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- PDB-3t35: Arabidopsis thaliana dynamin-related protein 1A in postfission state -

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Basic information

Entry
Database: PDB / ID: 3t35
TitleArabidopsis thaliana dynamin-related protein 1A in postfission state
ComponentsDynamin-related protein 1A, LINKER, Dynamin-related protein 1A
KeywordsMOTOR PROTEIN / dynamin-like protein 1A / GTPase / membrane fission
Function / homology
Function and homology information


cell plate formation involved in plant-type cell wall biogenesis / stigma development / regulation of plant-type cell wall organization or biogenesis / regulation of lipid localization / cell plate / regulation of phragmoplast microtubule organization / trichome branching / root hair initiation / cytokinesis by cell plate formation / xylem and phloem pattern formation ...cell plate formation involved in plant-type cell wall biogenesis / stigma development / regulation of plant-type cell wall organization or biogenesis / regulation of lipid localization / cell plate / regulation of phragmoplast microtubule organization / trichome branching / root hair initiation / cytokinesis by cell plate formation / xylem and phloem pattern formation / response to boron-containing substance / cellular response to boron-containing substance levels / phragmoplast / protein histidine kinase binding / embryo development ending in seed dormancy / clathrin-coated endocytic vesicle / plasmodesma / plant-type vacuole / clathrin-dependent endocytosis / clathrin-coated vesicle / regulation of establishment of cell polarity / plastid / clathrin binding / chloroplast thylakoid membrane / regulation of endocytosis / intracellular protein transport / cell cortex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / GTPase activity / GTP binding / plasma membrane / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / 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 / Phragmoplastin DRP1A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.592 Å
AuthorsYan, L.M. / Ma, Y.Y. / Sun, Y.N. / Lou, Z.Y.
CitationJournal: J Mol Cell Biol / Year: 2011
Title: Structural basis for mechanochemical role of Arabidopsis thaliana dynamin-related protein in membrane fission
Authors: Yan, L.M. / Ma, Y.Y. / Sun, Y.N. / Gao, J. / Chen, X. / Liu, J. / Wang, C. / Rao, Z. / Lou, Z.Y.
History
DepositionJul 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
B: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
C: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
D: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4208
Polymers159,6474
Non-polymers1,7734
Water6,864381
1
A: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
B: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7104
Polymers79,8232
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-25 kcal/mol
Surface area30660 Å2
MethodPISA
2
C: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
D: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7104
Polymers79,8232
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-20 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.157, 146.157, 204.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A


Mass: 39911.703 Da / Num. of mol.: 4 / Fragment: UNP residues 1-325, 579-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P42697
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 3.94 Å3/Da / Density % sol: 68.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 160mM sodium formate, 16%(w/v) polyethylene glycol 3350, 40mM magnesium chloride, 6%(w/v) 2-Propanol, 20mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.592→50 Å / Num. obs: 28872 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X2E

2x2e


Resolution: 3.592→43.323 Å / SU ML: 0.6 / σ(F): 0.05 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2907 1276 5.08 %random
Rwork0.238 ---
obs0.2407 25139 87.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.2 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0361 Å2-0 Å20 Å2
2--4.0361 Å2-0 Å2
3---6.8555 Å2
Refinement stepCycle: LAST / Resolution: 3.592→43.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10544 0 112 381 11037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210808
X-RAY DIFFRACTIONf_angle_d1.73514616
X-RAY DIFFRACTIONf_dihedral_angle_d20.8794148
X-RAY DIFFRACTIONf_chiral_restr0.1041712
X-RAY DIFFRACTIONf_plane_restr0.0071864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.592-3.73570.33131390.2461266988
3.7357-3.90570.31731220.279234077
3.9057-4.11140.34041030.2383169056
4.1114-4.36880.2891260.1961255084
4.3688-4.70570.26651340.163282192
4.7057-5.17860.20741800.1692280594
5.1786-5.92630.28061530.1921293396
5.9263-7.46040.27891590.2158297698
7.4604-43.32630.20031600.2013079100

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