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- PDB-5a3f: Crystal structure of the dynamin tetramer -

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Basic information

Entry
Database: PDB / ID: 5a3f
TitleCrystal structure of the dynamin tetramer
ComponentsDYNAMIN 3
KeywordsENDOCYTOSIS / MEMBRANE REMODELING / GTPASE
Function / homology
Function and homology information


synaptic vesicle budding from presynaptic endocytic zone membrane / dynamin GTPase / Retrograde neurotrophin signalling / Toll Like Receptor 4 (TLR4) Cascade / filopodium assembly / Recycling pathway of L1 / synapse assembly / MHC class II antigen presentation / receptor internalization / endocytosis ...synaptic vesicle budding from presynaptic endocytic zone membrane / dynamin GTPase / Retrograde neurotrophin signalling / Toll Like Receptor 4 (TLR4) Cascade / filopodium assembly / Recycling pathway of L1 / synapse assembly / MHC class II antigen presentation / receptor internalization / endocytosis / presynapse / Clathrin-mediated endocytosis / microtubule binding / dendritic spine / microtubule / postsynaptic density / GTPase activity / synapse / GTP binding / perinuclear region of cytoplasm / extracellular exosome / 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 / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsReubold, T.F. / Faelber, K. / Plattner, N. / Posor, Y. / Branz, K. / Curth, U. / Schlegel, J. / Anand, R. / Manstein, D.J. / Noe, F. ...Reubold, T.F. / Faelber, K. / Plattner, N. / Posor, Y. / Branz, K. / Curth, U. / Schlegel, J. / Anand, R. / Manstein, D.J. / Noe, F. / Haucke, V. / Daumke, O. / Eschenburg, S.
CitationJournal: Nature / Year: 2015
Title: Crystal Structure of the Dynamin Tetramer
Authors: Reubold, T.F. / Faelber, K. / Plattner, N. / Posor, Y. / Ketel, K. / Curth, U. / Schlegel, J. / Anand, R. / Manstein, D.J. / Noe, F. / Haucke, V. / Daumke, O. / Eschenburg, S.
History
DepositionMay 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DYNAMIN 3
B: DYNAMIN 3
C: DYNAMIN 3
D: DYNAMIN 3


Theoretical massNumber of molelcules
Total (without water)343,3774
Polymers343,3774
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-40.5 kcal/mol
Surface area128920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.696, 98.002, 401.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein
DYNAMIN 3 / DYNAMIN


Mass: 85844.289 Da / Num. of mol.: 4 / Fragment: DYNAMIN 3 - DELTA PRD, UNP RESIDUES 1-764 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UQ16, dynamin GTPase
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.9 % / Description: NONE
Crystal growpH: 6.5 / Details: 15% MPD, 100MM MES/NAOH (PH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2011 / Details: MIRRORS
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→49.47 Å / Num. obs: 42081 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.83 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2AKA, 3SNH, 1DYN

