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- PDB-6uqq: Crystal Structure of GTPase Domain of Human Septin 7 / Septin 3 T... -

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Basic information

Entry
Database: PDB / ID: 6uqq
TitleCrystal Structure of GTPase Domain of Human Septin 7 / Septin 3 T282Y Heterocomplex
Components
  • Neuronal-specific septin-3
  • Septin-7
KeywordsSTRUCTURAL PROTEIN / cytoskeleton protein / septin
Function / homology
Function and homology information


regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / septin ring / cytoskeleton-dependent cytokinesis / non-motile cilium / cell division site / cleavage furrow / axoneme ...regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / septin ring / cytoskeleton-dependent cytokinesis / non-motile cilium / cell division site / cleavage furrow / axoneme / cilium assembly / stress fiber / MAPK6/MAPK4 signaling / kinetochore / spindle / intracellular protein localization / presynapse / microtubule cytoskeleton / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Septin 3 / Septin 7 / 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 / Septin-7 / Neuronal-specific septin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBragnara, G. / Pereira, H.M. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 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 21, 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 1.3Apr 14, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 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-7
B: Septin-7
C: Neuronal-specific septin-3
D: Neuronal-specific septin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1258
Polymers133,3524
Non-polymers1,7734
Water2,702150
1
A: Septin-7
hetero molecules

C: Neuronal-specific septin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5624
Polymers66,6762
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area4870 Å2
ΔGint-24 kcal/mol
Surface area24980 Å2
MethodPISA
2
B: Septin-7
hetero molecules

D: Neuronal-specific septin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5624
Polymers66,6762
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
Buried area4550 Å2
ΔGint-23 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.390, 85.526, 152.051
Angle α, β, γ (deg.)90.000, 90.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Septin-7 / CDC10 protein homolog


Mass: 32757.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT7, CDC10 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q16181
#2: Protein Neuronal-specific septin-3


Mass: 33918.562 Da / Num. of mol.: 2 / Mutation: T282Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN3, SEP3, SEPT3 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UH03
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole pH 6.5 and 20mM 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: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.75→61.381 Å / Num. obs: 38827 / % possible obs: 94.8 % / Redundancy: 3.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.098 / Rrim(I) all: 0.197 / Net I/σ(I): 5.7
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
2.75-2.873.60.9221706847890.6040.5481.081.396.4
9.53-61.383.50.05633029390.9940.0340.06616.591.6

