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- PDB-4tt3: The Pathway of Binding of the Intrinsically Disordered Mitochondr... -

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Basic information

Entry
Database: PDB / ID: 4tt3
TitleThe Pathway of Binding of the Intrinsically Disordered Mitochondrial Inhibitor Protein to F1-ATPase
Components
  • (ATP synthase subunit ...) x 3
  • ATPase inhibitor, mitochondrial
KeywordsHYDROLASE / inhibitor protein
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / heme biosynthetic process / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / heme biosynthetic process / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Single helix bin / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 ...Single helix bin / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.21 Å
AuthorsBason, J.V. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Pathway of binding of the intrinsically disordered mitochondrial inhibitor protein to F1-ATPase.
Authors: Bason, J.V. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Dec 6, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Dec 20, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
D: ATP synthase subunit beta, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
H: ATPase inhibitor, mitochondrial
I: ATPase inhibitor, mitochondrial
J: ATPase inhibitor, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,94522
Polymers373,26310
Non-polymers2,68212
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44900 Å2
ΔGint-229 kcal/mol
Surface area110670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.385, 154.545, 272.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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ATP synthase subunit ... , 3 types, 7 molecules ABCDEFG

#1: Protein ATP synthase subunit alpha, mitochondrial


Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Heart / Tissue: muscle / References: UniProt: P19483
#2: Protein ATP synthase subunit beta, mitochondrial


Mass: 51615.684 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Heart / Tissue: muscle
References: UniProt: P00829, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit gamma, mitochondrial / F-ATPase gamma subunit


Mass: 30300.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Heart / Tissue: Muscle / References: UniProt: P05631

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Protein , 1 types, 3 molecules HIJ

#4: Protein ATPase inhibitor, mitochondrial / Inhibitor of F(1)F(o)-ATPase / IF1


Mass: 7403.996 Da / Num. of mol.: 3 / Fragment: UNP residues 36-85 / Mutation: K39A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: muscle / Gene: ATPIF1, ATPI / Organ: Heart / Production host: Escherichia coli (E. coli) / References: UniProt: P01096

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Non-polymers , 5 types, 40 molecules

#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE NUMBERING: BY CONVENTION, THE FIFTH AMINO ACID (SERINE) IN THE BETA SUBUNITS (CHAINS D,E,F) ...RESIDUE NUMBERING: BY CONVENTION, THE FIFTH AMINO ACID (SERINE) IN THE BETA SUBUNITS (CHAINS D,E,F) IS RESIDUE 1 AND THE FIRST FOUR AMINO ACIDS ARE NUMBERED -4 TO -1. REFERENCE FOR THE ALPHA SUBUNIT J. E. WALKER, S. J. POWELL,O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY,VOL 28,PP 4702-4708, 1989. SER 481 GLY IN CHAINS A, B AND C WAS IDENTIFIED AS A GLY FROM THE PROTEIN SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS RESIDUE WAS AGC SER IN THREE CLONES WHILE IN TWO OTHERS IT WAS GGC GLY. THE DIFFERENCE WAS THOUGHT TO BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN THIS POSITION.

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.2
Details: PEG 4000, Tris-HCl, magnesium chloride, EDTA, ATP, NaCl, spermidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.21→67.12 Å / Num. obs: 73010 / % possible obs: 97.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.6
Reflection shellResolution: 3.21→3.28 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Coot0.8model building
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v7q

2v7q


Resolution: 3.21→136.02 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.872 / SU B: 29.017 / SU ML: 0.479 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2834 3688 5.1 %RANDOM
Rwork0.2422 69297 --
obs0.2443 72985 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.61 Å2 / Biso mean: 93.079 Å2 / Biso min: 34.36 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å2-0 Å20 Å2
2--3.38 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 3.21→136.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23918 0 181 11 24110
Biso mean--80.71 51.23 -
Num. residues----3134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01924521
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224143
X-RAY DIFFRACTIONr_angle_refined_deg0.7321.98733041
X-RAY DIFFRACTIONr_angle_other_deg0.655355474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.66553117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.04524.1011029
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.612154336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.46415185
X-RAY DIFFRACTIONr_chiral_restr0.0640.23826
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02127469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025237
X-RAY DIFFRACTIONr_mcbond_it0.9469.36112584
X-RAY DIFFRACTIONr_mcbond_other0.9459.36112583
X-RAY DIFFRACTIONr_mcangle_it1.6911415619
LS refinement shellResolution: 3.21→3.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 259 -
Rwork0.339 5182 -
all-5441 -
obs--98.75 %

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