2aka

3snh

1dyn


Resolution: 3.7→49.465 Å / SU ML: 0.56 / σ(F): 1.99 / Phase error: 29.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 2086 5 %
Rwork0.2316 --
obs0.2339 42058 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→49.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18654 0 0 0 18654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.78610.37481500.3272622X-RAY DIFFRACTION99
3.7861-3.88070.33321380.31522601X-RAY DIFFRACTION100
3.8807-3.98560.34631540.28932605X-RAY DIFFRACTION99
3.9856-4.10280.30161380.27372617X-RAY DIFFRACTION100
4.1028-4.23520.25691130.24992653X-RAY DIFFRACTION100
4.2352-4.38640.27051300.23522607X-RAY DIFFRACTION99
4.3864-4.5620.23431270.21642650X-RAY DIFFRACTION99
4.562-4.76940.22121410.19182639X-RAY DIFFRACTION99
4.7694-5.02060.26581580.20782612X-RAY DIFFRACTION100
5.0206-5.33490.33451420.22732674X-RAY DIFFRACTION100
5.3349-5.74620.33221500.27032693X-RAY DIFFRACTION100
5.7462-6.32340.3411290.26622658X-RAY DIFFRACTION100
6.3234-7.2360.36661300.25932717X-RAY DIFFRACTION100
7.236-9.10730.27791340.21052753X-RAY DIFFRACTION100
9.1073-49.46920.22341520.20732871X-RAY DIFFRACTION99
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)
10.37070.27420.76912.43080.85251.61370.90021.00520.25330.5971-0.0662-0.59-0.8905-3.6723-0.05742.04730.9416-0.32883.58020.72762.2967-23.95927.6345-137.2335
24.6856-0.7686-1.12228.61730.12011.2950.02760.65890.30070.6826-0.4338-0.96510.5520.93910.00191.56750.2459-0.43522.55570.36321.7844-43.896350.9446-147.3686
32.9658-0.3021.15043.44441.90038.236-0.07690.03060.0784-0.6088-0.22150.2848-1.11330.3616-0.01861.3986-0.03140.07120.61130.03871.3446-8.425925.8118-82.7027
46.351-0.5267-0.99476.7745-0.61236.3540.4416-0.06790.45070.6527-0.41680.5424-0.654-0.49740.00051.74550.05740.1571.0620.13591.3905-3.301453.2904-90.661
51.91281.1863-0.74440.7707-0.59690.8577-0.92530.4370.85370.95990.9069-0.15851.89990.7352-0.20253.39661.3065-0.48522.47820.34542.41373.09790.474336.8596
63.3499-0.4479-1.77962.9415-0.59989.411-0.2069-0.5668-0.1631-0.0139-0.0209-0.0159-0.1931.30650.00710.6093-0.0216-0.0391.4346-0.03851.33031.768816.8358-18.336
78.253-0.99340.83743.30740.37532.5403-0.35550.81540.4930.22850.0192-0.4247-1.1646-0.40450.00122.72490.2476-0.33791.46950.36711.816526.3281-19.602946.9838
86.4371-0.26451.93675.03351.55996.8782-0.47230.6192-0.67680.05450.6796-0.34050.35320.9320.0060.98290.0296-0.08151.8798-0.18971.380628.739121.0599-9.7121
93.70711.70151.37330.84210.13763.6320.622-0.24450.716-0.0255-1.0867-0.131-0.3659-0.3549-0.06181.21510.29410.07670.72710.46721.375117.0433-18.1754-2.9838
101.52911.27530.94171.58080.71710.5704-0.255-2.09130.47041.8426-0.28930.2794-0.9443-0.30940.00433.5316-0.22510.30172.68860.30252.4521-7.8656-12.5403-22.9549
114.3940.9225-0.87813.0467-1.19793.7367-0.0211-0.1195-0.4065-0.1263-0.1739-0.7032-0.15780.76130.00041.3016-0.1150.12060.9947-0.01811.37563.49229.8958-70.2033
120.72110.6843-0.65251.5612-0.66960.58860.23451.7899-0.2083-1.8305-0.9574-0.85550.90230.17460.03651.86960.1434-0.12813.1464-0.17441.9223-37.044616.6811-77.7659
131.65972.2025-0.49353.7972-1.26382.4748-1.4877-0.65460.4184-0.15371.2413-0.6370.0879-0.1187-0.02440.80640.1528-0.4091.5371-0.03691.2722-42.494241.8056-97.4307
143.1641.88061.07424.92081.55065.5611-0.10540.0680.7696-0.0568-0.0330.5531-0.75470.1892-0.00411.0541-0.05310.02831.1551-0.07681.4299-14.561727.9859-30.1961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 6:31 OR RESSEQ 295:320 OR RESSEQ 699:735)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 32:294)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 321:507 OR RESSEQ 635:698)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 508:634)
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESSEQ 6:31 OR RESSEQ 295:320 OR RESSEQ 699:735)
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESSEQ 321:507 OR RESSEQ 635:698)
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESSEQ 32:294)
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESSEQ 508:634)
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESSEQ 32:294)
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESSEQ 6:31 OR RESSEQ 295:320 OR RESSEQ 699:735)
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESSEQ 321:507 OR RESSEQ 635:698)
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESSEQ 6:31 OR RESSEQ 295:320 OR RESSEQ 699:735)
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESSEQ 32:294)
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESSEQ 321:507 OR RESSEQ 635:698)

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