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- PDB-4tvs: LAP1(aa356-583), H.sapiens, bound to VHH-BS1 -

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Basic information

Entry
Database: PDB / ID: 4tvs
TitleLAP1(aa356-583), H.sapiens, bound to VHH-BS1
Components
  • Torsin-1A-interacting protein 1
  • VHH Domain BS-1
KeywordsMEMBRANE PROTEIN / nuclear envelope protein / AAA+-associated / activator
Function / homology
Function and homology information


nuclear membrane organization / protein localization to nuclear envelope / lamin binding / positive regulation of ATP-dependent activity / nuclear inner membrane / ATPase activator activity / protein localization to nucleus / cytoskeletal protein binding / ATPase binding / nuclear membrane ...nuclear membrane organization / protein localization to nuclear envelope / lamin binding / positive regulation of ATP-dependent activity / nuclear inner membrane / ATPase activator activity / protein localization to nucleus / cytoskeletal protein binding / ATPase binding / nuclear membrane / membrane => GO:0016020 / nucleus
Similarity search - Function
Rossmann fold - #12190 / Torsin-1A-interacting protein 1/2 / Lamina-associated polypeptide 1, AAA+ activator domain / LAP1C-like, C-terminal domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Torsin-1A-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSosa, B.A. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
Dystonia Medical Research Foundation United States
CitationJournal: Elife / Year: 2014
Title: How lamina-associated polypeptide 1 (LAP1) activates Torsin.
Authors: Sosa, B.A. / Demircioglu, F.E. / Chen, J.Z. / Ingram, J. / Ploegh, H.L. / Schwartz, T.U.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Oct 29, 2014Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Torsin-1A-interacting protein 1
B: Torsin-1A-interacting protein 1
a: VHH Domain BS-1
b: VHH Domain BS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8479
Polymers81,3834
Non-polymers4645
Water11,043613
1
A: Torsin-1A-interacting protein 1
a: VHH Domain BS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8754
Polymers40,6912
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Torsin-1A-interacting protein 1
b: VHH Domain BS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9725
Polymers40,6912
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.786, 74.021, 85.425
Angle α, β, γ (deg.)90.00, 108.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Torsin-1A-interacting protein 1 / Lamin-associated protein 1B / LAP1B


Mass: 26001.145 Da / Num. of mol.: 2 / Fragment: UNP residues 356-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOR1AIP1, LAP1 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR(DE3)-RIL / References: UniProt: Q5JTV8
#2: Antibody VHH Domain BS-1


Mass: 14690.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR(DE3)RIL
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, 20% 0.1M BIS-TRIS 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2548 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2548 Å / Relative weight: 1
ReflectionResolution: 1.6→66.1 Å / Num. all: 105976 / Num. obs: 105565 / % possible obs: 97.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.412 / Mean I/σ(I) obs: 1.1 / % possible all: 94.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZQ
