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- PDB-8dkt: Crystal Structure of Septin1 - Septin2 heterocomplex from Drosoph... -

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Basic information

Entry
Database: PDB / ID: 8dkt
TitleCrystal Structure of Septin1 - Septin2 heterocomplex from Drosophila melanogaster
Components
  • Septin-1
  • Septin-2
KeywordsCELL CYCLE / Septin
Function / homology
Function and homology information


growth of a germarium-derived egg chamber / imaginal disc development / cellularization / septin complex / imaginal disc-derived wing morphogenesis / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / cell division site / cleavage furrow ...growth of a germarium-derived egg chamber / imaginal disc development / cellularization / septin complex / imaginal disc-derived wing morphogenesis / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / cell division site / cleavage furrow / protein localization / spindle / microtubule cytoskeleton / synaptic vesicle / molecular adaptor activity / regulation of cell cycle / positive regulation of apoptotic process / GTPase activity / ubiquitin protein ligase binding / GTP binding / protein homodimerization activity
Similarity search - Function
Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Septin-1 / Septin-2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
Authorsde Freitas, A.F. / Leonardo, D.A. / Cavini, I.A. / Pereira, H.M. / Garratt, R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2020/02897-1 Brazil
CitationJournal: Cytoskeleton (Hoboken) / Year: 2023
Title: Conservation and divergence of the G-interfaces of Drosophila melanogaster septins.
Authors: de Freitas Fernandes, A. / Leonardo, D.A. / Cavini, I.A. / Rosa, H.V.D. / Vargas, J.A. / D'Muniz Pereira, H. / Nascimento, A.S. / Garratt, R.C.
History
DepositionJul 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-1
B: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9265
Polymers63,9352
Non-polymers9913
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-34 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.577, 149.423, 155.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Septin-1 / / DIFF6 protein homolog / Protein innocent bystander


Mass: 31558.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sep1, Diff6, iby, CG1403 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P42207
#2: Protein Septin-2 /


Mass: 32377.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sep2, CG4173 / Plasmid: pET Duet / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P54359

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Non-polymers , 4 types, 42 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol; 0.1 M MES/imidazole pH 6.5; 0.02 M of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium l-tartrate, sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.38→42.56 Å / Num. obs: 15075 / % possible obs: 43.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 57.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.041 / Rrim(I) all: 0.159 / Net I/σ(I): 11.1
Reflection shellResolution: 2.38→2.747 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.548 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9267 / CC1/2: 0.632 / Rpim(I) all: 0.459 / Rrim(I) all: 1.616 / % possible all: 6.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UPQ

6upq


Resolution: 2.38→42.56 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 750 4.98 %
Rwork0.2168 14316 -
obs0.2188 15066 43.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.89 Å2 / Biso mean: 69.4938 Å2 / Biso min: 22.82 Å2
Refinement stepCycle: final / Resolution: 2.38→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 61 39 4194
Biso mean--53.56 46.07 -
Num. residues----526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.38-2.560.265290.38412152243
2.56-2.820.4586420.373375679812
2.82-3.220.3857840.32861702178626
3.22-4.060.29522450.25264817506273
4.06-42.560.22213700.188268267196100
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)
18.06161.2574-0.97130.482-1.23374.15390.09340.37330.0707-1.6808-0.12830.281-0.5858-0.15860.04551.0113-0.031-0.17360.3403-0.030.3318-24.468713.4537-29.307
22.96681.5241-0.45993.54170.09191.8561-0.10230.02040.0706-0.3741-0.0104-0.2351-0.60790.01790.060.70540.0112-0.06080.18-0.00840.2753-21.413912.8658-15.1612
35.48971.2277-0.64732.18970.09871.94140.43370.05330.33630.0575-0.16780.2848-0.5853-0.394-0.24320.97790.1547-0.20110.2745-0.02840.3993-30.5620.7384-17.5449
40.36660.00021.02872.12231.09413.4138-0.0398-0.0188-0.43220.0876-0.55331.33450.3459-1.09670.42220.5044-0.1627-0.03720.3896-0.18210.866-41.6269-14.2017-9.7652
57.23615.12260.28784.6023-0.48211.09070.04250.1523-1.59010.2725-0.2011-0.4650.6305-0.35210.14740.655-0.167-0.03370.3189-0.1430.504-33.1967-14.9967-12.2461
60.57161.61-0.28664.7347-0.33421.13340.4303-0.58740.01660.9287-0.1544-0.69610.5735-0.2429-0.15730.6656-0.2574-0.07660.4586-0.12860.772-32.2878-31.8336-12.8071
71.3034-3.0481-1.87419.22413.6912.932-0.4157-0.82510.42841.3911-0.10511.37670.6577-0.05510.44710.7562-0.28070.00970.6336-0.13860.9458-41.2199-37.0819-10.7081
81.78691.3205-0.19531.69780.0051.4873-0.18080.8479-0.4628-0.5678-0.23180.0275-0.068-0.36850.26210.3687-0.0676-0.18120.5761-0.18490.6477-35.4181-11.6533-23.7131
92.59630.145-0.7051.3496-0.92383.5458-0.56170.2864-0.4001-0.59320.0960.78060.135-1.0651-0.13330.4864-0.1254-0.3740.6711-0.21140.8554-44.4013-13.6895-30.8177
101.6127-0.1448-0.21550.01070.020.0262-0.1280.35680.0935-0.3575-0.28191.2267-0.1212-1.10710.37490.44190.1158-0.17670.9157-0.14720.9976-54.85060.6221-19.0226
111.76910.1332-0.33960.3201-0.16362.2548-0.22540.0725-0.19090.1691-0.23380.6820.6985-0.6353-0.12510.5595-0.3465-0.14530.5506-0.24141.1628-40.9055-29.1555-21.718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 99 )A34 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 219 )A100 - 219
3X-RAY DIFFRACTION3chain 'A' and (resid 220 through 304 )A220 - 304
4X-RAY DIFFRACTION4chain 'B' and (resid 41 through 89 )B41 - 89
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 116 )B90 - 116
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 135 )B117 - 135
7X-RAY DIFFRACTION7chain 'B' and (resid 136 through 150 )B136 - 150
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 191 )B151 - 191
9X-RAY DIFFRACTION9chain 'B' and (resid 192 through 243 )B192 - 243
10X-RAY DIFFRACTION10chain 'B' and (resid 244 through 271 )B244 - 271
11X-RAY DIFFRACTION11chain 'B' and (resid 272 through 308 )B272 - 308

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