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- PDB-6upa: Crystal Structure of GTPase Domain of Human Septin 2/Septin 6 Het... -

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Basic information

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


septin collar / regulation of L-glutamate import across plasma membrane / sperm annulus / septin complex / photoreceptor connecting cilium / septin ring / cytoskeleton-dependent cytokinesis / non-motile cilium / ciliary membrane / smoothened signaling pathway ...septin collar / regulation of L-glutamate import across plasma membrane / sperm annulus / septin complex / photoreceptor connecting cilium / septin ring / cytoskeleton-dependent cytokinesis / non-motile cilium / ciliary membrane / smoothened signaling pathway / cell division site / cleavage furrow / mitotic cytokinesis / axoneme / cilium assembly / intercellular bridge / enzyme regulator activity / axon terminus / Anchoring of the basal body to the plasma membrane / kinetochore / spindle / synaptic vesicle / intracellular protein localization / actin cytoskeleton / regulation of protein localization / microtubule cytoskeleton / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cilium / cadherin binding / GTPase activity / synapse / GTP binding / cell surface / 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-6 / Septin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsRosa, H.V.D. / Brandao-Neto, J. / Martins, C. / Araujo, A.P.U. / Pereira, H.M. / 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 17, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Septin-6
A: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3455
Polymers66,3552
Non-polymers9913
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-34 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.730, 82.730, 170.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein Septin-6


Mass: 32081.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN6, KIAA0128, SEP2, SEPT6 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q14141
#2: Protein Septin-2 / Neural precursor cell expressed developmentally down-regulated protein 5 / NEDD-5


Mass: 34273.066 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: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15019

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Non-polymers , 4 types, 35 molecules

#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM bicine/Trizma base pH 8.5, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD and 20mM of each d-glucose, d-mannose,d-galactose, l-fucose, d-xylose, N-acetyld-glucosamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.51→37.21 Å / Num. obs: 21021 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.044 / Rrim(I) all: 0.159 / Net I/σ(I): 11.6 / Num. measured all: 269502
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
2.51-2.5813.32.2352014315160.5640.6352.3241.299.9
11.23-37.219.70.04429032990.9990.0140.04637.697.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QNR, 4KVA

2qnr

4kva


Resolution: 2.51→37.209 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 1036 4.94 %Randon selection
Rwork0.2241 ---
obs0.226 20952 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.86 Å2 / Biso mean: 71.3535 Å2 / Biso min: 33.05 Å2
Refinement stepCycle: final / Resolution: 2.51→37.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3951 0 61 32 4044
Biso mean--52.07 57.79 -
Num. residues----508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5101-2.64240.39341440.32472779
2.6424-2.80790.33751300.31362795
2.8079-3.02460.34671690.29842767
3.0246-3.32880.30311500.26432817
3.3288-3.81010.27521580.21992818
3.8101-4.79870.23281440.19032880
4.7987-37.2090.2271410.20083060
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)
15.43691.10510.33073.7433-0.48372.65770.0045-0.2061-0.45150.0281-0.082-0.37040.37050.28090.13740.65670.0365-0.03410.42180.0090.49774.005521.4433-14.1243
26.6349-6.9198-4.37968.35976.32144.4455-0.2535-0.1904-0.25310.73340.1845-0.20040.0820.23890.19290.69840.01470.01960.43550.00940.47866.23088.55-24.2129
32.47990.0551-1.1723.7759-0.03691.1322-0.1610.0009-0.3154-0.55650.05950.29560.2816-0.31920.06880.5536-0.0739-0.10050.38310.01140.4714-12.730222.5005-20.5898
43.1904-2.8179-3.13156.45655.30636.4945-0.2656-0.1373-0.67920.1792-0.05630.6340.8362-0.25830.36990.7091-0.0698-0.00370.43260.120.6458-8.659816.17-11.9833
55.55613.53970.18412.2783-1.16056.70270.19920.22520.3432-0.2997-0.11080.7822-0.3874-0.8659-0.0720.70610.1439-0.00050.60610.01410.4902-12.991951.187-20.9822
63.721-3.9916-2.5489.31946.28668.84430.3080.63750.0702-0.4986-0.3477-0.45180.1156-0.35550.00080.71720.01050.02130.49250.05760.6222-5.553346.2395-29.9993
78.5074-0.12390.35977.44322.13698.24080.02420.32610.7464-0.3676-0.3857-0.5319-0.36360.85120.33140.7068-0.07570.06360.5970.11260.64591.268363.1011-32.1017
81.78242.2794-0.51735.3985-2.39863.1304-0.03130.1640.4207-0.24350.23220.2444-0.4199-0.1962-0.20530.51840.01150.03340.3787-0.01790.4433-0.399553.5457-19.6455
95.15981.4344-2.03218.0455-1.10586.0620.0444-0.1409-0.00970.707-0.4046-1.0238-0.66810.76840.31840.5135-0.1017-0.17730.63570.01410.57755.151948.6685-7.5421
107.62713.06740.36248.04940.38686.0337-0.0143-0.71250.6070.6309-0.24860.5136-0.8148-0.54430.27570.62670.05670.02270.5074-0.01380.4165-13.752947.4598-4.4029
118.83316.3029-8.43779.601-7.09419.32160.2840.1950.72950.41450.051-0.1407-0.8533-0.1438-0.28280.771-0.023-0.22530.42320.06770.57530.703964.5832-18.1622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 41 through 113 )B41 - 113
2X-RAY DIFFRACTION2chain 'B' and (resid 114 through 155 )B114 - 155
3X-RAY DIFFRACTION3chain 'B' and (resid 156 through 242 )B156 - 242
4X-RAY DIFFRACTION4chain 'B' and (resid 243 through 305 )B243 - 305
5X-RAY DIFFRACTION5chain 'A' and (resid 37 through 68 )A37 - 68
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 115 )A69 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 133 )A116 - 133
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 188 )A134 - 188
9X-RAY DIFFRACTION9chain 'A' and (resid 189 through 224 )A189 - 224
10X-RAY DIFFRACTION10chain 'A' and (resid 225 through 272 )A225 - 272
11X-RAY DIFFRACTION11chain 'A' and (resid 273 through 306 )A273 - 306

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