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- PDB-6n0b: Structure of GTPase Domain of Human Septin 7 at High Resolution -

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Basic information

Entry
Database: PDB / ID: 6n0b
TitleStructure of GTPase Domain of Human Septin 7 at High Resolution
ComponentsSeptin-7
KeywordsSTRUCTURAL PROTEIN / cytoskeleton component septin GTPase
Function / homology
Function and homology information


regulation of embryonic cell shape / sperm annulus / septin complex / positive regulation of non-motile cilium assembly / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / cleavage furrow ...regulation of embryonic cell shape / sperm annulus / septin complex / positive regulation of non-motile cilium assembly / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / cleavage furrow / cilium assembly / stress fiber / MAPK6/MAPK4 signaling / spindle / kinetochore / microtubule cytoskeleton / midbody / spermatogenesis / cell differentiation / molecular adaptor activity / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Septin 7 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Septin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.739 Å
AuthorsBrognara, 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.Struct.Biol. / Year: 2019
Title: Revisiting SEPT7 and the slippage of beta-strands in the septin family.
Authors: Brognara, G. / Pereira, H.M. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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
C: Septin-7
A: Septin-7
B: Septin-7
D: Septin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,8028
Polymers131,0294
Non-polymers1,7734
Water15,979887
1
C: Septin-7
hetero molecules

D: Septin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4014
Polymers65,5152
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area4610 Å2
ΔGint-24 kcal/mol
Surface area23280 Å2
MethodPISA
2
A: Septin-7
B: Septin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4014
Polymers65,5152
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-21 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.513, 68.866, 150.519
Angle α, β, γ (deg.)90.000, 112.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Septin-7 / / CDC10 protein homolog


Mass: 32757.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT7, CDC10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16181
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.1 M MOPS/HEPES-Na pH 7.5, 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 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.739→69.85 Å / Num. obs: 146736 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 28.89 Å2 / CC1/2: 0.0998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Net I/σ(I): 14
Reflection shellResolution: 1.739→1.79 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.063 / Num. unique obs: 10760 / CC1/2: 0.825 / Rpim(I) all: 0.447 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QNR

