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- PDB-5cyp: GTPase domain of Septin 9 in complex with GTP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 5cyp
TitleGTPase domain of Septin 9 in complex with GTP-gamma-S
ComponentsSeptin-9
KeywordsHYDROLASE / Septin 9 GTPase domain
Function / homology
Function and homology information


positive regulation of non-motile cilium assembly / septin complex / septin ring / cytoskeleton-dependent cytokinesis / non-motile cilium / cell division site / axoneme / stress fiber / microtubule cytoskeleton / protein localization ...positive regulation of non-motile cilium assembly / septin complex / septin ring / cytoskeleton-dependent cytokinesis / non-motile cilium / cell division site / axoneme / stress fiber / microtubule cytoskeleton / protein localization / actin cytoskeleton / microtubule / molecular adaptor activity / cadherin binding / GTPase activity / GTP binding / perinuclear region of cytoplasm / cytoplasm
Similarity search - Function
Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Septin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.893 Å
AuthorsMatos, S.S. / Leonardo, D.A. / Pereira, H.M. / Horjales, E. / Araujo, A.P.U. / Garratt, R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
CitationJournal: Iucrj / Year: 2020
Title: A complete compendium of crystal structures for the human SEPT3 subgroup reveals functional plasticity at a specific septin interface
Authors: Castro, D.K.S.V. / da Silva, S.M.O. / Pereira, H.M. / Macedo, J.N.A. / Leonardo, D.A. / Valadares, N.F. / Kumagai, P.S. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.6May 13, 2020Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.7Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-9
B: Septin-9
C: Septin-9
D: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,16212
Polymers127,9074
Non-polymers2,2548
Water00
1
A: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5403
Polymers31,9771
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5403
Polymers31,9771
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5403
Polymers31,9771
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5403
Polymers31,9771
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.587, 79.156, 108.217
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer confirmed by gel filtration

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Components

#1: Protein
Septin-9 / MLL septin-like fusion protein MSF-A / MLL septin-like fusion protein / Ovarian/Breast septin / ...MLL septin-like fusion protein MSF-A / MLL septin-like fusion protein / Ovarian/Breast septin / Ov/Br septin / Septin D1


