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- PDB-6wcu: Crystal structure of coiled coil region of human septin 5 -

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Basic information

Entry
Database: PDB / ID: 6wcu
TitleCrystal structure of coiled coil region of human septin 5
ComponentsSeptin-5
KeywordsSTRUCTURAL PROTEIN / Coiled coil / Septin
Function / homology
Function and homology information


septin complex / synaptic vesicle targeting / septin ring / cytoskeleton-dependent cytokinesis / regulation of exocytosis / regulation of synaptic vesicle exocytosis / cell division site / adult behavior / social behavior / microtubule cytoskeleton ...septin complex / synaptic vesicle targeting / septin ring / cytoskeleton-dependent cytokinesis / regulation of exocytosis / regulation of synaptic vesicle exocytosis / cell division site / adult behavior / social behavior / microtubule cytoskeleton / protein localization / synaptic vesicle / molecular adaptor activity / GTPase activity / GTP binding / structural molecule activity / identical protein binding / plasma membrane
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.8 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 31, 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
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Septin-5
B: Septin-5


Theoretical massNumber of molelcules
Total (without water)7,7772
Polymers7,7772
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-21 kcal/mol
Surface area5190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.593, 26.114, 45.468
Angle α, β, γ (deg.)90.000, 104.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Septin-5 / Cell division control-related protein 1 / CDCrel-1 / Peanut-like protein 1


Mass: 3888.561 Da / Num. of mol.: 2 / Fragment: Coiled coil region / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99719
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.67 Å3/Da / Density % sol: 26.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid pH 5.0, 1.6 M ammonium sulfate

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.49
ReflectionResolution: 1.8→26.11 Å / Num. obs: 4769 / % possible obs: 97.4 % / Redundancy: 3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Rrim(I) all: 0.073 / Net I/σ(I): 11.3 / Num. measured all: 14437
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
1.8-1.843.10.2139503060.9770.1450.2594.597.1
8.63-26.112.60.05105400.9970.0350.06216.782.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.8→22.465 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.08
RfactorNum. reflection% reflection
Rfree0.2432 252 5.29 %
Rwork0.2186 --
obs0.2267 4768 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.72 Å2 / Biso mean: 21.5542 Å2 / Biso min: 10.35 Å2
Refinement stepCycle: final / Resolution: 1.8→22.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms530 0 0 42 572
Biso mean---27.5 -
Num. residues----60
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8029-2.27050.28831160.25682267238393
2.2705-16.77870.25721310.20982226235791
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)
10.62210.01350.04520.83820.67564.0729-0.00510.0391-0.0276-0.15450.0183-0.1531-0.05520.02950.03590.19920.01570.030.0361-0.01080.1267-0.79345.567416.0608
20.55850.10130.03841.2504-0.24263.34620.07010.07510.041-0.2127-0.03330.13590.1298-0.01760.05930.22030.0086-0.02950.04170.01470.1343-10.40225.265115.916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 340 through 369 )A101 - 130
2X-RAY DIFFRACTION2chain 'B' and (resid 340 through 369 )B201 - 230

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