2qnr


Resolution: 1.739→62.877 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 7282 4.97 %Randon selection
Rwork0.174 ---
obs0.1754 146423 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.57 Å2 / Biso mean: 41.9481 Å2 / Biso min: 20.8 Å2
Refinement stepCycle: final / Resolution: 1.739→62.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8005 0 112 887 9004
Biso mean--28.92 47.6 -
Num. residues----1016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088337
X-RAY DIFFRACTIONf_angle_d0.96111330
X-RAY DIFFRACTIONf_chiral_restr0.0671286
X-RAY DIFFRACTIONf_plane_restr0.0051445
X-RAY DIFFRACTIONf_dihedral_angle_d14.5315060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7391-1.75890.37232430.32034498474197
1.7589-1.77960.31282350.286746474882100
1.7796-1.80130.2982280.265645724800100
1.8013-1.82410.28812350.255346254860100
1.8241-1.84810.28582380.231446574895100
1.8481-1.87340.24162460.219545294775100
1.8734-1.90020.24282140.226546804894100
1.9002-1.92860.28872500.27284593484399
1.9286-1.95870.23932450.208845674812100
1.9587-1.99080.21392460.194446214867100
1.9908-2.02510.23692920.18946044896100
2.0251-2.0620.22532530.197545874840100
2.062-2.10160.24672230.197346184841100
2.1016-2.14450.22162540.183946414895100
2.1445-2.19120.21372570.178945934850100
2.1912-2.24210.20172370.180346544891100
2.2421-2.29820.21142310.177646514882100
2.2982-2.36030.22012160.1746344850100
2.3603-2.42980.22382200.177846664886100
2.4298-2.50820.19942420.177946704912100
2.5082-2.59790.20412310.174546324863100
2.5979-2.70190.19922410.178446574898100
2.7019-2.82490.21522550.173746374892100
2.8249-2.97380.18682370.176446924929100
2.9738-3.16010.21052560.173946524908100
3.1601-3.40410.19322440.169446564900100
3.4041-3.74660.19122570.156446764933100
3.7466-4.28860.17772640.147546974961100
4.2886-5.40280.16632570.138147124969100
5.4028-62.9180.18942350.17784823505899
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)
15.5308-0.01422.94662.71743.44426.0472-0.02830.34070.0863-0.43670.11720.111-0.08060.1601-0.10890.3332-0.0474-0.01870.28870.03870.2283-9.3994-38.257542.6768
21.76680.13610.50380.92990.02810.9588-0.0066-0.09190.09690.00240.0540.13730.1315-0.0864-0.06090.233-0.04160.00860.2498-0.00370.1977-11.2327-36.196956.4834
36.8032-1.7234-0.8861.78830.75961.43390.02530.1317-0.33750.00680.02760.09360.293-0.07920.00150.3261-0.0461-0.020.2194-0.01020.1997-7.8366-46.152451.8641
43.23131.26310.90352.8952-1.31724.00010.0557-0.0657-0.21010.0775-0.0363-0.29950.34380.0906-0.03560.31030.0448-0.02810.2459-0.03590.2125-21.7047-41.111324.0682
53.40240.06310.64328.7666-4.99185.2184-0.1396-0.27240.2568-0.10090.67960.8284-0.1762-0.7142-0.39260.46010.0367-0.09090.4011-0.00290.3596-20.0425-38.974831.1812
64.6989-1.47311.01981.6458-1.06061.7213-0.0786-0.10710.42430.03890.0799-0.20510.11970.0752-0.00260.30430.0668-0.02780.3002-0.07910.2653-13.8388-31.323823.0648
74.71170.62980.29021.04580.25010.58020.0073-0.0345-0.0402-0.00790.0393-0.18580.07450.0672-0.04750.29240.0708-0.00520.3009-0.01760.2341-17.4824-35.037915.9997
87.20974.0402-1.36124.985-0.2522.79360.04070.8220.0547-0.38530.04760.01610.0556-0.0235-0.04870.35830.0604-0.0370.38240.0040.1974-30.2613-38.5723.0867
91.36842.00350.47558.77224.05432.1849-0.00950.1849-0.19770.35250.3296-0.45660.35520.0769-0.32420.33130.0536-0.0220.4334-0.02970.2333-18.9637-46.82714.238
105.06410.3301-0.76512.56270.26332.39850.2451-0.6433-1.12160.4206-0.24620.22760.36060.04750.04890.4589-0.0443-0.08540.32730.11130.4715-34.9391-52.383222.3289
119.14072.3332-0.33352.2215-0.44930.63780.06580.4348-0.498-0.04810.0307-0.26720.20670.1261-0.08320.34760.096-0.02050.3106-0.04080.1729-16.118-43.794615.2702
125.3299-0.6689-0.68544.71140.70054.24510.0740.3597-0.0409-0.3659-0.09870.35970.1137-0.42670.01730.2303-0.0028-0.03170.30540.05230.2325-52.0261-28.36277.0538
