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- PDB-5j1t: TorsinAdeltaE-LULL1 complex, H. sapiens, bound to VHH-BS2 -

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Basic information

Entry
Database: PDB / ID: 5j1t
TitleTorsinAdeltaE-LULL1 complex, H. sapiens, bound to VHH-BS2
Components
  • Torsin-1A
  • Torsin-1A-interacting protein 2
  • VHH domain BS-2
KeywordsHYDROLASE / AAA+ ATPase / Torsin / endoplasmic reticulum
Function / homology
Function and homology information


synaptic vesicle membrane organization / nuclear membrane organization / organelle organization / regulation of dopamine uptake involved in synaptic transmission / nuclear envelope organization / protein localization to nuclear envelope / protein deneddylation / intermediate filament cytoskeleton organization / regulation of protein localization to cell surface / positive regulation of synaptic vesicle endocytosis ...synaptic vesicle membrane organization / nuclear membrane organization / organelle organization / regulation of dopamine uptake involved in synaptic transmission / nuclear envelope organization / protein localization to nuclear envelope / protein deneddylation / intermediate filament cytoskeleton organization / regulation of protein localization to cell surface / positive regulation of synaptic vesicle endocytosis / misfolded protein binding / membrane organization / endoplasmic reticulum organization / positive regulation of ATP-dependent activity / wound healing, spreading of cells / synaptic vesicle transport / kinesin binding / ATPase activator activity / chaperone cofactor-dependent protein refolding / protein localization to nucleus / chaperone-mediated protein folding / ERAD pathway / cytoskeletal protein binding / secretory granule / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic vesicle membrane / neuron projection development / unfolded protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / nuclear envelope / ATPase binding / growth cone / nuclear membrane / response to oxidative stress / cytoskeleton / cell adhesion / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Torsin-1A-interacting protein 1/2, AAA+ activator domain / Torsin-1A-interacting protein 1/2, N-terminal / Lamina-associated polypeptide 1, N-terminal / Rossmann fold - #12190 / Torsin-1A-interacting protein 1/2 / Lamina-associated polypeptide 1, AAA+ activator domain / : / Torsin-1A, C-terminal domain / Torsin / Torsin 1/2 ...Torsin-1A-interacting protein 1/2, AAA+ activator domain / Torsin-1A-interacting protein 1/2, N-terminal / Lamina-associated polypeptide 1, N-terminal / Rossmann fold - #12190 / Torsin-1A-interacting protein 1/2 / Lamina-associated polypeptide 1, AAA+ activator domain / : / Torsin-1A, C-terminal domain / Torsin / Torsin 1/2 / LAP1C-like, C-terminal domain superfamily / Torsin / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Torsin-1A / Torsin-1A-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 Å
AuthorsDemircioglu, F.E. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR065484 United States
CitationJournal: Elife / Year: 2016
Title: Structures of TorsinA and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia.
Authors: Demircioglu, F.E. / Sosa, B.A. / Ingram, J. / Ploegh, H.L. / Schwartz, T.U.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Torsin-1A
B: Torsin-1A-interacting protein 2
C: VHH domain BS-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6268
Polymers72,6413
Non-polymers9855
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-37 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.435, 88.445, 105.331
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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Protein , 2 types, 2 molecules AB

#1: Protein Torsin-1A / Dystonia 1 protein / Torsin ATPase-1A / Torsin family 1 member A


Mass: 32614.311 Da / Num. of mol.: 1 / Mutation: E171Q, deltaE302/303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOR1A, DQ2, DYT1, TA, TORA / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
References: UniProt: O14656, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Torsin-1A-interacting protein 2 / Lumenal domain-like LAP1


Mass: 26729.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOR1AIP2, IFRG15, LULL1 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: Q8NFQ8

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Antibody , 1 types, 1 molecules C

#3: Antibody VHH domain BS-2


Mass: 13296.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR

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Non-polymers , 5 types, 636 molecules

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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 19 % PEG3350 200 mM ammonium sulfate 100 mM Bis-Tris/HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.402→67.733 Å / Num. obs: 134334 / % possible obs: 97.06 % / Redundancy: 12.4 % / Biso Wilson estimate: 16.72 Å2 / Rsym value: 0.1 / Net I/σ(I): 30.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.402→67.733 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18
RfactorNum. reflection% reflectionSelection details
Rfree0.1768 2182 1.62 %Random selection
Rwork0.148 ---
obs0.1485 134334 97.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.79 Å2 / Biso mean: 25.3491 Å2 / Biso min: 10.84 Å2
Refinement stepCycle: final / Resolution: 1.402→67.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 0 61 631 5716
Biso mean--20.65 35.47 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175496
X-RAY DIFFRACTIONf_angle_d1.7087485
X-RAY DIFFRACTIONf_chiral_restr0.089806
X-RAY DIFFRACTIONf_plane_restr0.009963
X-RAY DIFFRACTIONf_dihedral_angle_d14.6722013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4015-1.4320.29171140.27596985709983
1.432-1.46530.26051340.24228138827297
1.4653-1.5020.26411350.21018185832097
1.502-1.54260.22871370.18658202833997
1.5426-1.5880.21360.16978160829697
1.588-1.63920.19721340.1448264839898
1.6392-1.69780.16761360.13448273840998
1.6978-1.76580.19281370.12728319845698
1.7658-1.84620.18551380.11638330846898
1.8462-1.94350.15761370.11398253839097
1.9435-2.06530.15571390.11778396853599
2.0653-2.22480.15491400.12268406854699
2.2248-2.44860.1761370.13368356849398
2.4486-2.8030.20181390.15168539867899
2.803-3.53140.14811430.15378512865598
3.5314-67.81240.17361460.15748834898099

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