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- PDB-6b9f: Human ATL1 mutant - F151S bound to GDPAlF4- -

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Basic information

Entry
Database: PDB / ID: 6b9f
TitleHuman ATL1 mutant - F151S bound to GDPAlF4-
ComponentsAtlastin-1
KeywordsHYDROLASE / GTPase / dynamin related protein / HSP mutant / 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 / Golgi membrane / axon ...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 / Golgi membrane / axon / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / identical protein binding / membrane
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
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Atlastin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)106,76016
Polymers104,8832
Non-polymers1,87814
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-70 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.613, 115.721, 184.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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: 52441.285 Da / Num. of mol.: 2 / Fragment: residues 1-446 / Mutation: F151S
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

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Non-polymers , 5 types, 571 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#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-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
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M ammonium citrate tribasic pH 7, 0.1 M imidazole pH7, 20% PEG monomethyl ether 2,000, 1 mM GDP, 2 mM MgCl2, 2 mM AlCl2, 20 mM NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→49 Å / Num. obs: 83775 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.129 / Net I/σ(I): 10.7

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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: 4IDO

4ido


Resolution: 1.9→43.684 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.75
RfactorNum. reflection% reflection
Rfree0.2223 1997 2.39 %
Rwork0.1776 --
obs0.1787 83642 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6644 0 116 557 7317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076909
X-RAY DIFFRACTIONf_angle_d0.8659330
X-RAY DIFFRACTIONf_dihedral_angle_d16.0894152
X-RAY DIFFRACTIONf_chiral_restr0.0511018
X-RAY DIFFRACTIONf_plane_restr0.0051186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9460.36191184834X-RAY DIFFRACTION83
1.946-1.99860.36541415814X-RAY DIFFRACTION99
1.9986-2.05740.37091435830X-RAY DIFFRACTION100
2.0574-2.12380.2631425802X-RAY DIFFRACTION100
2.1238-2.19970.27141435820X-RAY DIFFRACTION100
2.1997-2.28780.27441425842X-RAY DIFFRACTION100
2.2878-2.39190.22541445875X-RAY DIFFRACTION100
2.3919-2.5180.2321455900X-RAY DIFFRACTION100
2.518-2.67580.28161425874X-RAY DIFFRACTION100
2.6758-2.88230.23311455907X-RAY DIFFRACTION100
2.8823-3.17230.26121455912X-RAY DIFFRACTION100
3.1723-3.63110.21331465970X-RAY DIFFRACTION100
3.6311-4.57410.13811470.12856001X-RAY DIFFRACTION100
4.5741-43.6840.18311546264X-RAY DIFFRACTION100
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)
11.1250.64250.26291.1020.01050.844-0.07010.1041-0.0836-0.16740.08650.0216-0.0202-0.06790.00130.152-0.0060.0340.1775-0.02510.152-52.8723-11.428133.9197
20.60260.21330.281.03490.04710.6576-0.00820.0302-0.1953-0.02850.0534-0.15440.07510.0442-00.15230.01320.03470.1626-0.00450.2325-44.3517-15.761745.5952
30.27210.02310.09080.62540.46620.3821-0.0456-0.12210.02790.07870.03120.0828-0.02620.0447-00.2283-0.00680.02550.26670.07180.2248-69.7736-25.467385.6307
40.2203-0.2204-0.29310.18910.34040.60150.07950.05390.2049-0.11470.03540.404-0.1014-0.0691-0.00010.2169-0.02340.01350.29720.08630.258-73.6144-24.229481.4079
50.44950.1808-0.30920.903-0.12290.83320.0322-0.0103-0.03780.22470.0131-0.2353-0.02830.08430.00130.1746-0.0089-0.06750.1550.01120.1513-37.13486.154771.2397
60.3655-0.13040.07060.73210.14970.6199-0.00240.05440.02730.04520.0143-0.0194-0.0537-0.0985-00.1392-0.0030.00090.16250.00950.1797-49.38277.320760.511
70.63080.2145-0.44060.18160.23760.6131-0.0183-0.1309-0.07490.20320.12090.09350.04050.0325-00.4438-0.0167-0.07940.26770.05650.181-47.55071.675181.5976
8-0.17530.17940.06980.915-0.0550.5136-0.19760.0512-0.0601-0.25580.1576-0.12470.2865-0.0721-0.00040.3077-0.02970.04290.26910.05490.1994-67.3848-41.00775.1259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 31:163)
2X-RAY DIFFRACTION2(chain A and resid 164:345)
3X-RAY DIFFRACTION3(chain A and resid 346:402)
4X-RAY DIFFRACTION4(chain A and resid 403:442)
5X-RAY DIFFRACTION5(chain B and resid 31:186)
6X-RAY DIFFRACTION6(chain B and resid 187:306)
7X-RAY DIFFRACTION7(chain B and resid 307:346)
8X-RAY DIFFRACTION8(chain B and resid 347:452)

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