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- PDB-5j1s: TorsinA-LULL1 complex, H. sapiens, bound to VHH-BS2 -

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Basic information

Entry
Database: PDB / ID: 5j1s
TitleTorsinA-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: 1.399 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
Revision 1.3Apr 3, 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_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_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.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

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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)73,5819
Polymers72,7703
Non-polymers8116
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-55 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.739, 90.659, 105.092
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: 32743.426 Da / Num. of mol.: 1 / Mutation: E171Q
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, 571 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.: 3 / 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 13 % PEG 6000 5 % MPD 100 mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.399→61.445 Å / Num. obs: 132851 / % possible obs: 93.03 % / Redundancy: 5.7 % / Biso Wilson estimate: 20.14 Å2 / Rsym value: 0.06 / Net I/σ(I): 33

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVS_A

Resolution: 1.399→61.445 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.05
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 2000 1.51 %Random Selection
Rwork0.1433 ---
obs0.144 132851 93.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.7 Å2 / Biso mean: 33.1887 Å2 / Biso min: 15.85 Å2
Refinement stepCycle: final / Resolution: 1.399→61.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5021 0 47 565 5633
Biso mean--28.1 41.32 -
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145424
X-RAY DIFFRACTIONf_angle_d1.257396
X-RAY DIFFRACTIONf_chiral_restr0.099803
X-RAY DIFFRACTIONf_plane_restr0.008957
X-RAY DIFFRACTIONf_dihedral_angle_d20.4071972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3991-1.43410.345850.27745575566056
1.4341-1.47280.28631140.23037410752475
1.4728-1.51620.2581270.19348354848184
1.5162-1.56510.23491400.16829179931992
1.5651-1.62110.24531490.15199778992798
1.6211-1.6860.18951530.139994810101100
1.686-1.76270.20631520.133996610118100
1.7627-1.85570.20731520.1316994910101100
1.8557-1.97190.18581530.1223998810141100
1.9719-2.12420.18031530.12251000410157100
2.1242-2.3380.16821530.1241005710210100
2.338-2.67630.17811550.13561006110216100
2.6763-3.37180.18761550.14951015610311100
3.3718-61.50390.17861590.1472104261058599

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