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- PDB-8sjj: X-ray structure of the metastable SEPT14-SEPT7 heterodimeric coil... -

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Basic information

Entry
Database: PDB / ID: 8sjj
TitleX-ray structure of the metastable SEPT14-SEPT7 heterodimeric coiled coil
Components
  • Septin 7
  • Septin-14
KeywordsCELL CYCLE / Septin / Coiled coil
Function / homology
Function and homology information


septin complex / protein localization to perinuclear region of cytoplasm / septin ring / cytoskeleton-dependent cytokinesis / motile cilium / cell division site / spermatid development / cleavage furrow / acrosomal vesicle / neuron migration ...septin complex / protein localization to perinuclear region of cytoplasm / septin ring / cytoskeleton-dependent cytokinesis / motile cilium / cell division site / spermatid development / cleavage furrow / acrosomal vesicle / neuron migration / kinetochore / spindle / microtubule cytoskeleton / midbody / perikaryon / spermatogenesis / molecular adaptor activity / cytoskeleton / axon / GTPase activity / dendrite / GTP binding / perinuclear region of cytoplasm / cytoplasm
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Septin / Septin-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsCavini, I.A. / Pereira, H.M. / Garratt, R.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)20/02897-1 Brazil
Sao Paulo Research Foundation (FAPESP)18/19992-7 Brazil
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: X-ray structure of the metastable SEPT14-SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization.
Authors: Cavini, I.A. / Winter, A.J. / D'Muniz Pereira, H. / Woolfson, D.N. / Crump, M.P. / Garratt, R.C.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-14
B: Septin-14
C: Septin 7
D: Septin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,76614
Polymers40,3704
Non-polymers39610
Water4,450247
1
A: Septin-14
C: Septin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3837
Polymers20,1852
Non-polymers1985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Septin-14
hetero molecules

D: Septin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3837
Polymers20,1852
Non-polymers1985
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_455-x-1,y+1/2,-z1
crystal symmetry operation2_355-x-2,y+1/2,-z1
Unit cell
Length a, b, c (Å)34.934, 50.811, 91.558
Angle α, β, γ (deg.)90.00, 94.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Septin-14 /


Mass: 9249.529 Da / Num. of mol.: 2 / Fragment: coiled coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN14, SEPT14 / Plasmid: pETSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6ZU15
#2: Protein Septin 7 /


Mass: 10935.504 Da / Num. of mol.: 2 / Fragment: residues 307-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A023T695
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Bis-Tris pH 5.0, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.781→91.294 Å / Num. obs: 22355 / % possible obs: 72.47 % / Redundancy: 6.83 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 10.602
Reflection shellResolution: 1.781→1.996 Å / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1118 / CC1/2: 0.5692 / Rpim(I) all: 0.535 / Rrim(I) all: 1.1289 / % possible all: 14.18

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
STARANISOdata scaling
autoPROCdata reduction
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.781→91.29 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.881 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2863 1141 5.1 %RANDOM
Rwork0.2206 ---
obs0.2238 22355 72.5 %-
Displacement parametersBiso mean: 32.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.4664 Å20 Å22.1453 Å2
2--0.155 Å20 Å2
3---2.3114 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.781→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 22 247 2878
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082705HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.853590HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1090SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes479HARMONIC5
X-RAY DIFFRACTIONt_it2705HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion18.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion335SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2669SEMIHARMONIC4
LS refinement shellResolution: 1.781→1.9 Å
RfactorNum. reflection% reflection
Rfree0.2485 -5.58 %
Rwork0.2148 423 -
obs--8.14 %
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)
10.60010.82881.26960.3550.9221.6076-0.1558-0.08850.0529-0.1881-0.0010.0184-0.4099-0.20780.1568-0.10150.0352-0.02460.0698-0.1208-0.03264.972540.379922.1596
22.4381.41912.19980.85421.27721.8914-0.33360.27510.1479-0.21410.17810.0792-0.4350.27030.1555-0.04890.0062-0.0314-0.0568-0.0267-0.04183.232514.3820.3236
31.14440.97541.85181.07511.80513.38910.01150.01960.09430.0702-0.14430.15840.2002-0.0030.1328-0.06880.0092-0.0531-0.025-0.0515-0.03976.197930.485618.7291
40.95370.50210.95460.18220.2880.72320.09470.363-0.30890.03060.2548-0.18090.05840.5014-0.3495-0.07970.0415-0.0448-0.0224-0.0944-0.0091-28.56675.587721.3029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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