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- PDB-6u1y: bcs1 AAA domain -

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Basic information

Entry
Database: PDB / ID: 6u1y
Titlebcs1 AAA domain
ComponentsMitochondrial chaperone BCS1
KeywordsHYDROLASE / bcs1 / AAA ATPase
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitochondrial chaperone BCS1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsTang, W.K. / Xia, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
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
DepositionAug 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.2Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 1.4Apr 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)223,56721
Polymers219,8537
Non-polymers3,71414
Water34,8771936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27790 Å2
ΔGint-185 kcal/mol
Surface area70200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.206, 207.253, 116.615
Angle α, β, γ (deg.)90.000, 95.980, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: 0 / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA165 - 42215 - 272
21LYSLYSBB165 - 42215 - 272
12LYSLYSAA165 - 42315 - 273
22LYSLYSCC165 - 42315 - 273
13LYSLYSAA165 - 42415 - 274
23LYSLYSDD165 - 42415 - 274
14LYSLYSAA165 - 42315 - 273
24LYSLYSEE165 - 42315 - 273
15LYSLYSAA165 - 42415 - 274
25LYSLYSFF165 - 42415 - 274
16LYSLYSAA165 - 42215 - 272
26LYSLYSGG165 - 42215 - 272
17LYSLYSBB165 - 42215 - 272
27LYSLYSCC165 - 42215 - 272
18LYSLYSBB165 - 42215 - 272
28LYSLYSDD165 - 42215 - 272
19GLUGLUBB163 - 42213 - 272
29GLUGLUEE163 - 42213 - 272
110LYSLYSBB165 - 42215 - 272
210LYSLYSFF165 - 42215 - 272
111GLYGLYBB164 - 42214 - 272
211GLYGLYGG164 - 42214 - 272
112LYSLYSCC165 - 42315 - 273
212LYSLYSDD165 - 42315 - 273
113LYSLYSCC165 - 42215 - 272
213LYSLYSEE165 - 42215 - 272
114LYSLYSCC165 - 42315 - 273
214LYSLYSFF165 - 42315 - 273
115LYSLYSCC165 - 42315 - 273
215LYSLYSGG165 - 42315 - 273
116LYSLYSDD165 - 42315 - 273
216LYSLYSEE165 - 42315 - 273
117LYSLYSDD165 - 42415 - 274
217LYSLYSFF165 - 42415 - 274
118LYSLYSDD165 - 42215 - 272
218LYSLYSGG165 - 42215 - 272
119LYSLYSEE165 - 42315 - 273
219LYSLYSFF165 - 42315 - 273
120GLYGLYEE164 - 42214 - 272
220GLYGLYGG164 - 42214 - 272
121LYSLYSFF165 - 42215 - 272
221LYSLYSGG165 - 42215 - 272

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

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


Mass: 31407.637 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) / References: UniProt: Q9CZP5
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1936 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH 7.5, 12% PEG 3350, 3% 1,6-hexanediol

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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: RAYONIX MX300-HS / Detector: CCD / Date: Jan 1, 2014
RadiationMonochromator: Rayonix MX300HS. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→44.46 Å / Num. obs: 88747 / % possible obs: 86.82 % / Redundancy: 1.5 % / CC1/2: 0.977 / Rmerge(I) obs: 0.07675 / Net I/σ(I): 4.45
Reflection shellResolution: 2.17→2.251 Å / Rmerge(I) obs: 0.699 / Num. unique obs: 7918 / CC1/2: 0.499

