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- PDB-6wb3: Crystal structure of coiled coil region of human septin 4 -

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Basic information

Entry
Database: PDB / ID: 6wb3
TitleCrystal structure of coiled coil region of human septin 4
ComponentsSeptin-4
KeywordsSTRUCTURAL PROTEIN / Coiled coil / Septin
Function / homology
Function and homology information


sperm annulus / protein localization => GO:0008104 / septin complex / spermatid differentiation / flagellated sperm motility / septin ring / cytoskeleton-dependent cytokinesis / Release of apoptotic factors from the mitochondria / regulation of exocytosis / SMAC, XIAP-regulated apoptotic response ...sperm annulus / protein localization => GO:0008104 / septin complex / spermatid differentiation / flagellated sperm motility / septin ring / cytoskeleton-dependent cytokinesis / Release of apoptotic factors from the mitochondria / regulation of exocytosis / SMAC, XIAP-regulated apoptotic response / cell division site / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / neuron migration / microtubule cytoskeleton / synaptic vesicle / perikaryon / regulation of apoptotic process / mitochondrial outer membrane / molecular adaptor activity / positive regulation of apoptotic process / axon / GTPase activity / apoptotic process / dendrite / GTP binding / structural molecule activity / magnesium ion binding / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
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
ACETATE ION / Septin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.35 Å
AuthorsCabrejos, D.A.L. / Cavini, I. / Sala, F.A. / Valadares, N.F. / Pereira, H.M. / Brandao-Neto, J. / Nascimento, A.F.Z. / Uson, I. / Araujo, A.P.U. / Garratt, R.C.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/04658-9 Brazil
Sao Paulo Research Foundation (FAPESP)2018/19992-7 Brazil
Sao Paulo Research Foundation (FAPESP)2015/00062-1 Brazil
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Orientational Ambiguity in Septin Coiled Coils and its Structural Basis.
Authors: Leonardo, D.A. / Cavini, I.A. / Sala, F.A. / Mendonca, D.C. / Rosa, H.V.D. / Kumagai, P.S. / Crusca Jr., E. / Valadares, N.F. / Marques, I.A. / Brandao-Neto, J. / Munte, C.E. / Kalbitzer, H. ...Authors: Leonardo, D.A. / Cavini, I.A. / Sala, F.A. / Mendonca, D.C. / Rosa, H.V.D. / Kumagai, P.S. / Crusca Jr., E. / Valadares, N.F. / Marques, I.A. / Brandao-Neto, J. / Munte, C.E. / Kalbitzer, H.R. / Soler, N. / Uson, I. / Andre, I. / Araujo, A.P.U. / D'Muniz Pereira, H. / Garratt, R.C.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-4
B: Septin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0616
Polymers7,7512
Non-polymers3104
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-36 kcal/mol
Surface area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.763, 41.463, 54.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Septin-4 / / Apoptosis-related protein in the TGF-beta signaling pathway / ARTS / Bradeion beta / Brain protein ...Apoptosis-related protein in the TGF-beta signaling pathway / ARTS / Bradeion beta / Brain protein H5 / CE5B3 beta / Cell division control-related protein 2 / hCDCREL-2 / Cerebral protein 7 / Peanut-like protein 2


Mass: 3875.542 Da / Num. of mol.: 2 / Fragment: Coiled coil region / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43236
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 0.2 M NH4SO4, 16% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→33.02 Å / Num. obs: 13442 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 18.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.022 / Rrim(I) all: 0.074 / Net I/σ(I): 16.2 / Num. measured all: 162112 / Scaling rejects: 32
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
1.35-1.3712.30.88880656540.9480.2610.9262.6100
7.39-33.029.30.06710361110.9980.0220.07136.499.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.35→33.02 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 658 4.96 %RANDOM
Rwork0.2215 ---
obs0.2227 13276 99 %-
Displacement parametersBiso max: 100.34 Å2 / Biso mean: 31.3 Å2 / Biso min: 16.87 Å2
Baniso -1Baniso -2Baniso -3
1--10.9664 Å20 Å20 Å2
2--7.4025 Å20 Å2
3---3.5639 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.35→33.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms509 0 18 44 571
Biso mean--56.45 36.22 -
Num. residues----63
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d231SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes97HARMONIC5
X-RAY DIFFRACTIONt_it542HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion69SEMIHARMONIC5
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_contact606SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d542HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg717HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion14.58
LS refinement shellResolution: 1.35→1.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 33
RfactorNum. reflection% reflection
Rfree0.2707 17 4.1 %
Rwork0.2458 398 -
all0.2469 415 -
obs--99.77 %
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)
15.10855.17081.925512.13194.13983.90490.4441-0.36570.16120.4904-0.41510.36720.1537-0.1827-0.02890.0563-0.03310.0216-0.0786-0.0101-0.080514.617327.91254.1593
23.58335.0311.73111.14244.81474.21860.3707-0.1347-0.3120.4979-0.1027-0.48920.21070.1207-0.2680.11810.0057-0.0478-0.0263-0.0014-0.024325.466327.93394.2215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A447 - 478
2X-RAY DIFFRACTION2{ B|* }B447 - 477

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