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- PDB-6xjo: Human atlastin-3 (residues 1-334) bound to GDP-Mg2+ exhibits an o... -

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Basic information

Entry
Database: PDB / ID: 6xjo
TitleHuman atlastin-3 (residues 1-334) bound to GDP-Mg2+ exhibits an ordered amino terminus
ComponentsAtlastin-3
KeywordsHYDROLASE / GTPase / fusogen
Function / homology
Function and homology information


positive regulation of endoplasmic reticulum tubular network organization / endoplasmic reticulum tubular network membrane / endoplasmic reticulum tubular network / endoplasmic reticulum organization / Golgi organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / GTPase activity / GTP binding / endoplasmic reticulum ...positive regulation of endoplasmic reticulum tubular network organization / endoplasmic reticulum tubular network membrane / endoplasmic reticulum tubular network / endoplasmic reticulum organization / Golgi organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / GTPase activity / GTP binding / endoplasmic reticulum / identical protein binding / membrane
Similarity search - Function
Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Atlastin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsO'Donnell, J.P. / Sondermann, H.
CitationJournal: J.Cell Biol. / Year: 2021
Title: The hypervariable region of atlastin-1 is a site for intrinsic and extrinsic regulation.
Authors: Kelly, C.M. / Byrnes, L.J. / Neela, N. / Sondermann, H. / O'Donnell, J.P.
History
DepositionJun 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atlastin-3
B: Atlastin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2086
Polymers75,2732
Non-polymers9354
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, The dimer assembly is true for ATL3 1-442 which was validated with FRET measurements and light scattering. ATL3 1-334 described here does not dimerize in solution but ...Evidence: light scattering, The dimer assembly is true for ATL3 1-442 which was validated with FRET measurements and light scattering. ATL3 1-334 described here does not dimerize in solution but represents a biologically relevant state
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-37 kcal/mol
Surface area25810 Å2
2
A: Atlastin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1043
Polymers37,6371
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Atlastin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1043
Polymers37,6371
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.480, 88.040, 168.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Atlastin-3


Mass: 37636.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DD88, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 187.5 mM Ammonium acetate, 21.5% PEG3350, 100 mM Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 39632 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 39.62 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.105 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 2864 / CC1/2: 0.665 / Rrim(I) all: 1.517

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VGR

5vgr


Resolution: 2.1→44.02 Å / SU ML: 0.2623 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0788
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2308 3775 5.06 %
Rwork0.1785 70826 -
obs0.1812 39632 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 58 240 5078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784947
X-RAY DIFFRACTIONf_angle_d0.91116718
X-RAY DIFFRACTIONf_chiral_restr0.054761
X-RAY DIFFRACTIONf_plane_restr0.0056847
X-RAY DIFFRACTIONf_dihedral_angle_d16.0168674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.34551390.3042606X-RAY DIFFRACTION99.82
2.13-2.150.3581350.28592612X-RAY DIFFRACTION100
2.15-2.180.30551410.28252617X-RAY DIFFRACTION99.78
2.18-2.220.26121390.26082663X-RAY DIFFRACTION99.93
2.22-2.250.29971400.25182622X-RAY DIFFRACTION100
2.25-2.280.28731400.24672569X-RAY DIFFRACTION99.93
2.28-2.320.27581420.24872674X-RAY DIFFRACTION100
2.32-2.360.29211410.24022651X-RAY DIFFRACTION100
2.36-2.40.28891420.22322556X-RAY DIFFRACTION99.82
2.4-2.450.26521420.22522685X-RAY DIFFRACTION99.86
2.45-2.50.30241400.21652599X-RAY DIFFRACTION100
2.5-2.550.26921370.20982618X-RAY DIFFRACTION99.96
2.55-2.610.27541450.21042657X-RAY DIFFRACTION100
2.61-2.680.26591400.20262606X-RAY DIFFRACTION100
2.68-2.750.2941430.19762650X-RAY DIFFRACTION99.96
2.75-2.830.23011390.20012617X-RAY DIFFRACTION99.96
2.83-2.920.26591410.19532617X-RAY DIFFRACTION99.93
2.92-3.030.23231330.19342610X-RAY DIFFRACTION99.93
3.03-3.150.23051430.16972637X-RAY DIFFRACTION100
3.15-3.290.21921330.17932637X-RAY DIFFRACTION100
3.29-3.470.24931430.16592628X-RAY DIFFRACTION100
3.47-3.680.22681450.15552638X-RAY DIFFRACTION99.96
3.68-3.970.16961420.14322612X-RAY DIFFRACTION99.93
3.97-4.370.19931360.12982610X-RAY DIFFRACTION99.82
4.37-50.18121420.13222654X-RAY DIFFRACTION100
5-6.290.20271340.17012627X-RAY DIFFRACTION99.96
6.29-44.020.21641380.17252554X-RAY DIFFRACTION97.5
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)
16.555395817150.632579393651-2.930893635235.730218902032.162327524642.41953553352-0.60088609471-1.14201349348-0.5657162140660.960059786745-0.002370515345040.7522732518942.205326764640.1196014741550.5017123648440.870403486676-0.01402217142370.06428161845590.6222529768320.1016214393530.53844759157655.2417530163-13.6049835187-45.5560484833
21.5465960288-0.178050489639-0.2403617836224.08460310761-1.333168037162.707452929070.1030306584450.1411045532220.366487389204-0.26581090144-0.0701377525134-0.326881187016-0.4715227544930.0889926859441-0.04478417061170.320552087634-0.007477163852850.03156899562260.2888846782760.03904551055320.38297747060239.80448539565.80454867048-14.5490773695
31.88958381728-0.0471369274059-0.2648103664423.08099400115-1.41990582022.935611713460.1186640944540.1711380315050.444378086822-0.1167006596170.0448596938563-0.161683367009-0.552213739663-0.0169467083914-0.1436710887960.3610777184550.02088575027550.03595819329590.2828793626846.33000025673E-50.37207924486536.09315852056.06609130056-12.9610772687
42.16652780152-0.3260156636720.4268476890782.46774824828-0.1230050403814.71906699259-0.00436262787943-0.3091356896720.1580134189760.568273833836-0.03554244480380.5313285797020.159924895288-0.5427324850520.06115553576590.339075732665-0.001822951404870.1287897214350.336275239439-0.06257355978430.33561111381640.0790541454-10.564230652128.9340770462
51.080995555870.131334936515-0.5820226008313.14008276329-0.1328818436484.40972654689-0.04909575570010.009623150061670.1322976717960.212514307779-0.04733186452610.0469622053478-0.139936409874-0.04471404431430.07242246806070.1912206812480.0316941950673-0.03709043787190.263344651108-0.02661367588280.26012610106450.1551941661-3.756878450419.6656777503
61.35812751479-0.1593540969790.4314400721761.93522124297-0.1379583636633.1572228535-0.0347010715786-0.1557963192910.1459253967220.298368265792-0.0134720283623-0.00812541113002-0.04003862797540.0981362354610.05427695623160.2470137172020.03689816877280.03460522413680.259030092335-0.01851313592030.26203605925248.5510755791-8.6585607594122.1859153506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:21)
2X-RAY DIFFRACTION2(chain A and resid 22:241)
3X-RAY DIFFRACTION3(chain A and resid 242:332)
4X-RAY DIFFRACTION4(chain B and resid 22:100)
5X-RAY DIFFRACTION5(chain B and resid 101:246)
6X-RAY DIFFRACTION6(chain B and resid 247:333)

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