135.3382-0.45672.22553.1840.85753.75320.07710.09670.1423-0.2376-0.06340.18560.1229-0.2949-0.00210.25590.0175-0.00710.32130.09010.2356-47.9464-21.5217.3183
142.4922-2.50240.31734.3324-0.82750.32630.0520.02730.2453-0.0603-0.00140.0733-0.0073-0.1697-0.05360.25620.05390.02590.38350.04970.272-51.5091-17.08917.2844
153.361-1.3788-0.58538.16834.524.5857-0.1771-0.6328-0.15290.55830.08850.03770.0339-0.31380.10520.39110.05980.01660.52160.09120.2368-45.068-32.50631.1591
163.8205-0.8851-1.69794.92931.57983.2699-0.0414-0.3612-0.37280.7332-0.02940.56450.2393-0.61670.01950.37790.06830.01320.58880.09230.3414-54.4362-27.587227.9582
176.03153.42872.59276.9712.76249.1164-0.08220.6259-0.9488-0.5526-0.13921.46910.7273-1.10920.16140.482-0.0993-0.11510.5058-0.08320.6929-52.387-47.3279.4927
186.2496-5.80440.00415.46850.01542.0325-0.0742-0.2428-0.6416-0.0750.28531.00220.1137-0.4953-0.29560.3108-0.09230.00730.47570.07070.5158-56.2701-39.69217.4207
191.1956-1.7393-0.65828.84520.60832.2233-0.2647-0.19930.14930.51230.22910.2288-0.1009-0.20270.02420.29540.12150.0230.48840.02990.4421-60.6728-9.67620.7542
206.14410.55990.73844.172-0.20033.0826-0.0203-0.1313-0.14610.25620.0777-0.31680.17060.3396-0.05110.23470.0174-0.00610.3568-0.08350.2111-55.471-62.070763.7889
217.5619-2.0048-0.37324.35610.08663.8262-0.1429-0.3068-0.49030.34340.2613-0.79470.39810.7084-0.09610.32260.0608-0.05250.5766-0.1320.5228-44.3046-60.051665.7235
221.36071.99250.37513.67950.18520.3465-0.03020.10940.0845-0.05650.0761-0.2153-0.00910.1816-0.0590.228-0.03030.03450.3864-0.05940.2903-56.1916-51.607254.7831
232.32361.2233-1.01433.1059-3.37353.7197-0.08570.5274-0.0796-0.99990.0480.01460.0840.21780.05510.3932-0.06430.05640.5328-0.11150.2759-61.3691-65.105238.4132
241.95791.0101-0.31166.4015-1.87162.4990.00580.1632-0.3881-0.48460.0146-0.6820.35770.61710.1070.27710.05810.03760.4972-0.14480.3117-52.7945-71.683850.8809
251.53091.5920.48125.48160.53110.2574-0.10590.2163-0.221-0.36490.2087-0.96080.00310.3507-0.09290.3093-0.03130.0860.5656-0.120.3849-47.1986-59.00150.8624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 48 through 102 )C48 - 102
2X-RAY DIFFRACTION2chain 'C' and (resid 103 through 243 )C103 - 243
3X-RAY DIFFRACTION3chain 'C' and (resid 244 through 316 )C244 - 316
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 71 )A48 - 71
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 100 )A72 - 100
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 145 )A101 - 145
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 200 )A146 - 200
8X-RAY DIFFRACTION8chain 'A' and (resid 201 through 217 )A201 - 217
9X-RAY DIFFRACTION9chain 'A' and (resid 218 through 243 )A218 - 243
10X-RAY DIFFRACTION10chain 'A' and (resid 244 through 267 )A244 - 267
11X-RAY DIFFRACTION11chain 'A' and (resid 268 through 316 )A268 - 316
12X-RAY DIFFRACTION12chain 'B' and (resid 49 through 82 )B49 - 82
13X-RAY DIFFRACTION13chain 'B' and (resid 83 through 127 )B83 - 127
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 200 )B128 - 200
15X-RAY DIFFRACTION15chain 'B' and (resid 201 through 217 )B201 - 217
16X-RAY DIFFRACTION16chain 'B' and (resid 218 through 248 )B218 - 248
17X-RAY DIFFRACTION17chain 'B' and (resid 249 through 267 )B249 - 267
18X-RAY DIFFRACTION18chain 'B' and (resid 268 through 293 )B268 - 293
19X-RAY DIFFRACTION19chain 'B' and (resid 294 through 316 )B294 - 316
20X-RAY DIFFRACTION20chain 'D' and (resid 49 through 93 )D49 - 93
21X-RAY DIFFRACTION21chain 'D' and (resid 94 through 113 )D94 - 113
22X-RAY DIFFRACTION22chain 'D' and (resid 114 through 200 )D114 - 200
23X-RAY DIFFRACTION23chain 'D' and (resid 201 through 217 )D201 - 217
24X-RAY DIFFRACTION24chain 'D' and (resid 218 through 267 )D218 - 267
25X-RAY DIFFRACTION25chain 'D' and (resid 268 through 316 )D268 - 316

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