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: mBcs1-ATPgS

Resolution: 2.17→44.46 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.633 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.237
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 4596 5.2 %RANDOM
Rwork0.1809 ---
obs0.1838 84108 86.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.07 Å2 / Biso mean: 40.849 Å2 / Biso min: 19.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.8 Å2
2--0.12 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 2.17→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13632 0 287 1936 15855
Biso mean--30.16 49.47 -
Num. residues----1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01314293
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712989
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.65119458
X-RAY DIFFRACTIONr_angle_other_deg1.2961.57530036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92351715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69720.553814
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.663152301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.87415133
X-RAY DIFFRACTIONr_chiral_restr0.0680.21801
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023225
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A77980.04
12B77980.04
21A78210.03
22C78210.03
31A78410.04
32D78410.04
41A78130.04
42E78130.04
51A78070.05
52F78070.05
61A77710.04
62G77710.04
71B78040.03
72C78040.03
81B78040.03
82D78040.03
91B78720.02
92E78720.02
101B78180.03
102F78180.03
111B78330.03
112G78330.03
121C78500.03
122D78500.03
131C78400.03
132E78400.03
141C78440.04
142F78440.04
151C78350.04
152G78350.04
161D78600.03
162E78600.03
171D78920.04
172F78920.04
181D78500.03
182G78500.03
191E78390.03
192F78390.03
201E78340.03
202G78340.03
211F78280.02
212G78280.02
LS refinement shellResolution: 2.171→2.227 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 299 -
Rwork0.336 5434 -
all-5733 -
obs--76.91 %
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)
10.10180.01770.00860.5654-0.13940.6522-0.02160.0061-0.0395-0.0171-0.0028-0.0453-0.02220.0040.02440.02810.03220.01860.1022-0.01280.03594.2667-34.028721.5684
20.00950.01240.05540.7382-0.26020.5220.0022-0.0101-0.005-0.01020.0084-0.1127-0.0113-0.0128-0.01060.0205-0.03540.01390.0911-0.04290.05323.680527.155152.0702
30.00880.0496-0.0240.6510.07120.4902-0.002-0.01490.0130.00790.0388-0.0070.03240.0963-0.03680.00380.0037-0.010.1299-0.02970.04973.5686-0.426865.0532
40.0934-0.1493-0.05230.62940.0520.42660.0243-0.0026-0.0115-0.02660.0217-0.0335-0.03250.0277-0.04590.03060.01980.01640.1269-0.01150.03544.4333-14.648-1.9636
50.0263-0.0712-0.08870.6755-0.2780.88020.0039-0.00220.00320.0298-0.0487-0.0317-0.02450.08140.04480.0453-0.04050.03810.1267-0.00880.0443.63834.413722.4946
60.0635-0.1627-0.1720.62630.25050.64350.0107-0.01750.0045-0.01770.02010.0116-0.02930.0972-0.03070.04560.01420.04140.11840.00370.03983.983515.9175-1.692
70.05390.03190.03070.25560.11130.6187-0.0195-0.01030.0235-0.0107-0.01450.03010.05020.1020.0340.03520.03990.00390.1241-0.00260.01933.9367-27.588251.303
80.88320.15860.31261.81070.66760.3204-0.0122-0.0116-0.12590.18580.01010.11610.05950.00020.00210.080.04430.05230.06270.03660.0525-10.4495-48.837344.5597
90.77680.4012-0.160.38810.44391.5922-0.0044-0.07360.0407-0.0733-0.01420.0312-0.17380.07770.01860.0977-0.0390.02830.0407-0.02880.0406-10.948650.47137.7684
101.03310.04760.52881.2383-0.32640.8495-0.044-0.01120.14080.15370.04930.0735-0.0025-0.0032-0.00530.0325-0.00350.00540.0677-0.05620.0771-11.038125.431974.0255
110.703-0.08210.08890.449-0.12381.10770.02510.0581-0.09530.00750.01990.02370.051-0.1108-0.04510.01810.00620.00890.0965-0.04040.057-10.2652-41.95740.8539
121.46020.5267-0.25951.43110.09270.2172-0.137-0.02630.0619-0.16210.08550.04810.0370.00490.05150.07070.0090.03320.10460.02850.0523-11.058137.6046-4.7873
130.7761-0.4317-0.431.1242-0.31770.9159-0.02490.1258-0.0674-0.0387-0.02840.0458-0.0219-0.06980.05330.03920.0316-0.00340.15-0.02070.0105-10.1567-3.7677-21.1447
141.5089-0.4040.81541.32240.03130.4955-0.0595-0.0691-0.03470.10350.06640.0754-0.0057-0.0075-0.00690.0480.03630.01720.1206-0.00580.0112-11.2253-18.930877.031
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A165 - 355
2X-RAY DIFFRACTION1A800 - 2000
3X-RAY DIFFRACTION2B165 - 355
4X-RAY DIFFRACTION2B800
5X-RAY DIFFRACTION3C165 - 355
6X-RAY DIFFRACTION3C800
7X-RAY DIFFRACTION4D165 - 355
8X-RAY DIFFRACTION4D800
9X-RAY DIFFRACTION5E165 - 355
10X-RAY DIFFRACTION5E800
11X-RAY DIFFRACTION6F165 - 355
12X-RAY DIFFRACTION6F800
13X-RAY DIFFRACTION7G165 - 355
14X-RAY DIFFRACTION7G800
15X-RAY DIFFRACTION8A357 - 423
16X-RAY DIFFRACTION9B357 - 423
17X-RAY DIFFRACTION10C357 - 423
18X-RAY DIFFRACTION11D357 - 423
19X-RAY DIFFRACTION12E357 - 423
20X-RAY DIFFRACTION13F357 - 423
21X-RAY DIFFRACTION14G357 - 423

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