Resolution: 1.6→66.068 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 2810 2.66 %Random selection
Rwork0.1811 ---
obs0.1824 105565 97.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→66.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5504 0 29 613 6146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195655
X-RAY DIFFRACTIONf_angle_d1.6567646
X-RAY DIFFRACTIONf_dihedral_angle_d14.372069
X-RAY DIFFRACTIONf_chiral_restr0.091839
X-RAY DIFFRACTIONf_plane_restr0.01995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62730.41621340.3944791X-RAY DIFFRACTION91
1.6273-1.65690.38491360.37554990X-RAY DIFFRACTION95
1.6569-1.68880.3781390.36745082X-RAY DIFFRACTION96
1.6888-1.72330.42661400.37285073X-RAY DIFFRACTION96
1.7233-1.76070.37411350.32945039X-RAY DIFFRACTION96
1.7607-1.80170.28731390.28015111X-RAY DIFFRACTION97
1.8017-1.84680.28841410.24155141X-RAY DIFFRACTION98
1.8468-1.89670.23221420.22375162X-RAY DIFFRACTION98
1.8967-1.95250.25261400.20275130X-RAY DIFFRACTION98
1.9525-2.01550.26141390.19095107X-RAY DIFFRACTION97
2.0155-2.08760.21881410.18255142X-RAY DIFFRACTION98
2.0876-2.17120.25561430.16865191X-RAY DIFFRACTION98
2.1712-2.270.22811400.15845182X-RAY DIFFRACTION98
2.27-2.38970.22981420.16345185X-RAY DIFFRACTION98
2.3897-2.53940.21421410.16595137X-RAY DIFFRACTION97
2.5394-2.73550.21981430.17135254X-RAY DIFFRACTION99
2.7355-3.01080.23771440.17565242X-RAY DIFFRACTION99
3.0108-3.44640.23231430.16975251X-RAY DIFFRACTION99
3.4464-4.3420.18481420.14995234X-RAY DIFFRACTION98
4.342-66.12470.2011460.15815311X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.00030.91290.9191.32790.36353.00120.1213-0.5606-0.49160.2432-0.0664-0.00310.3808-0.1242-0.00650.327-0.0358-0.00490.23030.02140.302181.2525.645215.3086
23.44970.83280.84894.9934-0.14783.5161-0.08560.2467-0.1238-0.26470.007-0.14820.30410.30390.04830.2710.0174-0.00650.2583-0.04160.304887.116928.74366.7642
32.1061-0.59951.80342.9683-0.96834.0783-0.00490.4887-0.0834-0.1593-0.0381-0.33490.08120.41180.02910.2293-0.00990.03370.3145-0.0520.256979.216528.9685-7.4589
40.66060.04240.87570.3190.1272.3712-0.04690.1568-0.05240.07320.0074-0.0594-0.0377-0.12890.03240.2224-0.00250.02230.1494-0.0330.280874.377131.52850.2589
55.8003-0.1851-0.96161.2982-0.0882.9445-0.3985-0.89530.58660.4642-0.0762-0.6949-1.15660.73090.25580.6354-0.0234-0.16940.2901-0.00570.580386.930547.837611.9371
63.1781-0.27752.34071.8827-0.90318.3047-0.5184-0.29240.63570.2506-0.00590.1644-1.2792-0.66210.49530.50220.0599-0.06630.2191-0.06190.401576.139847.12856.3626
70.8628-0.24621.421.3872-0.36073.34710.02120.2020.089-0.1433-0.0757-0.0955-0.12630.12540.03760.26270.0052-0.00270.208-0.03210.249978.177839.40132.1957
86.59154.22560.75536.2214-0.22123.35140.52060.0012-1.18950.7785-0.053-0.57110.56030.5751-0.43430.39740.007-0.08330.64970.15470.6112110.8327-17.764136.9181
96.56280.52460.64861.4192-0.92362.85740.1336-1.2491-0.06530.45240.07370.3006-0.3137-0.3761-0.16430.447-0.0144-0.00280.65480.09340.3556105.3584-9.217338.9414
106.14790.01430.28573.63840.33354.6680.3941-0.5874-1.01911.0673-0.34620.24710.5389-0.3701-0.14430.3376-0.0209-0.00140.38940.02180.401496.3325-10.360230.7376
113.3842-0.28411.0694.04860.29173.1726-0.0514-0.0574-0.0032-0.06710.1231-0.24550.00830.5601-0.08420.27480.0216-0.01980.5142-0.03330.327110.6514-7.983927.9344
122.35510.551.49980.6992-0.32352.76620.03960.6673-0.00950.0996-0.4785-0.3043-0.2191.22510.37540.322-0.00880.02260.5461-0.05110.4324106.9405-5.754415.7431