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QNR, 4Z54

2qnr

4z54


Resolution: 2.75→61.381 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.52
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 1902 4.91 %Random selection
Rwork0.197 ---
obs0.1999 38766 94.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.22 Å2 / Biso mean: 61.6106 Å2 / Biso min: 5.15 Å2
Refinement stepCycle: final / Resolution: 2.75→61.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8162 0 112 150 8424
Biso mean--49.84 44.26 -
Num. residues----1049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038470
X-RAY DIFFRACTIONf_angle_d0.55911508
X-RAY DIFFRACTIONf_chiral_restr0.0451298
X-RAY DIFFRACTIONf_plane_restr0.0041485
X-RAY DIFFRACTIONf_dihedral_angle_d15.6275097
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.81880.36571340.3065265495
2.8188-2.8950.33471590.2908262996
2.895-2.98020.34591330.2635266396
2.9802-3.07640.34461470.2548266895
3.0764-3.18630.34311510.2535261295
3.1863-3.31390.29911270.2325264195
3.3139-3.46470.29741330.2174266595
3.4647-3.64730.26741340.1903265195
3.6473-3.87580.26091460.1855263094
3.8758-4.1750.21061010.1681263794
4.175-4.5950.20441370.146261393
4.595-5.25960.20581260.1524262293
5.2596-6.62530.24181320.194257891
6.6253-61.3810.19131420.1761260190
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)
11.8992.5159-1.39675.90441.86486.78110.11470.1012-0.5723-0.1024-0.1902-0.22130.50140.10790.04270.38660.0822-0.12370.3294-0.00660.5143-4.4841-27.892-22.5964
24.69611.19323.02662.26661.57626.70650.05370.3597-0.2782-0.5701-0.12220.4369-0.14740.35320.09630.40070.1107-0.13150.3163-0.0720.4091-0.2483-19.8448-30.0531
31.93730.6206-1.73381.0351-1.60258.38880.06550.28220.0458-0.2357-0.13230.16750.1681-0.15170.0120.37460.0669-0.14510.2792-0.05370.4242-4.9437-14.4072-25.461
43.9755-1.16680.01732.0521-2.08322.99370.29850.15080.1231-0.5215-0.39720.3011-0.4505-0.38650.22890.52520.1994-0.11260.3624-0.05650.4279-12.8128-5.4661-16.7836
54.47041.1478-1.42093.77570.5775.34850.01920.1323-0.0813-0.90290.02761.31130.5197-1.2259-0.10450.2298-0.0582-0.13870.5997-0.03890.6687-19.8035-21.8927-9.815
61.8193-0.6451-0.3841.511-1.90089.1842-0.09260.7767-0.055-0.51060.14310.446-0.3173-1.0569-0.10550.69140.1509-0.31430.5196-0.08250.5598-11.1634-13.674-33.6605
74.99681.05051.1881.6992-0.16243.5231-0.5563-0.92530.7470.50940.41210.17060.221-0.35210.14390.88290.1441-0.06161.10590.11480.4966-30.2331-4.6096-70.1836
83.6540.97171.35111.63350.3170.5516-0.4185-0.1326-0.04270.5121-0.02540.1815-1.11150.33570.42440.98250.0793-0.10530.97350.12680.4815-23.7235-6.6247-74.9938
93.40940.49943.24651.1287-0.54544.02370.1219-0.2279-0.16130.38320.0452-0.0302-0.0834-0.1256-0.12680.86560.0211-0.15220.90790.14760.4648-20.2519-13.1356-70.0649
104.59120.1035-1.91980.42390.14020.9493-0.50760.188-0.04240.72190.7467-0.1340.8725-0.0872-0.18521.1581-0.0157-0.23850.9820.29280.666-29.4899-27.1642-75.8454
116.14782.6354-0.82891.49581.3157.57250.6195-1.317-1.52772.0345-0.00290.7720.82350.069-0.15381.15460.09410.04561.26660.30540.5933-37.6846-21.2532-69.3777
126.976-0.6660.6627.84153.22362.3235-0.4778-0.09220.48770.7960.97560.16070.721-1.1447-0.29350.71080.00960.03491.54890.32960.6609-51.3636-8.058-75.4152
131.66260.05152.38451.35250.08953.07140.3672-0.3686-0.29810.85470.08680.18870.2834-0.7539-0.51821.2341-0.0552-0.04781.24670.21060.4762-28.7912-16.1499-64.7901
142.2243-1.4507-1.51112.3061-1.14046.78840.0061-0.02870.28150.04920.067-0.1331-0.54210.5056-0.10750.2509-0.0491-0.07470.3597-0.00060.4236-3.962736.5662-7.313
