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- PDB-6b9d: Human ATL1 mutant - R77A bound to GDP -

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Basic information

Entry
Database: PDB / ID: 6b9d
TitleHuman ATL1 mutant - R77A bound to GDP
ComponentsAtlastin-1
KeywordsHYDROLASE / GTPase / dynamin related protein / hydrolysis-deficient
Function / homology
Function and homology information


endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / axon / Golgi membrane ...endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / axon / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / membrane / identical protein binding
Similarity search - Function
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-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsO'Donnell, J.P. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
Spastic Paraplegia Foundation United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A hereditary spastic paraplegia-associated atlastin variant exhibits defective allosteric coupling in the catalytic core.
Authors: O'Donnell, J.P. / Byrnes, L.J. / Cooley, R.B. / Sondermann, H.
History
DepositionOct 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atlastin-1
B: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,49212
Polymers105,0052
Non-polymers1,48810
Water5,062281
1
A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2466
Polymers52,5021
Non-polymers7445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2466
Polymers52,5021
Non-polymers7445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.058, 68.429, 75.883
Angle α, β, γ (deg.)117.00, 89.81, 99.04
Int Tables number1
Space group name H-MP1

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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: 52502.340 Da / Num. of mol.: 2 / Fragment: residues 1-446 / Mutation: R77A
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 / Guanosine 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium malonate pH 6, 20% PEG3350, 1 mM GDP, 2 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→42.36 Å / Num. obs: 63315 / % possible obs: 96.4 % / Redundancy: 2.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.103 / Net I/σ(I): 7.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q5E

3q5e


Resolution: 1.95→25.18 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.82
RfactorNum. reflection% reflection
Rfree0.2387 1576 2.49 %
Rwork0.2045 --
obs0.2053 63245 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5872 0 94 281 6247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076071
X-RAY DIFFRACTIONf_angle_d0.9298206
X-RAY DIFFRACTIONf_dihedral_angle_d21.4072182
X-RAY DIFFRACTIONf_chiral_restr0.056929
X-RAY DIFFRACTIONf_plane_restr0.0061031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01290.34741320.30345586X-RAY DIFFRACTION96
2.0129-2.08480.2791390.26465592X-RAY DIFFRACTION96
2.0848-2.16830.32081620.23955591X-RAY DIFFRACTION96
2.1683-2.26690.2891380.22575576X-RAY DIFFRACTION96
2.2669-2.38630.25461350.2255643X-RAY DIFFRACTION97
2.3863-2.53570.29411520.21975660X-RAY DIFFRACTION97
2.5357-2.73130.23061400.2165567X-RAY DIFFRACTION96
2.7313-3.00570.251470.22085625X-RAY DIFFRACTION96
3.0057-3.43970.26851440.20025638X-RAY DIFFRACTION97
3.4397-4.33010.20591460.17485606X-RAY DIFFRACTION97
4.3301-25.18180.18371410.18065585X-RAY DIFFRACTION96
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)
12.30640.1004-0.15422.61611.38435.0076-0.09060.0610.0813-0.23460.1045-0.2985-0.1390.2541-0.01270.25250.04180.00710.179-0.02260.1975-3.7893-26.4581.65
21.9577-0.73041.03821.7012-1.70664.92950.1130.1372-0.2194-0.5061-0.1327-0.19160.40260.21990.00730.3270.01850.04070.2175-0.04390.2084-9.438-40.5533-9.5808
32.2581-0.56941.99161.13-0.91424.2829-0.2584-0.5205-0.17960.27530.1906-0.1326-0.2825-0.22350.04490.28010.1299-0.0010.2996-0.00880.2776-0.0701-36.436419.9441
43.4945-0.54090.60573.62881.08044.5335-0.03980.0769-0.17890.0429-0.04530.27670.3936-0.20860.06010.23720.00180.00250.21130.00620.1329-19.1897-72.959933.3891
51.9546-1.5073-0.77323.09230.40571.44160.13860.40.0591-0.6156-0.11340.08530.1629-0.1852-0.01610.37350.0319-0.0460.267-0.01890.1719-10.8337-71.654814.1746
63.1964-2.2469-0.38913.13980.71381.7321-0.2968-0.19480.28260.33340.22030.0504-0.0786-0.2760.0730.27120.0522-0.04470.29220.01440.2003-24.8547-56.254532.7828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 29:183)
2X-RAY DIFFRACTION2(chain A and resid 184:289)
3X-RAY DIFFRACTION3(chain A and resid 290:438)
4X-RAY DIFFRACTION4(chain B and resid 29:144)
5X-RAY DIFFRACTION5(chain B and resid 145:278)
6X-RAY DIFFRACTION6(chain B and resid 279:439)

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