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- PDB-6uko: Structure analysis of full-length mouse bcs1 complex -

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Basic information

Entry
Database: PDB / ID: 6uko
TitleStructure analysis of full-length mouse bcs1 complex
ComponentsMitochondrial chaperone BCS1
KeywordsCHAPERONE / Rieske / cytochrome bc1
Function / homology
Function and homology information


mitochondrial protein-transporting ATPase activity / protein insertion into mitochondrial inner membrane from matrix / mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex I assembly / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding
Similarity search - Function
BCS1, N-terminal / BCS1 N terminal / BCS1_N / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Mitochondrial chaperone BCS1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å
AuthorsXia, D. / Esser, L.
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structures of AAA protein translocase Bcs1 suggest translocation mechanism of a folded protein.
Authors: Wai Kwan Tang / Mario J Borgnia / Allen L Hsu / Lothar Esser / Tara Fox / Natalia de Val / Di Xia /
Abstract: The mitochondrial membrane-bound AAA protein Bcs1 translocate substrates across the mitochondrial inner membrane without previous unfolding. One substrate of Bcs1 is the iron-sulfur protein (ISP), a ...The mitochondrial membrane-bound AAA protein Bcs1 translocate substrates across the mitochondrial inner membrane without previous unfolding. One substrate of Bcs1 is the iron-sulfur protein (ISP), a subunit of the respiratory Complex III. How Bcs1 translocates ISP across the membrane is unknown. Here we report structures of mouse Bcs1 in two different conformations, representing three nucleotide states. The apo and ADP-bound structures reveal a homo-heptamer and show a large putative substrate-binding cavity accessible to the matrix space. ATP binding drives a contraction of the cavity by concerted motion of the ATPase domains, which could push substrate across the membrane. Our findings shed light on the potential mechanism of translocating folded proteins across a membrane, offer insights into the assembly process of Complex III and allow mapping of human disease-associated mutations onto the Bcs1 structure.
History
DepositionOct 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial chaperone BCS1
B: Mitochondrial chaperone BCS1
C: Mitochondrial chaperone BCS1
D: Mitochondrial chaperone BCS1
E: Mitochondrial chaperone BCS1
F: Mitochondrial chaperone BCS1
G: Mitochondrial chaperone BCS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,19021
Polymers338,0297
Non-polymers3,16114
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40100 Å2
ΔGint-282 kcal/mol
Surface area135540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.055, 161.127, 132.595
Angle α, β, γ (deg.)90.000, 107.268, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALAchain 'A'AA1029 - 128629 - 286
12LEULEUARGARGchain 'A'AA1307 - 1418307 - 418
13ADPADPADPADPchain 'A'AH1800
24LEULEUALAALAchain 'B'BB1029 - 128629 - 286
25LEULEUARGARGchain 'B'BB1307 - 1418307 - 418
26ADPADPADPADPchain 'B'BJ1800
37LEULEUALAALAchain 'C'CC1029 - 128629 - 286
38LEULEUARGARGchain 'C'CC1307 - 1418307 - 418
39ADPADPADPADPchain 'C'CL1800
410LEULEUALAALAchain 'D'DD1029 - 128629 - 286
411LEULEUARGARGchain 'D'DD1307 - 1418307 - 418
412ADPADPADPADPchain 'D'DN1800
513LEULEUALAALAchain 'E'EE1029 - 128629 - 286
514LEULEUARGARGchain 'E'EE1307 - 1418307 - 418
515ADPADPADPADPchain 'E'EP1800
616LEULEUALAALAchain 'F'FF1029 - 128629 - 286
617LEULEUARGARGchain 'F'FF1307 - 1418307 - 418
618ADPADPADPADPchain 'F'FR1800
719LEULEUALAALAchain 'G'GG1029 - 128629 - 286
720LEULEUARGARGchain 'G'GG1307 - 1418307 - 418
721ADPADPADPADPchain 'G'GT1800

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Components

#1: Protein
Mitochondrial chaperone BCS1 / BCS1-like protein


Mass: 48289.887 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcs1l / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q9CZP5
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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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: 3.83 Å3/Da / Density % sol: 67.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein was premixed with 2mM ATP-gamma-S and 20 mM MgCl2 incubated for 30 min on ice, then centrifuged and the supernatant was mixed with 100 mM Tris pH 9.0, 100 mM NaCl, 60 mM MgCl2, 15% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013
RadiationMonochromator: Si mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.4→50 Å / Num. obs: 32257 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Χ2: 1.003 / Net I/σ(I): 19.09
Reflection shellResolution: 4.4→4.56 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 3169 / CC1/2: 0.306 / Χ2: 0.883 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: cryoEM

Resolution: 4.4→24.91 Å / SU ML: 1.1028 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 54.9189
RfactorNum. reflection% reflection
Rfree0.4067 1056 3.27 %
Rwork0.3568 --
obs0.3584 32257 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 258.69 Å2
Refinement stepCycle: LAST / Resolution: 4.4→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20930 0 196 0 21126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003521644
X-RAY DIFFRACTIONf_angle_d0.797729393
X-RAY DIFFRACTIONf_chiral_restr0.04553192
X-RAY DIFFRACTIONf_plane_restr0.00423745
X-RAY DIFFRACTIONf_dihedral_angle_d15.89837973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4-4.60.4611320.47963897X-RAY DIFFRACTION99.88
4.6-4.840.45661310.43143895X-RAY DIFFRACTION99.93
4.84-5.140.38771310.40713854X-RAY DIFFRACTION99.65
5.14-5.530.46321310.40363887X-RAY DIFFRACTION99.43
5.53-6.080.42281320.40953891X-RAY DIFFRACTION99.93
6.08-6.950.43121320.40673917X-RAY DIFFRACTION99.75
6.95-8.690.42611330.38313908X-RAY DIFFRACTION99.88
8.69-24.910.37381340.2933952X-RAY DIFFRACTION99.37

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