153.5159-0.09753.80722.2144-1.34347.7706-0.2678-0.2596-0.0463-0.08650.1177-0.0133-0.3723-0.4780.16070.19960.0349-0.00810.1607-0.08770.4171-15.492635.0624-6.5909
163.1609-0.78381.35542.0576-0.21292.94680.1539-0.2588-0.4393-0.18270.13960.18180.4152-0.3249-0.28460.2422-0.0268-0.0310.21630.01570.3907-11.39521.6424-6.3723
176.34392.32691.95681.8977-0.32090.9648-0.03350.8094-0.4838-0.22290.2164-0.2750.20430.4643-0.10650.30020.04910.07420.4382-0.08250.44383.269619.5015-12.7867
186.9287-0.70652.36881.1277-0.8422.50370.01060.40570.1529-0.09860.00470.01810.17860.1050.04070.2693-0.0214-0.02050.1787-0.04990.2739-12.856625.2981-13.9715
191.59390.6359-0.41833.3549-0.33984.21360.31670.0908-0.2737-0.238-0.05330.08730.8123-0.5973-0.23970.4475-0.0067-0.11910.6021-0.15270.4545-24.029921.3759-49.1052
208.27464.36090.64185.6828-0.48367.7916-0.00260.7723-1.38280.13790.7852-1.16130.52141.6093-0.64580.53770.1283-0.10250.7307-0.24180.5866-19.328417.1017-39.4277
214.48542.28663.4752.57422.15562.9124-0.14160.3313-0.223-0.33040.06470.2342-0.1528-1.11960.08490.39790.0438-0.09270.7926-0.04680.5144-36.288927.3461-44.5479
221.58970.8169-1.20733.9528-5.63796.98520.1378-0.0077-0.1371-0.29240.12080.29660.6528-0.041-0.23070.3581-0.0821-0.0730.5019-0.05350.3537-26.139524.4465-32.682
233.46660.13270.19872.62241.00676.9595-0.10290.48590.1296-0.29180.1847-0.0967-0.8870.1316-0.05280.5311-0.0516-0.060.5244-0.0240.3813-20.886740.0994-50.6476
241.833-0.0275-2.72621.3019-0.01194.14580.10490.6643-0.6604-0.3343-0.0741-0.51630.25451.0687-0.06440.49250.1772-0.04581.1829-0.29380.632-8.206126.5883-55.0267
255.5474-3.0178-4.82898.91534.3185.37830.4558-0.9125-0.2580.089-0.17020.51660.029-0.2404-0.25730.52840.0108-0.22020.5185-0.01680.4001-28.191933.5849-31.1293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 101 )A49 - 101
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 145 )A102 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 200 )A146 - 200
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 232 )A201 - 232
5X-RAY DIFFRACTION5chain 'A' and (resid 233 through 281 )A233 - 281
6X-RAY DIFFRACTION6chain 'A' and (resid 282 through 316 )A282 - 316
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 100 )B49 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 127 )B101 - 127
9X-RAY DIFFRACTION9chain 'B' and (resid 128 through 200 )B128 - 200
10X-RAY DIFFRACTION10chain 'B' and (resid 201 through 234 )B201 - 234
11X-RAY DIFFRACTION11chain 'B' and (resid 235 through 252 )B235 - 252
12X-RAY DIFFRACTION12chain 'B' and (resid 253 through 267 )B253 - 267
13X-RAY DIFFRACTION13chain 'B' and (resid 268 through 316 )B268 - 316
14X-RAY DIFFRACTION14chain 'C' and (resid 59 through 112 )C59 - 112
15X-RAY DIFFRACTION15chain 'C' and (resid 113 through 156 )C113 - 156
16X-RAY DIFFRACTION16chain 'C' and (resid 157 through 244 )C157 - 244
17X-RAY DIFFRACTION17chain 'C' and (resid 245 through 282 )C245 - 282
18X-RAY DIFFRACTION18chain 'C' and (resid 283 through 338 )C283 - 338
19X-RAY DIFFRACTION19chain 'D' and (resid 59 through 105 )D59 - 105
20X-RAY DIFFRACTION20chain 'D' and (resid 106 through 125 )D106 - 125
21X-RAY DIFFRACTION21chain 'D' and (resid 126 through 156 )D126 - 156
22X-RAY DIFFRACTION22chain 'D' and (resid 157 through 178 )D157 - 178
23X-RAY DIFFRACTION23chain 'D' and (resid 179 through 256 )D179 - 256
24X-RAY DIFFRACTION24chain 'D' and (resid 257 through 308 )D257 - 308
25X-RAY DIFFRACTION25chain 'D' and (resid 309 through 329 )D309 - 329

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