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- PDB-3zvr: Crystal structure of Dynamin -

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Basic information

Entry
Database: PDB / ID: 3zvr
TitleCrystal structure of Dynamin
ComponentsDYNAMIN-1
KeywordsHYDROLASE / DRP1 / DRP / ENDOCYTOSIS / MITOCHONDRIAL FISSION / GTPASE / STALK / PH / BSE / MEMBRANE FISSION
Function / homology
Function and homology information


positive regulation of synaptic vesicle recycling / Toll Like Receptor 4 (TLR4) Cascade / clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / Gap junction degradation / Formation of annular gap junctions / presynaptic endocytic zone membrane / varicosity / MHC class II antigen presentation ...positive regulation of synaptic vesicle recycling / Toll Like Receptor 4 (TLR4) Cascade / clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / Gap junction degradation / Formation of annular gap junctions / presynaptic endocytic zone membrane / varicosity / MHC class II antigen presentation / dynamin GTPase / chromaffin granule / regulation of vesicle size / Recycling pathway of L1 / endosome organization / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / photoreceptor ribbon synapse / membrane coat / G protein-coupled receptor internalization / regulation of synaptic vesicle endocytosis / clathrin-coated vesicle / nitric-oxide synthase binding / phosphatidylinositol-3,4,5-trisphosphate binding / response to amyloid-beta / synaptic vesicle endocytosis / endocytic vesicle / D2 dopamine receptor binding / protein serine/threonine kinase binding / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / photoreceptor inner segment / receptor-mediated endocytosis / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / SH3 domain binding / endocytosis / GDP binding / : / synaptic vesicle / presynapse / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / synapse / protein-containing complex binding / GTP binding / protein kinase binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFord, M.G.J. / Jenni, S. / Nunnari, J.
CitationJournal: Nature / Year: 2011
Title: The Crystal Structure of Dynamin
Authors: Ford, M.G.J. / Jenni, S. / Nunnari, J.
History
DepositionJul 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other
Revision 1.2Oct 12, 2011Group: Database references / Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0774
Polymers88,3631
Non-polymers7153
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)178.450, 191.610, 60.520
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 / B-DYNAMIN / D100 / DYNAMIN\ / BRAIN


Mass: 88362.633 Da / Num. of mol.: 1 / Fragment: DYNAMIN 1 G397D DELTA PRD, RESIDUES 1-752 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P21575, dynamin GTPase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 397 TO ASP

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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: 2.93 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 7.7
Details: 52.5 MM TRIS.HCL PH 7.7, 175 MM NACL, 32.5 MM NANO3, 20 % V/V PEG 400, 0.97 MM BETA-MERCAPTOETHANOL, 31.9 MICROM DYN1 G397D DELTA PRD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9488
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9488 Å / Relative weight: 1
ReflectionResolution: 3.1→95.8 Å / Num. obs: 18735 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 101.701 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.9 / % possible all: 66.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AKA CHAIN B, PDB ENTRY 2DYN CHAIN B, PDB ENTRY 3LJB CHAIN B

