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- PDB-6upq: Crystal Structure of GTPase Domain of Human Septin 2 / Septin 11 ... -

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Basic information

Entry
Database: PDB / ID: 6upq
TitleCrystal Structure of GTPase Domain of Human Septin 2 / Septin 11 Heterocomplex
Components
  • Septin-11
  • Septin-2
KeywordsSTRUCTURAL PROTEIN / cytoskeleton protein / septin
Function / homology
Function and homology information


postsynaptic specialization of symmetric synapse / sperm annulus / protein localization => GO:0008104 / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane ...postsynaptic specialization of symmetric synapse / sperm annulus / protein localization => GO:0008104 / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / cell division site / axoneme / cleavage furrow / cilium assembly / GABA-ergic synapse / stress fiber / Anchoring of the basal body to the plasma membrane / kinetochore / spindle / microtubule cytoskeleton / actin cytoskeleton / synaptic vesicle / midbody / spermatogenesis / dendritic spine / molecular adaptor activity / cell differentiation / cadherin binding / axon / GTPase activity / glutamatergic synapse / GTP binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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-11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3315
Polymers65,3412
Non-polymers9913
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-31 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.654, 81.859, 68.221
Angle α, β, γ (deg.)90.000, 97.130, 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-11


Mass: 33649.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN11, SEPT11 / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9NVA2

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Non-polymers , 4 types, 501 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-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


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


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES/imidazole pH 6.5, 10% PEG 20000, 20% PEG 550 MME and 30mM of each sodium nitrate, disodium hydrogen phosphate and ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.86→67.7 Å / Num. obs: 51728 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.973 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.08 / Rrim(I) all: 0.208 / Net I/σ(I): 5.8 / Num. measured all: 347126 / Scaling rejects: 910
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.86-1.916.83.1262567637980.4531.2923.3870.998.9
8.32-67.76.40.0639146110.9960.0260.06515.599.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UPA