Mass: 31976.834 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT9, KIAA0991, MSF / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHD8
#2: Chemical
ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 20% PEG1500, 20% Glycerol / PH range: 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. all: 27269 / Num. obs: 27269 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.25 % / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.145 / Χ2: 0.944 / Net I/σ(I): 8.57 / Num. measured all: 85852
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.89-3.070.8140.6521.913284448342660.78995.2
3.07-3.280.9210.4192.9913113419541570.50699.1
3.28-3.540.960.264.6812274392638760.31398.7
3.54-3.880.9870.1487.4211240360435560.17898.7
3.88-4.330.9950.0910.9810219329232290.10998.1
4.33-4.990.9970.06514.368961291028480.07897.9
4.99-6.10.9960.0713.367494245423880.08597.3
6.1-8.550.9980.05316.025909193618660.06396.4
8.550.9990.02628.223358113910830.03295.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.893→45.654 Å / FOM work R set: 0.6839 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2974 1362 5.01 %Random selection
Rwork0.2522 25819 --
obs0.2544 27181 97.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.72 Å2 / Biso mean: 60.85 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.893→45.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7117 0 132 0 7249
Biso mean--42.45 --
Num. residues----940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027376
X-RAY DIFFRACTIONf_angle_d0.59410043
X-RAY DIFFRACTIONf_chiral_restr0.0231192
X-RAY DIFFRACTIONf_plane_restr0.0021269
X-RAY DIFFRACTIONf_dihedral_angle_d12.2772617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.893-2.99640.40331280.35462438256692
2.9964-3.11630.32281380.33132609274799
3.1163-3.25810.37571370.30712589272699
3.2581-3.42980.35311370.2912602273999
3.4298-3.64460.28071350.25422580271598
3.6446-3.92590.32181380.24912604274298
3.9259-4.32070.24981360.22152594273098
4.3207-4.94520.24621380.20422613275198
4.9452-6.2280.29181370.23962582271997
6.228-45.65930.27881380.23222608274696
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)
16.40570.5415-6.53644.0076-1.61977.5002-0.63141.54030.0101-0.12670.29610.61090.2772-0.84520.03430.2301-0.0123-0.03060.54360.23970.3983-27.816810.52936.3161
26.1515-1.93021.7325.42531.88274.0902-0.28160.0141-0.8735-0.06680.3367-0.4858-0.0553-0.0786-0.08870.20530.07150.00980.5150.02030.7874-14.97796.37319.0741
33.86222.0949-4.65763.9673-1.87065.82160.040.5948-0.0919-0.22520.3866-0.39370.2426-0.2789-0.59680.44130.1507-0.12740.5223-0.1670.7887-15.70099.60611.9284
41.16081.9073-1.93384.4546-1.59985.0656-0.00360.3866-2.0691-0.57210.38080.1785-0.2096-0.1751-0.37810.39650.0352-0.13870.9834-0.23820.9334-22.7779.8436-9.0826
50.4345-0.5631-0.72622.8442-0.08112.6219-0.1760.26110.3509-0.31190.1218-0.010.21560.02060.07030.251-0.03030.01990.63410.0610.6651-17.361817.71980.285
62.2817-0.69650.11154.2733-0.10523.5709-0.4260.3889-0.00140.23120.2786-0.885-0.32390.6041-0.4040.35620.05330.05830.56390.1340.6665-8.173531.44087.8013
70.01520.03130.09110.07120.20320.5549-0.07780.09410.9774-0.35910.43481.1255-0.5131-0.5697-0.45120.30390.0207-0.0210.71330.21041.0717-24.504129.78130.9344
83.6119-4.8659-2.31786.61483.3192.1267-0.4686-0.85910.17860.46620.79510.4669-0.5616-0.5035-0.37680.30720.10530.04610.61680.09310.7299-21.393427.878511.6966
90.2690.4947-0.26811.26170.69514.8756-0.32420.16850.0247-0.1909-0.14320.1484-0.4644-0.40840.19910.27980.07030.08190.55890.0450.7637-22.177617.49119.5727
105.1688-0.2419-2.17475.31740.532.71970.05120.00041.76910.1075-0.20090.3263-0.1879-0.28860.18340.34740.02570.05240.58360.02871.044417.015226.14215.4582
111.42941.83872.70942.39483.59696.97310.81961.3441-0.58940.2841-0.3020.08510.4762-0.8572-0.40540.45380.0635-0.00071.10670.2950.811418.89222.363-8.5818
125.54512.8859-5.28282.446-1.10138.1541-0.08360.8535-0.9743-0.08870.2459-0.8982-1.19950.769-0.43840.4334-0.10370.17010.8607-0.00480.876835.218925.4462-6.2907
133.62670.1788-0.07631.9933-0.33111.19380.06440.2798-0.5648-0.4933-0.196-0.0458-0.1505-0.1954-0.22840.12620.1495-0.04740.7612-0.19710.898710.356612.44673.1891
140.35520.385-0.59741.3573-2.51964.80860.41570.3185-0.03250.03230.2236-0.8685-0.20180.1386-0.51670.35590.01360.01780.6895-0.23490.809915.04353.81286.7704
155.6134-6.97360.53648.6673-0.8483.2249-0.6914-1.0971-0.86670.69290.86390.62030.14220.4825-0.14750.34750.1265-0.03540.74540.02860.994620.9016.948612.9554
164.1411-0.2996-1.7551.8297-0.51695.4835-0.1236-0.14420.239-0.2323-0.16370.01890.8210.27620.1970.31240.0940.11140.63580.16241.063727.859215.04653.3895
175.917-1.28840.75772.3280.69043.7237-0.0608-0.3263-0.76950.1008-0.1039-0.13610.1187-0.50370.03370.26040.037-0.1115-0.0519-0.01390.67820.523520.264858.9074
182.61230.1798-0.26523.8141-0.06461.34730.3304-0.2788-0.8510.3529-0.1152-0.76580.29310.0834-0.04030.3228-0.0652-0.1162-0.10870.02091.066712.51116.886159.2664
