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- PDB-6upr: Crystal Structure of GTPase Domain of Human Septin 2 / Septin 8 H... -

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Basic information

Entry
Database: PDB / ID: 6upr
TitleCrystal Structure of GTPase Domain of Human Septin 2 / Septin 8 Heterocomplex
Components
  • Septin-2
  • Septin-8
KeywordsSTRUCTURAL PROTEIN / cytoskeleton protein / septin
Function / homology
Function and homology information


regulation of SNARE complex assembly / sperm annulus / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway ...regulation of SNARE complex assembly / sperm annulus / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge / cell division site / regulation of intracellular protein transport / axoneme / cleavage furrow / cilium assembly / Anchoring of the basal body to the plasma membrane / regulation of protein stability / protein localization / synaptic vesicle membrane / kinetochore / spindle / microtubule cytoskeleton / actin cytoskeleton / synaptic vesicle / presynapse / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cadherin binding / axon / GTPase activity / GTP binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Septin 8 / Septin 2 / 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-2 / Septin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsLeonardo, D.A. / Pereira, H.M. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
Sao Paulo Research Foundation (FAPESP)2016/04658-9 Brazil
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Molecular Recognition at Septin Interfaces: The Switches Hold the Key.
Authors: Rosa, H.V.D. / Leonardo, D.A. / Brognara, G. / Brandao-Neto, J. / D'Muniz Pereira, H. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionOct 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-2
B: Septin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3125
Polymers65,3212
Non-polymers9913
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-29 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.754, 82.773, 78.144
Angle α, β, γ (deg.)90.000, 103.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Septin-2 / / Neural precursor cell expressed developmentally down-regulated protein 5 / NEDD-5


Mass: 31691.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN2, DIFF6, KIAA0158, NEDD5, SEPT2 / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15019
#2: Protein Septin-8 /


Mass: 33630.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN8, KIAA0202, SEPT8 / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92599

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Non-polymers , 4 types, 90 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.: 87 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES/imidazole pH 6.5, 10% PEG 8000, 20% ethylene glycol and 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol and 1,3-propanediol

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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 X 16M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.299→82.8 Å / Num. obs: 28853 / % possible obs: 99.2 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.054 / Rrim(I) all: 0.142 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1 / % possible all: 99.5

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.3-2.367.11.6881495121080.7820.681.8211
10.29-82.86.20.04721613480.9940.0210.05234.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UPQ

6upq


Resolution: 2.299→55.959 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 1394 4.86 %Random selection
Rwork0.2083 ---
obs0.2105 28678 98.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.01 Å2 / Biso mean: 63.0132 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.299→55.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 0 61 87 4427
Biso mean--52.56 51.63 -
Num. residues----537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2994-2.38160.37831460.3406266797
2.3816-2.47690.37411430.3146266498
2.4769-2.58970.43231540.2968270598
2.5897-2.72620.32171440.2762268898
2.7262-2.8970.32511400.2679272498
2.897-3.12070.3011160.2542272298
3.1207-3.43470.31781360.2254276499
3.4347-3.93160.23161390.1943276299
3.9316-4.95290.17561280.1576278399
4.9529-55.9590.19981480.1702280599
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)
14.53871.3528-2.15434.9513-3.33815.5560.0884-0.23640.12060.33320.09940.1612-0.9669-0.488-0.2250.59030.1256-0.10480.5173-0.07490.43152.342811.292813.6275
24.97541.10763.16082.79612.47194.773-0.1421-0.25080.2397-0.13570.02590.2056-0.2385-0.76250.03810.43820.0777-0.06260.5574-0.05360.4794-6.17932.74595.9844
32.1290.56551.31072.6342-0.10512.70920.19230.4538-0.3212-0.10490.0152-0.37770.29950.374-0.20020.47390.1029-0.080.5325-0.10760.427716.30872.79915.4947
49.09596.22744.54465.53632.8133.7787-0.28861.02150.0483-0.44880.41570.1629-0.04470.3091-0.14030.46280.1488-0.0330.5413-0.11710.42068.94954.88510.0724
53.35991.028-1.28283.4066-1.88544.46650.26630.4523-0.40670.06440.0697-0.32540.53150.5291-0.38520.6730.1351-0.20610.5913-0.1050.536525.672-2.246232.3601
62.5484-1.41461.51472.2836-1.26538.89150.04580.1851-0.1553-0.2541-0.0527-0.02450.74740.2878-0.01060.65610.0554-0.16560.4046-0.04060.466921.377-5.73341.5928
70.18030.4402-0.57210.869-0.90681.85730.09740.1056-0.0520.0717-0.0661-0.039-0.0473-0.1191-0.03360.64620.0765-0.16250.5746-0.06930.489117.08856.009438.8173
89.51861.43960.94318.5207-0.34348.73230.4279-1.08350.76771.6590.1895-0.8446-0.54020.2409-0.58340.83130.1263-0.07760.7481-0.18660.523922.551718.239546.55
91.32710.6753-2.23781.7431-1.61633.77580.1333-0.2013-0.04860.4387-0.1028-0.2846-0.35690.49410.01740.5333-0.0081-0.15760.5746-0.10080.482831.237112.119532.2916
105.0498-1.0956-0.01816.8182-4.57656.44420.1140.2032-0.6329-0.176-0.22060.741-0.0923-0.3034-0.06010.7180.0889-0.17710.6191-0.16160.625911.681-3.723757.8509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 81 )A36 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 147 )A82 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 257 )A148 - 257
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 305 )A258 - 305
5X-RAY DIFFRACTION5chain 'B' and (resid 39 through 78 )B39 - 78
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 132 )B79 - 132
7X-RAY DIFFRACTION7chain 'B' and (resid 133 through 207 )B133 - 207
8X-RAY DIFFRACTION8chain 'B' and (resid 208 through 230 )B208 - 230
9X-RAY DIFFRACTION9chain 'B' and (resid 231 through 291 )B231 - 291
10X-RAY DIFFRACTION10chain 'B' and (resid 292 through 307 )B292 - 307

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