6upa


Resolution: 1.86→56.216 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.59
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 2567 4.97 %Random selection
Rwork0.1867 ---
obs0.1882 51621 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.71 Å2 / Biso mean: 37.0276 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: final / Resolution: 1.86→56.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 61 498 4689
Biso mean--21.2 41.32 -
Num. residues----517
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.86-1.89570.39171430.3696268798
1.8957-1.93440.39811610.3687264298
1.9344-1.97640.33251560.2835268799
1.9764-2.02240.30181340.2581272899
2.0224-2.0730.29151350.2376271699
2.073-2.1290.2631370.2312271099
2.129-2.19170.24231390.2131270899
2.1917-2.26240.29811390.2618272799
2.2624-2.34330.23961350.2007268499
2.3433-2.43710.22471440.197274099
2.4371-2.5480.251460.18442729100
2.548-2.68240.20381370.18272724100
2.6824-2.85040.21261330.17872764100
2.8504-3.07050.20091380.17512724100
3.0705-3.37950.19021350.16462753100
3.3795-3.86840.19261660.15452746100
3.8684-4.87330.1751290.14092785100
4.8733-56.2160.17031600.1612800100
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)
17.72013.06760.77435.35253.52582.8564-0.09360.15690.2093-0.22420.10920.0851-0.2163-0.16320.01860.14160.02470.01910.15420.0010.14537.15739.8846.9492
24.0408-0.89732.6552.096-0.57584.8431-0.1264-0.36460.22950.10910.034-0.081-0.4515-0.6218-0.02950.28060.10060.01370.4257-0.04110.31433.279712.152919.5096
35.5579-0.27891.61815.8366-1.56947.27640.08451.04690.6879-0.6104-0.1850.2122-1.15820.12490.09770.48190.0742-0.02150.5280.09750.4177-0.36414.7634-0.1286
40.27210.2702-0.0730.4915-0.7221.73150.2986-0.8087-0.15690.0171-0.09780.05390.5722-0.9776-0.19780.3408-0.0697-0.03760.39180.05270.30123.9681-0.526321.2737
56.18921.30861.51881.77821.06622.4086-0.22470.22380.4073-0.26390.00840.5207-0.3369-0.71110.12030.2730.0376-0.07650.386-0.01440.3595-11.71210.91291.826
64.37251.30660.75860.9421-0.07891.41360.09110.0491-0.2213-0.0919-0.0168-0.01890.171-0.012-0.10410.20080.01790.00580.1834-0.03960.192712.2656-1.04299.4198
79.03487.45791.07578.70631.51993.7476-0.04820.5989-1.1049-0.24170.1732-0.84080.35130.3893-0.06840.25360.1186-0.00090.2688-0.07290.30523.1827-5.04126.2482
83.24170.52811.07212.1681.80311.63310.01240.9196-0.1537-1.2878-0.2054-0.18820.63630.35960.13350.54010.07040.03580.4695-0.07690.302511.1904-5.4291-7.2257
92.16480.51350.76772.9480.71921.9009-0.01420.6512-0.2071-0.7538-0.0648-0.0487-0.12590.1929-0.0010.33790.04550.02710.4675-0.03290.212218.3665.5254-4.9757
101.4646-1.5711.71782.0304-0.49047.1901-0.08250.83650.8548-0.9193-0.1749-0.7591-0.52250.68630.01720.4406-0.06480.02010.36890.14030.477324.196223.38094.6454
115.21563.30141.90233.46941.1891.512-0.20550.5370.0057-0.26520.23650.1433-0.06080.0513-0.0120.20210.0310.01170.2464-0.00260.18057.7143.5911-1.7007
124.9071.96821.45872.76981.05773.81260.10660.2793-0.2670.10840.1042-0.3560.33890.5696-0.24740.20690.0802-0.0170.23110.01470.23933.3076-1.690927.9244
133.2316-1.25671.83512.5359-0.04884.78750.12710.2311-0.11390.1665-0.0363-0.29540.29420.5146-0.07320.26660.0125-0.01460.23840.05240.261627.5165-5.982430.8072
140.4599-0.51241.16941.7378-2.78945.351-0.0161-0.0409-0.03130.1078-0.037-0.106-0.0543-0.00670.02280.22460.0137-0.02110.1897-0.01570.217525.6363-0.773839.3667
156.4660.6501-3.76684.4383-2.38963.8129-0.0587-0.050.54460.07150.23860.1724-0.6588-0.5806-0.3320.30160.0788-0.05690.2313-0.03740.277118.818318.099327.0725
162.59060.378-2.68761.2944-0.71485.21280.0025-0.15130.17980.1746-0.0291-0.2429-0.12720.197-0.07040.2050.0171-0.0450.2108-0.00640.250633.773711.17224.0711
170.57410.7181-1.21322.1064-3.83188.59380.0855-0.1717-0.00690.5116-0.2883-0.2746-0.82590.62990.15440.27680.0217-0.03910.2508-0.00830.267133.2788.556235.6691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 58 )A36 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 81 )A59 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 101 )A82 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 115 )A102 - 115
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 147 )A116 - 147
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 188 )A148 - 188
7X-RAY DIFFRACTION7chain 'A' and (resid 189 through 205 )A189 - 205
8X-RAY DIFFRACTION8chain 'A' and (resid 206 through 221 )A206 - 221
9X-RAY DIFFRACTION9chain 'A' and (resid 222 through 244 )A222 - 244
10X-RAY DIFFRACTION10chain 'A' and (resid 245 through 258 )A245 - 258
11X-RAY DIFFRACTION11chain 'A' and (resid 259 through 305 )A259 - 305
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 72 )B40 - 72
13X-RAY DIFFRACTION13chain 'B' and (resid 73 through 114 )B73 - 114
14X-RAY DIFFRACTION14chain 'B' and (resid 115 through 189 )B115 - 189
15X-RAY DIFFRACTION15chain 'B' and (resid 190 through 206 )B190 - 206
16X-RAY DIFFRACTION16chain 'B' and (resid 207 through 255 )B207 - 255
17X-RAY DIFFRACTION17chain 'B' and (resid 256 through 300 )B256 - 300

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