwork0.254 ---
obs0.254 15266 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1652 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-14.9 Å20 Å20 Å2
2---0.53 Å20 Å2
3----14.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.5→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 23 70 3599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.493 85 4.1 %
Rwork0.363 2004 -
obs--76.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3mal_xplor.parammal_xplor.top

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