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- PDB-3tw4: Crystal Structure of Human Septin 7 GTPase Domain -

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Basic information

Entry
Database: PDB / ID: 3tw4
TitleCrystal Structure of Human Septin 7 GTPase Domain
ComponentsSeptin-7
KeywordsCELL CYCLE / GTPase / Septins
Function / homology
Function and homology information


regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / cleavage furrow ...regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / cleavage furrow / cilium assembly / stress fiber / MAPK6/MAPK4 signaling / kinetochore / spindle / microtubule cytoskeleton / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / identical protein binding / nucleus / cytosol
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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Septin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å
AuthorsSerrao, V.H.B. / Alessandro, F. / Pereira, H.M. / Thiemann, O.T. / Garratt, R.C.
CitationJournal: Febs Lett. / Year: 2011
Title: Promiscuous interactions of human septins: The GTP binding domain of SEPT7 forms filaments within the crystal.
Authors: Serrao, V.H. / Alessandro, F. / Caldas, V.E. / Marcal, R.L. / D'Muniz Pereira, H. / Thiemann, O.H. / Garratt, R.C.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_residues / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin-7
B: Septin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1644
Polymers62,2772
Non-polymers8862
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-21 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.510, 82.510, 210.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPHEPHEchain A and (resseq 30:52 or resseq 88:98 or resseq...AA30 - 522 - 24
12LEULEUPHEPHEchain A and (resseq 30:52 or resseq 88:98 or resseq...AA88 - 9860 - 70
13ASNASNTHRTHRchain A and (resseq 30:52 or resseq 88:98 or resseq...AA106 - 20978 - 181
14LEULEUGLYGLYchain A and (resseq 30:52 or resseq 88:98 or resseq...AA217 - 231189 - 203
15ASNASNLEULEUchain A and (resseq 30:52 or resseq 88:98 or resseq...AA257 - 270229 - 242
16METMETALAALAchain A and (resseq 30:52 or resseq 88:98 or resseq...AA275 - 297247 - 269
21PHEPHEPHEPHEchain B and (resseq 30:52 or resseq 88:98 or resseq...BB30 - 522 - 24
22LEULEUPHEPHEchain B and (resseq 30:52 or resseq 88:98 or resseq...BB88 - 9860 - 70
23ASNASNTHRTHRchain B and (resseq 30:52 or resseq 88:98 or resseq...BB106 - 20978 - 181
24LEULEUGLYGLYchain B and (resseq 30:52 or resseq 88:98 or resseq...BB217 - 231189 - 203
25ASNASNLEULEUchain B and (resseq 30:52 or resseq 88:98 or resseq...BB257 - 270229 - 242
26METMETALAALAchain B and (resseq 30:52 or resseq 88:98 or resseq...BB275 - 297247 - 269

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Components

#1: Protein Septin-7 / CDC10 protein homolog


Mass: 31138.682 Da / Num. of mol.: 2 / Fragment: UNP residues 48-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT7, CDC10 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16181
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 100mM Tris pH 8.4; 16% Glycerol; 1.5M Amonium Sulphate; 500mM GDP; 12.5% Isopropanol and 7mg/mL SETPT7G, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2010
RadiationMonochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 3.35→42.42 Å / Num. all: 11558 / Num. obs: 11558 / % possible obs: 98.7 % / Observed criterion σ(F): 2.885 / Observed criterion σ(I): -3 / Redundancy: 3.01 % / Biso Wilson estimate: 112 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.35-3.550.661.595443182597.8
3.55-3.790.373.125549177499.8
3.79-4.090.2085.274862163498.7
4.09-4.480.09410.874459148599.1
4.48-50.05317.864241137099.3
5-5.760.04619.333434118598.2
5.76-7.020.03925.643288103899.7
7.02-9.80.01846.69223877796.5
9.80.01266.17133247097.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing
DMphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QNR

