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- PDB-3snh: Crystal structure of nucleotide-free human dynamin1 -

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Basic information

Entry
Database: PDB / ID: 3snh
TitleCrystal structure of nucleotide-free human dynamin1
ComponentsDynamin-1
KeywordsENDOCYTOSIS / HYDROLASE
Function / homology
Function and homology information


clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / photoreceptor ribbon synapse / Retrograde neurotrophin signalling ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / photoreceptor ribbon synapse / Retrograde neurotrophin signalling / Formation of annular gap junctions / endosome organization / Gap junction degradation / membrane coat / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / synaptic vesicle endocytosis / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / receptor-mediated endocytosis / photoreceptor inner segment / cell projection / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / endocytosis / GDP binding / : / presynapse / Clathrin-mediated endocytosis / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / GTP binding / protein kinase binding / protein homodimerization activity / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Dynamin, middle 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, middle 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.7 Å
AuthorsFaelber, K. / Daumke, O.
CitationJournal: Nature / Year: 2011
Title: Crystal structure of nucleotide-free dynamin.
Authors: Faelber, K. / Posor, Y. / Gao, S. / Held, M. / Roske, Y. / Schulze, D. / Haucke, V. / Noe, F. / Daumke, O.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynamin-1


Theoretical massNumber of molelcules
Total (without water)85,0711
Polymers85,0711
Non-polymers00
Water0
1
A: Dynamin-1

A: Dynamin-1


Theoretical massNumber of molelcules
Total (without water)170,1422
Polymers170,1422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)155.056, 201.993, 59.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dynamin-1 /


Mass: 85071.148 Da / Num. of mol.: 1 / Fragment: UNP residues 6-746 / Mutation: I395A,H396A,G397A,I398A,R399A,K562E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM, DNM1 / Plasmid: pET46-EK/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2-DE3 / References: UniProt: Q05193, dynamin GTPase

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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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 9% PEG400, 6% isopropanol, 100 mM HEPES/NaOH (pH 7.3), 10 mM MgCl2, 10 mM KCl. , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Aug 20, 2010 / Details: MIRROR
RadiationMonochromator: DOUBLE SI-111 CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.7→35 Å / Num. all: 10295 / Num. obs: 10214 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Redundancy: 4 % / Biso Wilson estimate: 111 Å2 / Rsym value: 0.076 / Net I/σ(I): 13.1
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.14 / Num. unique all: 717 / Rsym value: 0.665 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.51 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.6 Å33.67 Å
Translation3.6 Å33.67 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2AKA, 2DYN and 3LJB

2aka

2dyn

3ljb


Resolution: 3.7→32.59 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / WRfactor Rfree: 0.3028 / WRfactor Rwork: 0.2688 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.68 / SU B: 162.775 / SU ML: 1.049 / SU R Cruickshank DPI: 0.8175 / SU Rfree: 0.918 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.918 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3305 487 4.8 %RANDOM
Rwork0.2882 ---
obs0.2903 10214 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 436.07 Å2 / Biso mean: 176.8996 Å2 / Biso min: 72.73 Å2
Baniso -1Baniso -2Baniso -3
1-7.18 Å20 Å20 Å2
2---8.74 Å20 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 3.7→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 0 0 0 5285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225360
X-RAY DIFFRACTIONr_bond_other_d0.0060.023781
X-RAY DIFFRACTIONr_angle_refined_deg0.9821.9747203
X-RAY DIFFRACTIONr_angle_other_deg0.85339203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2375640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02324.248266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.204151039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1251547
X-RAY DIFFRACTIONr_chiral_restr0.060.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025808
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021051
LS refinement shellResolution: 3.7→3.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 22 -
Rwork0.397 688 -
all-710 -
obs-710 99.72 %
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)
10.1262-0.06020.37591.3922-0.29551.6225-0.01910.1412-0.07080.096-0.05780.1235-0.26170.37360.07690.2702-0.133-0.06380.4298-0.00110.269125.2722-56.85965.4237
21.0758-0.8480.2530.6718-0.16570.5544-0.38860.00610.1830.30540.0618-0.1333-0.4347-0.0280.32670.7574-0.3289-0.13570.3382-0.10520.166127.6102-29.920758.3461
31.82760.0812-2.13141.2311-0.92763.0761-0.15310.0527-0.31760.0853-0.08370.0712-0.0194-0.04620.23680.2545-0.00840.03730.41670.05450.224345.4886-10.83685.0855
42.05050.42990.49160.6655-0.36470.8646-0.0672-0.00910.0104-0.03610.19980.10350.05210.0001-0.13260.346-0.04390.0590.34860.0480.280366.1764-29.78398.3597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 294
2X-RAY DIFFRACTION2A6 - 32
3X-RAY DIFFRACTION2A295 - 314
4X-RAY DIFFRACTION2A716 - 746
5X-RAY DIFFRACTION3A320 - 499
6X-RAY DIFFRACTION3A653 - 708
7X-RAY DIFFRACTION4A518 - 631

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