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- PDB-4h1u: Nucleotide-free human dynamin-1-like protein GTPase-GED fusion -

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Basic information

Entry
Database: PDB / ID: 4h1u
TitleNucleotide-free human dynamin-1-like protein GTPase-GED fusion
ComponentsDynamin-1-like protein
KeywordsHYDROLASE / GTPase domain / GTPase
Function / homology
Function and homology information


mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / regulation of mitophagy / GTP-dependent protein binding ...mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / regulation of mitophagy / GTP-dependent protein binding / protein localization to mitochondrion / mitochondrial fission / positive regulation of neutrophil chemotaxis / regulation of mitochondrion organization / positive regulation of mitochondrial fission / intracellular distribution of mitochondria / heart contraction / necroptotic process / positive regulation of release of cytochrome c from mitochondria / brush border / localization / positive regulation of intrinsic apoptotic signaling pathway / clathrin-coated pit / mitochondrion organization / GTPase activator activity / release of cytochrome c from mitochondria / positive regulation of protein secretion / synaptic vesicle membrane / small GTPase binding / endocytosis / peroxisome / rhythmic process / calcium ion transport / protein complex oligomerization / microtubule binding / regulation of gene expression / protein-containing complex assembly / microtubule / mitochondrial outer membrane / membrane fusion / molecular adaptor activity / positive regulation of apoptotic process / intracellular membrane-bounded organelle / GTPase activity / lipid binding / ubiquitin protein ligase binding / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / mitochondrion / membrane / identical protein binding / cytosol / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Dynamin-1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsWenger, J. / Klinglmayr, E. / Puehringer, S. / Goettig, P.
CitationJournal: Plos One / Year: 2013
Title: Functional Mapping of Human Dynamin-1-Like GTPase Domain Based on X-ray Structure Analyses.
Authors: Wenger, J. / Klinglmayr, E. / Frohlich, C. / Eibl, C. / Gimeno, A. / Hessenberger, M. / Puehringer, S. / Daumke, O. / Goettig, P.
History
DepositionSep 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Dynamin-1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1682
Polymers40,9791
Non-polymers1891
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.500, 151.430, 42.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1013-

HOH

DetailsFull-length protein exists mainly as tetramer

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Components

#1: Protein Dynamin-1-like protein / Dnm1p/Vps1p-like protein / DVLP / Dynamin family member proline-rich carboxyl-terminal domain less ...Dnm1p/Vps1p-like protein / DVLP / Dynamin family member proline-rich carboxyl-terminal domain less / Dymple / Dynamin-like protein / Dynamin-like protein 4 / Dynamin-like protein IV / HdynIV / Dynamin-related protein 1


Mass: 40978.852 Da / Num. of mol.: 1 / Fragment: chimeric construct: unp residues 1-327/711-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1L, DLP1, DRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00429, dynamin GTPase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE (SEQRES) CORRESPONDS TO A CHIMERIC CONSTRUCT.

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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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate, 27.5% PEG 3000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 2, 2012 / Details: MIRRORS
RadiationMonochromator: Si 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.3→75.715 Å / Num. all: 15371 / Num. obs: 15371 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.118 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.423.50.4491.7778322040.44996.8
2.42-2.573.50.3352.1748421170.33597
2.57-2.753.50.262.9698419750.2696.9
2.75-2.973.50.2093.6667218910.20997.5
2.97-3.253.60.1365.6600016890.13696.7
3.25-3.643.50.0937.9547515480.09396.9
3.64-4.23.50.0719.5482313680.07196.6
4.2-5.143.50.0619.8409911660.06196.3
5.14-7.273.50.06210.432319140.06294.8
7.27-36.7153.50.04411.817284990.04490.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.69 Å
Translation2.5 Å43.69 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SNH

3snh


Resolution: 2.3→19.853 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.809 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 772 5.04 %RANDOM
Rwork0.2299 ---
obs0.2317 15331 95.25 %-
all-15337 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.71 Å2 / Biso mean: 24.3911 Å2 / Biso min: 0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 13 129 2908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052812
X-RAY DIFFRACTIONf_angle_d0.9763806
X-RAY DIFFRACTIONf_chiral_restr0.063454
X-RAY DIFFRACTIONf_plane_restr0.007496
X-RAY DIFFRACTIONf_dihedral_angle_d15.9141097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.38210.3417660.30871451151796
2.3821-2.47740.327830.2761414149796
2.4774-2.58990.3318860.27631431151797
2.5899-2.72610.2819810.26861475155696
2.7261-2.89640.326830.27441427151096
2.8964-3.11920.3038880.24391450153896
3.1192-3.43170.269620.22791470153296
3.4317-3.92490.2251890.19961457154695
3.9249-4.93240.2262670.18281484155194
4.9324-19.85410.2232670.20581500156790

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