2qnr


Resolution: 3.35→42.42 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 1.17 / σ(F): 1.99 / Phase error: 41.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3652 577 5 %Random
Rwork0.2892 ---
all0.2927 11538 --
obs0.2927 11538 98.52 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 268.675 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 413.38 Å2 / Biso mean: 144.4312 Å2 / Biso min: 49.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.6112 Å2-0 Å20 Å2
2---2.6112 Å20 Å2
3---5.2224 Å2
Refinement stepCycle: LAST / Resolution: 3.35→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 56 0 3039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083089
X-RAY DIFFRACTIONf_angle_d1.5444234
X-RAY DIFFRACTIONf_chiral_restr0.086522
X-RAY DIFFRACTIONf_plane_restr0.01538
X-RAY DIFFRACTIONf_dihedral_angle_d22.7761003
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1285X-RAY DIFFRACTIONPOSITIONAL0.063
12B1285X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.35-3.68410.44681430.35992713285698
3.6841-4.21680.38281440.32262748289299
4.2168-5.31110.34241450.25582753289899
5.3111-42.43040.3551450.28282747289298
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)
18.4087-4.904-0.31683.3938-1.43617.713-0.4453-0.6856-0.02781.54711.54610.38030.1542-0.0764-0.52291.1998-0.20360.09720.58790.10890.8279-44.03756.0277-6.9468
23.58172.4082-0.74753.16380.20290.7559-0.31250.1603-0.41520.35470.0525-0.5563-0.3512-0.1733-0.48321.3984-1.2609-0.31640.7472-0.32640.907-35.4434-3.1058-10.0312
32.6406-1.9509-1.45567.9042-3.72794.3759-0.03-0.9147-1.00811.6099-0.41450.04511.36490.330.29151.7663-0.6983-0.23120.97250.3880.9635-41.2393-18.9428-7.887
42.3083-0.5036-0.90144.25480.11460.8391-0.65160.52741.1476-1.0230.54540.10770.0442-0.26550.05941.1215-1.0778-0.29611.2433-0.16561.006-38.822410.6286-24.0769
56.6709-0.57761.22430.6939-0.90241.2108-0.63471.0416-0.1677-0.8371-0.10790.6416-0.6714-1.18870.79171.6587-0.496-0.74211.7173-0.36981.3291-49.28760.5974-27.9347
61.7024-0.2397-1.26632.8419-1.76673.4875-0.29680.6852.0324-0.09830.36741.913-0.4892-0.48030.1231.3792-0.7048-0.46110.76710.24122.1402-52.756515.2928-17.8037
78.11188.8536-8.48879.8405-9.73041.999-0.74411.04672.3772-1.39811.79611.06920.20620.1398-0.74620.6808-0.34120.2732.172-0.03061.3834-55.36674.7306-15.9257
80.80330.16971.28525.04012.40052.97040.19470.2868-1.56920.2090.1106-0.61980.36590.307-0.48081.4175-0.8984-0.07081.0711-0.18711.584-40.1173-12.3666-20.0493
91.64030.3380.27120.06930.05160.05340.01410.44580.5517-1.08540.62110.8307-0.440.00830.57611.2351-0.6590.14260.67930.23170.9946-25.419636.4716-25.0852
102.1434-1.6184-1.84497.0428-3.36335.4752-0.52090.2971-0.0531-1.02980.7117-0.4905-0.9490.4601-0.59951.0658-0.2455-0.21451.6595-0.54850.6168-20.070518.8139-19.0975
112.34870.7478-0.3374.3533-1.08991.0746-0.13330.22310.1615-0.18-0.1542-1.1515-0.3470.28730.04241.6916-1.10350.2542-0.6127-0.14790.7423-14.485333.7547-16.9922
123.4281.3721-0.87144.2203-0.0144.11240.1093-0.8310.06361.9851-0.62781.3023-0.29970.0836-0.55211.823-0.2010.3340.4635-0.00911.1225-30.963429.7725-6.5598
137.01812.74790.22282.2822-0.25360.9322-0.0438-0.60620.58371.1128-0.22541.8499-0.7251-0.3131-0.18961.5952-0.26830.43750.567-0.19631.2423-29.137442.3924-10.75
142.52080.68911.17144.42551.77361.4131-0.07280.171-0.4381-0.02450.4379-2.06730.59780.1482-0.30211.9435-0.6752-0.06090.6629-0.1851.2419-3.323537.5685-10.8272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 30:78)A30 - 78
2X-RAY DIFFRACTION2chain 'A' and (resseq 79:126)A79 - 126
3X-RAY DIFFRACTION3chain 'A' and (resseq 127:140)A127 - 140
4X-RAY DIFFRACTION4chain 'A' and (resseq 141:199)A141 - 199
5X-RAY DIFFRACTION5chain 'A' and (resseq 200:220)A200 - 220
6X-RAY DIFFRACTION6chain 'A' and (resseq 221:262)A221 - 262
7X-RAY DIFFRACTION7chain 'A' and (resseq 263:273)A263 - 273
8X-RAY DIFFRACTION8chain 'A' and (resseq 274:297)A274 - 297
9X-RAY DIFFRACTION9chain 'B' and (resseq 30:94)B30 - 94
10X-RAY DIFFRACTION10chain 'B' and (resseq 95:108)B95 - 108
11X-RAY DIFFRACTION11chain 'B' and (resseq 109:164)B109 - 164
12X-RAY DIFFRACTION12chain 'B' and (resseq 165:199)B165 - 199
13X-RAY DIFFRACTION13chain 'B' and (resseq 200:284)B200 - 284
14X-RAY DIFFRACTION14chain 'B' and (resseq 285:297)B285 - 297

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