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- PDB-5vgr: Human Atlastin-3, GDP-bound -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5vgr
TitleHuman Atlastin-3, GDP-bound
ComponentsAtlastin-3
KeywordsHYDROLASE / G proteins / GTPase / membrane fusion
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: 2.096 Å
AuthorsO'Donnell, J.P. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008500 United States
CitationJournal: Structure / Year: 2017
Title: Timing and Reset Mechanism of GTP Hydrolysis-Driven Conformational Changes of Atlastin.
Authors: O'Donnell, J.P. / Cooley, R.B. / Kelly, C.M. / Miller, K. / Andersen, O.S. / Rusinova, R. / Sondermann, H.
History
DepositionApr 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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-3
B: Atlastin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2364
Polymers98,3492
Non-polymers8862
Water4,306239
1
A: Atlastin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6182
Polymers49,1751
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Atlastin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6182
Polymers49,1751
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.666, 57.057, 143.423
Angle α, β, γ (deg.)90.00, 116.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Atlastin-3


Mass: 49174.582 Da / Num. of mol.: 2 / Fragment: residues 21-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL3 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21
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 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M NaCl, 0.1 M Tris pH 8.5, 25% PEG3350, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6362 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6362 Å / Relative weight: 1
ReflectionResolution: 2.096→29.305 Å / Num. obs: 55378 / % possible obs: 98.41 % / Redundancy: 4.5 % / Net I/σ(I): 12.43
Reflection shellResolution: 2.096→2.171 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 4912 / % possible all: 88.17

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q5E

3q5e


Resolution: 2.096→29.305 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.228 1992 3.61 %
Rwork0.1975 --
obs0.1986 55138 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.096→29.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 56 0 239 6259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116166
X-RAY DIFFRACTIONf_angle_d1.0518359
X-RAY DIFFRACTIONf_dihedral_angle_d8.4464412
X-RAY DIFFRACTIONf_chiral_restr0.078925
X-RAY DIFFRACTIONf_plane_restr0.0071069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.096-2.14830.35611200.32173167X-RAY DIFFRACTION83
2.1483-2.20630.31491430.29323810X-RAY DIFFRACTION99
2.2063-2.27120.29221380.27013811X-RAY DIFFRACTION100
2.2712-2.34450.26151460.25323832X-RAY DIFFRACTION100
2.3445-2.42830.24591420.24773818X-RAY DIFFRACTION100
2.4283-2.52540.27471440.23663839X-RAY DIFFRACTION100
2.5254-2.64030.27021460.22173860X-RAY DIFFRACTION100
2.6403-2.77940.22341450.21643805X-RAY DIFFRACTION100
2.7794-2.95340.27241430.2213879X-RAY DIFFRACTION100
2.9534-3.18120.23361440.20463842X-RAY DIFFRACTION100
3.1812-3.50080.23941470.18773855X-RAY DIFFRACTION100
3.5008-4.00630.20481400.16473894X-RAY DIFFRACTION100
4.0063-5.04340.1871490.15833903X-RAY DIFFRACTION100
5.0434-29.3050.20771450.18713831X-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)
13.28540.6383-0.34212.6462-0.96663.38130.0286-0.42990.13820.4384-0.0219-0.093-0.0094-0.2290.00410.2371-0.0353-0.04430.2829-0.04410.2333133.8037.947918.8497
22.08651.0732-0.50832.388-0.92362.64990.031-0.09120.10980.22810.00760.13610.056-0.5557-0.02920.2183-0.0396-0.01830.3604-0.04560.2774128.32347.910316.1784
38.1169-0.7105-3.36230.53150.043.1451-0.07010.14640.3338-0.00520.025-0.1187-0.17190.16080.04440.3091-0.0811-0.03130.2555-0.02090.4548156.744126.41314.6045
43.1341-0.6641-0.97670.69240.92172.8272-0.07360.25090.24360.05590.06230.0705-0.5226-0.12080.00850.7113-0.12330.02130.42210.09980.3174169.041629.748243.917
59.56652.3409-1.14333.00362.05694.5469-0.1536-0.454-0.56821.4957-0.3243-0.76230.38370.28260.47871.37090.1470.09420.67520.34011.1079156.868347.45341.2546
66.63850.3742-2.9421.3484-0.10893.80960.10770.28270.9534-0.36670.42110.4133-0.2493-0.6633-0.52831.01260.1083-0.03990.57260.07450.5863147.568445.018758.8652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 22:232)
2X-RAY DIFFRACTION2(chain A and resid 233:331)
3X-RAY DIFFRACTION3(chain A and resid 332:438)
4X-RAY DIFFRACTION4(chain B and resid 22:328)
5X-RAY DIFFRACTION5(chain B and resid 329:333)
6X-RAY DIFFRACTION6(chain B and resid 334:421)

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