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- PDB-6b9g: human ATL1 GTPase domain bound to GDP -

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Basic information

Entry
Database: PDB / ID: 6b9g
Titlehuman ATL1 GTPase domain bound to GDP
ComponentsAtlastin-1
KeywordsHYDROLASE / GTPase / dynamin related protein / GTPase domain
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: 3 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 ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)158,08312
Polymers156,2134
Non-polymers1,8708
Water1,65792
1
B: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5213
Polymers39,0531
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5213
Polymers39,0531
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5213
Polymers39,0531
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5213
Polymers39,0531
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)308.032, 308.032, 308.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11D-506-

HOH

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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: 39053.188 Da / Num. of mol.: 4 / Fragment: residue 1-339
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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M DL-malic acid pH 7, 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: Sep 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3→48.7 Å / Num. obs: 48244 / % possible obs: 99.9 % / Redundancy: 25.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.197 / Rrim(I) all: 0.201 / Net I/σ(I): 22.8

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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: 3Q5D

3q5d


Resolution: 3→48.7 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.77
RfactorNum. reflection% reflection
Rfree0.2052 1997 4.15 %
Rwork0.1695 --
obs0.171 48124 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9730 0 116 92 9938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210066
X-RAY DIFFRACTIONf_angle_d0.53413646
X-RAY DIFFRACTIONf_dihedral_angle_d14.4235946
X-RAY DIFFRACTIONf_chiral_restr0.0431513
X-RAY DIFFRACTIONf_plane_restr0.0031723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.0760.31241430.31063244X-RAY DIFFRACTION99
3.076-3.15910.27411420.25473305X-RAY DIFFRACTION100
3.1591-3.25210.2781440.24013297X-RAY DIFFRACTION100
3.2521-3.3570.27421390.21913277X-RAY DIFFRACTION100
3.357-3.4770.2631400.22253268X-RAY DIFFRACTION100
3.477-3.61610.26531450.19313272X-RAY DIFFRACTION100
3.6161-3.78070.2711380.17563301X-RAY DIFFRACTION100
3.7807-3.97990.17451420.15723299X-RAY DIFFRACTION100
3.9799-4.22910.19851430.14053282X-RAY DIFFRACTION100
4.2291-4.55540.17781440.12593309X-RAY DIFFRACTION100
4.5554-5.01340.13881460.12963319X-RAY DIFFRACTION100
5.0134-5.73790.17531430.1523334X-RAY DIFFRACTION100
5.7379-7.22540.19981430.16673316X-RAY DIFFRACTION100
7.2254-48.70.16541450.15253304X-RAY DIFFRACTION97
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)
15.119-0.0716-0.23242.25230.0852.14750.09150.0486-0.3484-0.0963-0.1617-0.42890.13530.30790.05880.49320.11140.08920.39780.01360.346980.3836-45.1507-40.7795
20.92480.37580.33725.07361.78783.00990.01520.08280.06590.0335-0.2510.3958-0.049-0.09990.21630.33430.04130.050.3308-0.01630.272161.6829-18.2568-24.2452
31.08980.2421-0.29822.8205-1.80215.21630.01210.072-0.0894-0.04830.25130.1317-0.0285-0.4124-0.22520.35410.046-0.03920.26540.01850.333861.609-24.38218.1497
44.8534-0.254-0.03222.0476-0.06262.21480.0921-0.3626-0.05540.13140.0624-0.31280.10880.4117-0.15080.49630.1-0.1070.3466-0.0090.404280.3495-40.717345.1964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 30:338)
2X-RAY DIFFRACTION2(chain B and resid 31:338)
3X-RAY DIFFRACTION3(chain C and resid 31:338)
4X-RAY DIFFRACTION4(chain D and resid 31:338)

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