131.4226-0.65010.79726.0946-3.34973.49460.03980.4102-0.2936-0.4491-0.1438-0.13670.48440.21920.09230.34260.01930.02070.3547-0.05430.320698.6103-9.563112.0609
141.5672-0.28460.75360.53850.1492.0306-0.00780.1042-0.10580.10240.0093-0.006-0.07240.07870.01620.2576-0.00470.0160.2582-0.02650.279297.451-5.89921.6891
156.8880.50312.1432.5629-0.17344.4843-0.3325-1.00771.07040.3350.02510.1818-1.0343-0.13880.3410.7160.0129-0.08280.4455-0.15160.5152102.83749.379632.4812
161.4331-0.8116-0.16491.8284-0.85532.4109-0.4522-0.00521.21260.5852-0.11640.0186-1.6253-0.10920.4650.80630.022-0.12180.5819-0.07690.568291.52478.67212.1311
174.7325-1.34053.24281.2084-1.11784.1615-0.2199-0.89520.04080.11880.34970.0323-0.7632-0.5474-0.0970.4020.0582-0.00330.3785-0.05220.300393.06251.695728.0227
186.2705-0.8053-0.02086.61181.9443.03620.26370.6384-0.0333-0.8113-0.7998-0.1557-0.71070.17890.35480.45990.0241-0.08960.69220.05260.3787120.0048-2.246629.9628
195.89550.9076-2.17691.892-1.55325.7952-0.1346-0.04281.1790.266-0.0628-0.2285-1.25460.7170.03640.4828-0.0605-0.11910.2146-0.0590.551550.454447.005710.5222
202.61030.0458-0.24992.4372-1.61533.1579-0.2598-0.01950.31010.05220.1798-0.1128-0.2121-0.42290.03470.28230.0337-0.01960.2369-0.05240.263539.508338.181212.7095
212.1747-0.0462-0.060.5285-1.07944.40970.0119-0.01920.26630.2231-0.1524-0.0279-0.40490.632-0.02280.2785-0.02340.01660.18670.00990.291250.501636.35429.4322
220.9917-0.1947-0.49780.82011.24732.5022-0.4332-0.5193-0.06620.3156-0.0995-0.12380.00521.11720.43650.27790.03360.00710.37720.01530.245851.003129.597317.7452
234.00750.6785-0.32133.1097-1.17193.5324-0.11310.49-0.1837-0.0783-0.0598-0.16930.19490.58160.11440.22490.02180.01750.31980.00790.221949.294429.88291.2721
242.37251.7182-0.7732.6515-1.2844.1956-0.03730.1454-0.0451-0.1250.10190.18720.4004-0.2409-0.0230.2461-0.02060.03450.1757-0.00220.269342.832530.48876.8424
253.05842.8324-1.19995.7939-2.61762.61360.0622-0.1350.28510.0794-0.2989-0.1632-0.1788-0.05010.18370.26030.00860.00140.20510.02090.302841.011736.88917.6851
265.13720.7233.06562.3950.41877.72510.2708-0.299-0.92130.27030.2490.01810.9514-0.1251-0.44230.3249-0.0242-0.01580.35620.03260.317338.166125.913619.59
272.38870.1324-1.09630.5751-0.23753.1072-0.04070.26510.1184-0.098-0.0346-0.1939-0.02230.18340.09930.19790.00110.01480.2730.02590.229154.442933.71037.127
283.1649-0.37520.62495.351-0.53284.5982-0.16170.16190.83450.2836-0.107-0.4273-0.66170.64880.19740.3163-0.0509-0.04280.3126-0.00640.326155.504939.056112.9131
297.21840.01860.81734.53691.78335.05320.4968-0.75430.13750.62740.01410.0124-0.1107-0.6516-0.4280.28690.02490.00720.46320.01250.218338.022332.93823.8105
308.0822.8496-2.92665.4225-1.40495.2656-0.21190.04131.0918-0.14950.05810.0662-0.57350.34140.29740.51990.0222-0.05230.29130.01750.376974.01079.307831.8621
312.54141.1070.48942.4578-0.99943.4837-0.1415-0.24290.252-0.07560.10090.1483-0.1324-0.40180.03970.26750.04680.0060.3594-0.00910.250663.11910.833934.6772
321.05150.198-0.55550.9551-1.66413.363-0.0302-0.02190.04070.105-0.2523-0.1425-0.28950.35820.17710.2774-0.02990.01190.33540.04230.243873.8386-1.436231.0279
330.63060.34170.24990.29661.12548.5443-0.0347-0.2586-0.1350.1631-0.0487-0.07790.13891.03650.08420.27190.0204-0.00910.43550.03060.24374.1366-8.064739.3956
342.36510.3359-0.90352.283-1.66014.33370.08910.36510.075-0.4327-0.07590.06640.40770.4445-0.03290.28470.0131-0.00590.37270.00850.224572.2882-7.881222.8197