191.6139-1.5351-0.94283.56550.43516.9960.5190.2615-0.3043-0.5617-0.2095-0.0196-0.0376-0.0939-0.13490.357-0.0238-0.07510.15950.02230.12454.509119.71844.1873
200.8368-0.77-0.8042.1709-0.58712.6863-0.2349-0.1157-0.3629-0.28940.20770.64830.1953-0.67840.08890.2903-0.16410.06330.1519-0.14460.488-8.24116.774747.8002
214.47581.45941.46062.54740.68451.5322-0.4065-0.29011.2221-0.8920.172-0.5624-0.37650.1874-0.02160.2797-0.03180.0116-0.0659-0.29080.664519.569531.389457.3834
227.06971.57370.78150.59640.40590.29950.03540.68071.071-0.1544-0.14030.139-0.4098-0.10680.20310.4377-0.0377-0.01170.2709-0.08840.764715.884732.062147.8794
230.8393-0.7703-1.07962.09120.83031.4141-0.4711-0.29480.12630.3860.11040.10020.30020.0409-0.04730.2754-0.13360.10930.2867-0.09880.390216.366630.200461.6793
241.58130.11430.59692.10070.93781.52070.0071-0.38260.6876-0.1467-0.08450.1974-0.4078-0.29860.26690.39880.0833-0.0153-0.0671-0.19410.86618.768240.442760.0051
257.5094-7.0881-1.88157.57480.08783.6914-1.3686-1.83110.02611.50440.79730.0504-0.4140.0418-0.02390.60560.0319-0.08050.5917-0.25110.540213.662430.788470.4037
262.54350.8104-1.12511.25930.64091.4155-0.0581-0.22690.1010.0389-0.13770.1096-0.278-0.1750.06310.2331-0.0112-0.08460.1397-0.12310.37-1.006128.25953.7522
273.0192-0.2951-0.22590.86550.37283.1926-0.2564-0.32771.12350.29540.25420.1465-0.76880.2238-0.3080.26570.03050.01390.0139-0.19760.992943.45435.322960.4119
284.6622-1.77851.95634.547-0.49473.783-0.0873-0.22120.7362-0.27540.05180.063-0.63380.1174-0.07460.2777-0.02290.1475-0.01250.06440.98144.923235.754656.8106
291.9235-0.71831.34682.10890.82453.30970.18420.5370.0768-0.0156-0.14910.01050.030.5715-0.0489-0.05560.17040.06390.33330.23871.30450.734332.939944.5117
300.1751-0.480.06561.3869-0.63842.30110.0582-0.04930.2453-0.1311-0.213-0.6255-0.89690.86220.29890.422-0.457-0.00190.4178-0.15371.190763.029436.098147.9857
312.651-0.6853-0.29522.921-0.96492.62840.18360.14780.0413-0.3453-0.02020.271-0.29840.0577-0.12340.3518-0.0097-0.01350.1153-0.0270.855937.289121.51253.7415
321.671-0.7425-0.1583.0415-0.49641.62240.0062-0.3408-0.80170.1213-0.13020.18660.3528-0.03350.03370.25650.0704-0.0460.059-0.00340.585841.549416.416560.0425
333.0771-2.38831.59823.2303-1.84272.33610.0556-0.411-0.8547-0.0156-0.3769-0.53750.76310.17510.3490.4368-0.1030.28230.37650.40540.819254.512111.911764.8883
347.7175-1.8234-0.16772.4151-1.80833.0002-0.2933-1.5503-0.34640.3540.6816-0.8527-0.20510.0464-0.04110.2603-0.0371-0.00260.4969-0.05010.489446.931323.034968.0101
352.70140.32461.16720.7046-0.69241.55070.070.30250.7879-0.1303-0.3284-0.39580.29720.34040.14750.37220.0320.11380.24610.09650.597858.751824.552148.0456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 76 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 97 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 119 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 175 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 176 through 192 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 193 through 206 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 207 through 227 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 228 through 289 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 19 through 97 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 98 through 114 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 115 through 134 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 135 through 175 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 176 through 206 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 207 through 257 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 258 through 290 )B0
17X-RAY DIFFRACTION17chain 'C' and (resid 19 through 30 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 31 through 97 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 98 through 119 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 120 through 134 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 135 through 148 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 149 through 160 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 161 through 175 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 176 through 217 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 218 through 257 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 258 through 291 )C0
27X-RAY DIFFRACTION27chain 'D' and (resid 19 through 67 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 68 through 97 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 98 through 119 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 120 through 134 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 135 through 159 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 160 through 206 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 207 through 217 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 218 through 269 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 270 through 291 )D0

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