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- PDB-6wbe: Crystal structure of coiled coil region of human septin 1 -

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Basic information

Entry
Database: PDB / ID: 6wbe
TitleCrystal structure of coiled coil region of human septin 1
ComponentsSeptin-1
KeywordsSTRUCTURAL PROTEIN / Coiled coil / Septin
Function / homology
Function and homology information


meiotic metaphase chromosome alignment / protein localization => GO:0008104 / septin complex / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / spindle assembly involved in female meiosis / meiotic spindle / microtubule organizing center / cell division site ...meiotic metaphase chromosome alignment / protein localization => GO:0008104 / septin complex / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / spindle assembly involved in female meiosis / meiotic spindle / microtubule organizing center / cell division site / microtubule cytoskeleton / synaptic vesicle / midbody / molecular adaptor activity / GTPase activity / GTP binding / identical protein binding
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-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.1 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
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

Downloads & links

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Assembly

Deposited unit
A: Septin-1
B: Septin-1
C: Septin-1
D: Septin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,79016
Polymers15,0374
Non-polymers75312
Water57632
1
A: Septin-1
hetero molecules

C: Septin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,01610
Polymers7,5192
Non-polymers4988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area890 Å2
ΔGint-54 kcal/mol
Surface area5370 Å2
MethodPISA
2
B: Septin-1
hetero molecules

D: Septin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7746
Polymers7,5192
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465x-1/2,-y+3/2,-z1
Buried area950 Å2
ΔGint-70 kcal/mol
Surface area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.230, 60.450, 81.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 through 4 and (name N...
21(chain B and ((resid 2 through 4 and (name N...
31(chain C and ((resid 2 through 4 and (name N...
41(chain D and ((resid 2 through 4 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 2 through 4 and (name N...A2 - 4
121(chain A and ((resid 2 through 4 and (name N...A328 - 356
131(chain A and ((resid 2 through 4 and (name N...A328 - 356
141(chain A and ((resid 2 through 4 and (name N...A328 - 356
151(chain A and ((resid 2 through 4 and (name N...A328 - 356
211(chain B and ((resid 2 through 4 and (name N...B2 - 4
221(chain B and ((resid 2 through 4 and (name N...B329 - 354
231(chain B and ((resid 2 through 4 and (name N...B329 - 354
241(chain B and ((resid 2 through 4 and (name N...B329 - 354
251(chain B and ((resid 2 through 4 and (name N...B329 - 354
311(chain C and ((resid 2 through 4 and (name N...C2 - 4
321(chain C and ((resid 2 through 4 and (name N...C328 - 355
331(chain C and ((resid 2 through 4 and (name N...C328 - 355
341(chain C and ((resid 2 through 4 and (name N...C328 - 355
351(chain C and ((resid 2 through 4 and (name N...C328 - 355
411(chain D and ((resid 2 through 4 and (name N...D2 - 4
421(chain D and ((resid 2 through 4 and (name N...D328 - 355
431(chain D and ((resid 2 through 4 and (name N...D328 - 355
441(chain D and ((resid 2 through 4 and (name N...D328 - 355
451(chain D and ((resid 2 through 4 and (name N...D328 - 355

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Components

#1: Protein/peptide
Septin-1 / / LARP / Peanut-like protein 3 / Serologically defined breast cancer antigen NY-BR-24


Mass: 3759.312 Da / Num. of mol.: 4 / Fragment: coiled coil region / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WYJ6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M zinc acetate, 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.82652 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82652 Å / Relative weight: 1
ReflectionResolution: 2.1→81.64 Å / Num. obs: 7988 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.027 / Rrim(I) all: 0.066 / Net I/σ(I): 16.4 / Num. measured all: 45377 / Scaling rejects: 16
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
2.1-2.165.90.30637636400.9480.1360.3355.699
8.91-81.644.60.0296061310.9990.0160.0343297.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.1→40.82 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 388 4.87 %Random selection
Rwork0.208 ---
obs0.2102 7959 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.72 Å2 / Biso mean: 45.6428 Å2 / Biso min: 19.45 Å2
Refinement stepCycle: final / Resolution: 2.1→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 27 32 941
Biso mean--53.94 45.12 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015897
X-RAY DIFFRACTIONf_angle_d1.471179
X-RAY DIFFRACTIONf_chiral_restr0.051130
X-RAY DIFFRACTIONf_plane_restr0.008161
X-RAY DIFFRACTIONf_dihedral_angle_d21.704592
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A458X-RAY DIFFRACTION16.799TORSIONAL
12B458X-RAY DIFFRACTION16.799TORSIONAL
13C458X-RAY DIFFRACTION16.799TORSIONAL
14D458X-RAY DIFFRACTION16.799TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1003-2.40410.26461320.2089244198
2.4041-3.02880.28621170.2305251699
3.0288-40.820.2451390.1991261499
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)
13.0593-1.0546-0.16192.27242.31314.6225-0.14940.002-0.00451.52870.0592-0.43830.50660.1255-0.00910.46610.0312-0.02340.23380.04470.339717.09337.381717.4885
26.76260.0052-2.05533.737-3.52726.63990.1974-0.17570.14730.1241-0.08920.1882-0.2573-0.1578-0.13960.21480.0159-0.02170.2786-0.03920.18237.601646.71954.9181
31.72911.7635-0.03234.2482-2.64452.96090.2882-0.04530.28010.5854-0.12881.3129-0.643-0.36850.05910.60930.0157-0.00140.2177-0.04110.37399.457550.283616.6764
46.14272.15560.90223.6182.32226.6203-0.04-0.2371-0.3395-0.04420.2114-0.62630.08340.5418-0.18530.13430.0067-0.00040.2979-0.02810.203416.549244.18565.0746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 328 through 356 )A1 - 29
2X-RAY DIFFRACTION2chain 'B' and (resid 329 through 354 )B2 - 27
3X-RAY DIFFRACTION3chain 'C' and (resid 328 through 355 )C1 - 28
4X-RAY DIFFRACTION4chain 'D' and (resid 328 through 355 )D1 - 28

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