352.29751.5393-0.69832.8257-0.12994.1671-0.0338-0.1772-0.0814-0.1699-0.01090.02530.3678-0.2147-0.01540.2702-0.0302-0.01450.27460.04310.274866.0404-6.988628.4293
362.48981.2519-0.57614.0016-1.95143.7934-0.1408-0.18370.0781-0.09890.1139-0.0318-0.0675-0.51690.04580.24090.0311-0.03990.34340.04460.272664.339-0.54829.3353
371.796-0.59810.8540.29630.00412.22480.0026-0.1538-0.1321-0.07710.09530.07320.2051-0.3501-0.0860.276-0.04490.00970.42440.03540.243468.0025-5.806837.7226
382.18191.6344-2.00522.8922-0.09425.70440.0013-0.0145-0.0097-0.1853-0.2772-0.40740.20960.55630.22930.29850.06350.04840.42940.04090.28980.4828-7.108823.6811
393.3284-0.0676-1.12662.3602-0.1384.3918-0.0040.39270.36360.1467-0.1466-0.3957-0.40230.22770.20220.2757-0.026-0.02020.42070.03590.272779.06350.911134.3405
406.42220.35530.27753.67251.59634.05480.4116-0.7863-0.23880.488-0.24520.33350.4402-0.7479-0.07910.3343-0.0297-0.01370.60310.0710.263561.0929-4.459645.239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 360 through 415 )
2X-RAY DIFFRACTION2chain 'A' and (resid 416 through 437 )
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 471 )
4X-RAY DIFFRACTION4chain 'A' and (resid 472 through 513 )
5X-RAY DIFFRACTION5chain 'A' and (resid 514 through 524 )
6X-RAY DIFFRACTION6chain 'A' and (resid 525 through 542 )
7X-RAY DIFFRACTION7chain 'A' and (resid 543 through 583 )
8X-RAY DIFFRACTION8chain 'B' and (resid 362 through 378 )
9X-RAY DIFFRACTION9chain 'B' and (resid 379 through 399 )
10X-RAY DIFFRACTION10chain 'B' and (resid 400 through 415 )
11X-RAY DIFFRACTION11chain 'B' and (resid 416 through 437 )
12X-RAY DIFFRACTION12chain 'B' and (resid 438 through 453 )
13X-RAY DIFFRACTION13chain 'B' and (resid 454 through 471 )
14X-RAY DIFFRACTION14chain 'B' and (resid 472 through 513 )
15X-RAY DIFFRACTION15chain 'B' and (resid 514 through 539 )
16X-RAY DIFFRACTION16chain 'B' and (resid 540 through 553 )
17X-RAY DIFFRACTION17chain 'B' and (resid 554 through 570 )
18X-RAY DIFFRACTION18chain 'B' and (resid 571 through 583 )
19X-RAY DIFFRACTION19chain 'a' and (resid 1 through 8 )
20X-RAY DIFFRACTION20chain 'a' and (resid 9 through 29 )
21X-RAY DIFFRACTION21chain 'a' and (resid 30 through 40 )
22X-RAY DIFFRACTION22chain 'a' and (resid 41 through 52 )
23X-RAY DIFFRACTION23chain 'a' and (resid 53 through 61 )
24X-RAY DIFFRACTION24chain 'a' and (resid 62 through 77 )
25X-RAY DIFFRACTION25chain 'a' and (resid 78 through 84 )
26X-RAY DIFFRACTION26chain 'a' and (resid 85 through 92 )
27X-RAY DIFFRACTION27chain 'a' and (resid 93 through 111 )
28X-RAY DIFFRACTION28chain 'a' and (resid 112 through 121 )
29X-RAY DIFFRACTION29chain 'a' and (resid 122 through 128 )
30X-RAY DIFFRACTION30chain 'b' and (resid 1 through 8 )
31X-RAY DIFFRACTION31chain 'b' and (resid 9 through 29 )
32X-RAY DIFFRACTION32chain 'b' and (resid 30 through 40 )
33X-RAY DIFFRACTION33chain 'b' and (resid 41 through 52 )
34X-RAY DIFFRACTION34chain 'b' and (resid 53 through 61 )
35X-RAY DIFFRACTION35chain 'b' and (resid 62 through 77 )
36X-RAY DIFFRACTION36chain 'b' and (resid 78 through 84 )
37X-RAY DIFFRACTION37chain 'b' and (resid 85 through 101 )
38X-RAY DIFFRACTION38chain 'b' and (resid 102 through 111 )
39X-RAY DIFFRACTION39chain 'b' and (resid 112 through 121 )
40X-RAY DIFFRACTION40chain 'b' and (resid 122 through 128 )

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