2aka

2dyn

3ljb


Resolution: 3.1→95.805 Å / SU ML: 0.73 / σ(F): 1.34 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 956 5.1 %
Rwork0.2123 --
obs0.2153 18731 96.73 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.803 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 114.41 Å2
Baniso -1Baniso -2Baniso -3
1-9.0208 Å20 Å20 Å2
2--2.8708 Å20 Å2
3----11.8916 Å2
Refinement stepCycle: LAST / Resolution: 3.1→95.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5407 0 48 5 5460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085536
X-RAY DIFFRACTIONf_angle_d1.0987437
X-RAY DIFFRACTIONf_dihedral_angle_d16.0462168
X-RAY DIFFRACTIONf_chiral_restr0.057837
X-RAY DIFFRACTIONf_plane_restr0.004957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.26350.32851160.30281998X-RAY DIFFRACTION78
3.2635-3.4680.32081340.2822578X-RAY DIFFRACTION100
3.468-3.73580.33291330.24692596X-RAY DIFFRACTION100
3.7358-4.11170.27631550.22092587X-RAY DIFFRACTION100
4.1117-4.70670.27561330.18912616X-RAY DIFFRACTION100
4.7067-5.92980.28761460.21592631X-RAY DIFFRACTION100
5.9298-95.85070.22651390.18872769X-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)
15.97780.23381.91424.88531.71446.4055-0.26810.22630.13340.38630.0996-0.43570.31590.02140.1350.8062-0.2415-0.03150.6273-0.00310.628-27.756944.98022.3094
26.8030.65611.01758.7045-0.31227.6285-0.02391.2389-0.3902-0.01120.6862-1.73680.71510.2013-0.3490.5403-0.05830.15951.16680.03741.1041-16.10543.1484-3.0734
37.20050.28461.42536.33890.28796.5376-0.1833-0.15510.7347-0.4690.1108-0.13140.0506-0.71290.31220.8667-0.2777-0.05020.8302-0.07670.6674-31.348150.6257-4.6656
46.76882.46171.71778.38710.68449.0134-0.35490.35030.9853-0.01660.27570.8746-1.2814-0.3850.05010.7468-0.01730.01430.7191-0.02280.6982-39.410459.47455.171
57.06136.03694.52955.44454.2093.00180.9978-2.6893-2.3253-1.6095-0.0632-3.13911.7556-1.6866-0.78341.62550.13580.32231.99120.17062.0215-12.483761.36257.5368
63.4072-0.5804-0.73565.02290.57625.09960.1622-0.85950.29611.5163-0.32290.29560.1441-0.32060.1310.7482-0.11880.04330.7934-0.02080.6391-33.11150.561912.8911
75.59272.68640.89656.34825.01963.6541.06070.7956-2.01870.4803-0.8208-0.4184-0.33970.79320.01171.5490.0976-0.59361.4893-0.48371.6218-38.476913.0903-14.2889
83.757-3.41215.21968.1108-1.80096.7005-0.6029-1.10130.49670.72140.2188-0.30980.4589-0.0740.20131.1195-0.08030.11491.0012-0.08420.6588-49.50958.7631-31.0173
95.51-2.20915.27626.0161-2.41274.3856-0.2147-0.65971.4641-0.1366-0.2535-0.24430.2672-1.67280.61030.4590.1190.11870.7432-0.0680.922-66.807516.7445-57.064
102.5641-0.18282.01110.48781.71019.0111-0.24610.59911.2944-0.99971.5136-0.6523-0.08730.4363-1.24221.40420.16030.06231.37130.53231.115-69.95516.9428-82.0686
114.9177-5.8647-2.92697.28423.43342.0077-1.01682.48-1.6597-0.2598-3.3889-1.38371.27691.25773.68192.13010.14830.16382.04570.08951.6108-67.76025.8084-87.7351
124.5962-0.36552.0573.38780.32116.12950.19570.16930.53960.5158-0.11360.1304-0.00190.72370.0960.6046-0.0960.15850.49360.06930.5924-53.82110.7063-54.4871
135.4636-1.8053.33013.6279-4.57675.9999-0.50250.1011.3728-1.9070.79461.11670.1394-0.4065-0.19210.67010.00890.79860.3646-0.24650.913-98.501421.7547-100.5235
140.4672-0.9246-1.43063.24471.07598.8466-0.1282-2.55763.229-0.35020.27062.67380.51582.96910.5692.141-0.32050.26751.6325-0.20722.3248-98.346544.1388-97.9141
159.49582.0347-3.04754.28740.55618.41470.1455-0.09931.3954-0.09050.027-0.5526-0.13460.8972-0.06050.7614-0.14250.14920.7471-0.08091.3815-97.917830.1553-101.8119
162.90432.4624-1.60548.54541.01065.7869-0.0235-0.64671.86510.41370.1040.411-0.65720.61290.06450.59390.0140.0870.7068-0.05481.0244-101.393228.1354-95.931
178.80180.715.00123.97281.55649.66110.959-0.1452-0.5434-0.28110.07640.58370.9026-0.4121-0.19880.0592-0.06440.25660.2144-0.10140.3069-61.92946.1505-58.4366
183.85695.83664.9589.85946.89586.35390.58150.1553-0.72821.0450.5787-1.0953-0.0165-0.1478-0.70041.4753-0.1586-0.31371.96610.19791.3494-32.188311.4386-29.5027
193.7176-4.9355-3.10627.15195.16386.73650.47072.2107-1.5271-0.3963-0.58460.47890.6304-2.3552-0.69891.9098-0.0991-0.19731.7476-0.02951.3254-36.259924.6418-19.4131
202.4571-0.36580.83872.72352.46845.85270.94620.8303-0.8102-0.1043-0.0256-0.57172.14193.3816-1.11541.86160.027-0.34420.5211-0.33421.2166-33.621624.8486-2.3783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:75)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 76:114)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 115:161)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 162:236)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 237:246)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 247:307)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 308:324)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 325:357)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 358:382)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 383:393)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 394:406)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 407:493)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 494:528)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 529:538)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 539:594)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 595:654)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 655:705)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 706:719)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 720:725)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 726:743)

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