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- PDB-6xjn: Human atlastin-1 (residues 1-439) bound to GDP-Mg2+ exhibits an o... -

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Basic information

Entry
Database: PDB / ID: 6xjn
TitleHuman atlastin-1 (residues 1-439) bound to GDP-Mg2+ exhibits an ordered amino terminus
ComponentsAtlastin-1
KeywordsHYDROLASE / GTPase / fusogen
Function / homology
Function and homology information


endoplasmic reticulum tubular network membrane / endoplasmic reticulum tubular network membrane organization / Golgi cis cisterna membrane / GTPase-dependent fusogenic activity / endoplasmic reticulum tubular network / endoplasmic reticulum membrane fusion / endoplasmic reticulum organization / axonogenesis / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...endoplasmic reticulum tubular network membrane / endoplasmic reticulum tubular network membrane organization / Golgi cis cisterna membrane / GTPase-dependent fusogenic activity / endoplasmic reticulum tubular network / endoplasmic reticulum membrane fusion / endoplasmic reticulum organization / axonogenesis / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Golgi membrane / axon / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / Golgi apparatus / identical protein binding
Similarity search - Function
Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Atlastin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8733
Polymers50,4051
Non-polymers4682
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.170, 138.860, 202.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Atlastin-1 / Brain-specific GTP-binding protein / GTP-binding protein 3 / hGBP3 / Guanine nucleotide-binding ...Brain-specific GTP-binding protein / GTP-binding protein 3 / hGBP3 / Guanine nucleotide-binding protein 3 / Spastic paraplegia 3 protein A


Mass: 50405.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WXF7, 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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5 M sodium formate pH 7, crystals transferred to cryo solution supplemented with 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 39278 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 47.89 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.078 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.735 / Num. unique obs: 5640 / CC1/2: 0.902

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→40.86 Å / SU ML: 0.2439 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 1520 3.87 %
Rwork0.2007 37736 -
obs0.2021 39256 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 29 85 3397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743384
X-RAY DIFFRACTIONf_angle_d0.89824586
X-RAY DIFFRACTIONf_chiral_restr0.0529509
X-RAY DIFFRACTIONf_plane_restr0.0064583
X-RAY DIFFRACTIONf_dihedral_angle_d15.5353453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.28671340.24383370X-RAY DIFFRACTION99.83
2.27-2.350.29981370.24223391X-RAY DIFFRACTION100
2.35-2.450.29711360.24393361X-RAY DIFFRACTION99.91
2.45-2.560.34391370.25153420X-RAY DIFFRACTION100
2.56-2.690.26311370.24243383X-RAY DIFFRACTION99.89
2.69-2.860.31231370.24843406X-RAY DIFFRACTION99.97
2.86-3.080.28931380.24293411X-RAY DIFFRACTION100
3.08-3.390.2841380.23343454X-RAY DIFFRACTION99.97
3.39-3.880.20241390.1843444X-RAY DIFFRACTION100
3.88-4.890.17691410.15773464X-RAY DIFFRACTION99.89
4.89-40.860.22811460.1813632X-RAY DIFFRACTION99.76
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)
13.04099016359-3.500862412910.7988967327784.69184474773-0.5443050558511.603312931180.1370870091550.260595944091-0.3439066524120.16524198054-0.081175956119-0.7355394475920.4901199023860.3099379932410.03703077415210.581841552884-0.1458262911390.0315180658991.10305432308-0.2412146952110.74242281665253.398592256941.95979922377.2758037219
22.339340220090.07520083724840.3657901132532.909962949032.127324526924.57583139067-0.07248270811940.208870911203-0.136778691409-0.226740584014-0.06366143478330.0576703435202-0.05427336397710.07763471869080.113358093460.398735192805-0.01397770851750.01890491671570.309319661355-0.05585648243520.27341757455827.055508472351.254972217379.2411489483
33.283197599-2.88311608577-1.977614511774.854970968692.386530442352.86850025371-0.295584221060.11558834967-0.5067734696030.0696261210257-0.1879540752470.5472112330910.402460912702-0.1436758914950.4439676718730.707156150451-0.06856342959710.0462143556380.477455760723-0.2322635722250.52224215584727.007260632227.292700332956.5890850939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 19:35)
2X-RAY DIFFRACTION2(chain A and resid 36:334)
3X-RAY DIFFRACTION3(chain A and resid 335:439)

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