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- PDB-5cyo: High resolution Septin 9 GTPase domain in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 5cyo
TitleHigh resolution Septin 9 GTPase domain in complex with GDP
ComponentsSeptin-9
KeywordsHYDROLASE / septin 9 gtpase domain
Function / homology
Function and homology information


positive regulation of non-motile cilium assembly / septin complex / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / stress fiber / microtubule cytoskeleton / actin cytoskeleton ...positive regulation of non-motile cilium assembly / septin complex / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / stress fiber / microtubule cytoskeleton / 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
GUANOSINE-5'-DIPHOSPHATE / Septin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0354 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)2014/15556-1 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 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 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 1.5May 13, 2020Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7406
Polymers63,8052
Non-polymers9354
Water4,197233
1
A: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3703
Polymers31,9031
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Septin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3703
Polymers31,9031
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.497, 78.049, 77.443
Angle α, β, γ (deg.)90.000, 105.920, 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: 31902.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT9, KIAA0991, MSF / Plasmid: plasmid / Details (production host): pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHD8
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.035→65 Å / Num. all: 41927 / Num. obs: 41927 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.14 % / Biso Wilson estimate: 31.81 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.091 / Χ2: 0.986 / Net I/σ(I): 11.2 / Num. measured all: 131988
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
2.0354-2.160.6940.7241.9920750681166310.87597.4
2.16-2.310.8610.4433.2820268640563820.53699.6
2.31-2.490.9160.2934.7618817596459440.35599.7
2.49-2.730.9670.1827.1517318547154540.21999.7
2.73-3.050.9870.10411.4115722499349690.12699.5
3.05-3.520.9950.05818.3313767438743680.0799.6
3.52-4.310.9970.03926.0511546374037040.04799
4.31-6.070.9970.03329.088791291728690.0498.4
6.070.9990.02732.115009165316060.03397.2

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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: 2.0354→55.292 Å / FOM work R set: 0.8303 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2096 5 %Random selection
Rwork0.1833 39807 --
obs0.1856 41903 99.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.46 Å2 / Biso mean: 42.58 Å2 / Biso min: 16.03 Å2
Refinement stepCycle: final / Resolution: 2.0354→55.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 58 233 4437
Biso mean--25.85 44.12 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044316
X-RAY DIFFRACTIONf_angle_d0.8575858
X-RAY DIFFRACTIONf_chiral_restr0.035673
X-RAY DIFFRACTIONf_plane_restr0.004743
X-RAY DIFFRACTIONf_dihedral_angle_d14.481608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0354-2.08270.30221310.29752479261094
2.0827-2.13480.27471410.260226822823100
2.1348-2.19250.31411400.243326512791100
2.1925-2.2570.26141390.226326522791100
2.257-2.32990.28391390.21526282767100
2.3299-2.41320.28281410.213826912832100
2.4132-2.50980.25321410.205626682809100
2.5098-2.6240.27771400.196226682808100
2.624-2.76230.20771400.19482669280999
2.7623-2.93540.26241390.19422637277699
2.9354-3.1620.24911410.190426832824100
3.162-3.48020.21391400.1752662280299
3.4802-3.98370.20571400.15842659279999
3.9837-5.01850.1821410.14482681282299
5.0185-55.31210.19911430.16742697284098
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)
13.34750.23440.0721.6463-0.82294.7107-0.0713-0.30680.23960.24460.07060.1141-0.2911-0.1899-0.03670.3170.0323-0.02540.2062-0.03820.309626.7424-6.27819.9307
25.11420.51425.44161.95990.95348.0425-0.37750.06990.4722-0.02560.0096-0.0455-0.54660.54050.4090.3414-0.0645-0.08610.32720.02840.324645.7909-2.842821.1368
33.1250.5892.2620.99790.12432.9560.0379-0.0015-0.05370.1076-0.0302-0.07120.03110.0959-0.02260.2080.0161-0.0170.14890.01650.223435.6603-12.931415.4328
49.7688-0.46960.70861.94240.11871.65460.30380.4816-1.0127-0.21160.02780.17470.8083-0.0835-0.07890.3773-0.002-0.08530.21980.00050.314828.2049-27.35567.5464
54.4096-1.2706-0.51631.72170.56751.3685-0.0592-0.4475-0.25330.24070.1053-0.00210.1185-0.1149-0.08960.3333-0.00130.0080.25670.05960.252224.0552-21.58122.1698
69.47270.777-1.7975.6441-1.47356.29670.0153-0.4448-0.01230.1196-0.0004-0.3938-0.05690.275-0.030.31350.0179-0.09920.2423-0.0170.26346.8324-13.404125.1909
75.84651.15331.90373.4573-0.93126.50670.08430.2885-0.3225-0.29110.0870.17560.8552-0.2377-0.15830.4039-0.0591-0.03530.2041-0.01390.260415.8898-21.7485-14.5831
87.9954.73976.28793.74784.07285.0654-0.62590.6546-0.2057-0.55120.1749-0.0011-0.2920.5840.45530.3675-0.030.01760.36790.02380.395132.6648-11.3627-9.2184
90.6707-0.1476-0.00820.22110.79268.02110.00620.1797-0.0525-0.01310.0229-0.0050.10470.0165-0.01190.33290.0135-0.03250.24990.01370.273620.487-9.9185-18.553
105.94060.4858-4.09611.348-0.74763.36840.0071-0.2326-0.03550.6190.06320.2521-0.7598-0.2970.21110.34020.0337-0.02020.28710.00120.279612.596-1.02040.5844
117.2081-0.24471.77134.604-2.77454.02130.27270.89560.8868-1.0585-0.09840.4612-0.9372-0.88920.18890.60630.2438-0.09740.54470.0180.337311.13372.0654-17.338
123.29491.9761-1.32134.8054-2.38595.58330.13040.1078-0.092-0.5566-0.14930.74650.2214-0.9784-0.25450.36530.0266-0.08470.5007-0.0750.37725.3662-10.4792-8.5109
133.75621.7872-3.00231.9596-2.50327.0263-0.04140.3031-0.1753-0.01060.1020.10180.0412-0.8441-0.01580.26510.0031-0.05350.2817-0.05190.269610.6912-11.2984-15.8343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 101 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 120 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 175 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 192 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 266 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 293 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 87 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 88 through 101 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 102 through 175 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 176 through 192 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 193 through 206 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 207 through 239 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 240 through 293 )B0

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