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- PDB-6n12: Structure of GTPase Domain of Human Septin 7 at High Resolution -

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Basic information

Entry
Database: PDB / ID: 6n12
TitleStructure of GTPase Domain of Human Septin 7 at High Resolution
ComponentsSeptin-7
KeywordsSTRUCTURAL PROTEIN / cytoskeleton component septin GTPase
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 2.23 Å
AuthorsBrognara, G. / Pereira, H.M. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Revisiting SEPT7 and the slippage of beta-strands in the septin family.
Authors: Brognara, G. / Pereira, H.M. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)66,4506
Polymers65,5152
Non-polymers9354
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-43 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.815, 82.815, 209.021
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Septin-7 / / CDC10 protein homolog


Mass: 32757.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT7, CDC10 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q16181
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol 0.03 M of each CaCl2 and MgCl2, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.23→69.68 Å / Num. obs: 39079 / % possible obs: 99.2 % / Redundancy: 20.4 % / Biso Wilson estimate: 48.79 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.045 / Net I/σ(I): 8.6
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 20.6 % / Rmerge(I) obs: 2.26 / Num. unique obs: 2845 / CC1/2: 0.529 / Rpim(I) all: 0.509 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N06

6n06


Resolution: 2.23→40.618 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 1977 5.07 %Random selection
Rwork0.1813 ---
obs0.183 38992 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.01 Å2 / Biso mean: 68.1032 Å2 / Biso min: 36.88 Å2
Refinement stepCycle: final / Resolution: 2.23→40.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 58 179 4161
Biso mean--49.8 62.98 -
Num. residues----505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084054
X-RAY DIFFRACTIONf_angle_d0.9425502
X-RAY DIFFRACTIONf_chiral_restr0.058629
X-RAY DIFFRACTIONf_plane_restr0.005701
X-RAY DIFFRACTIONf_dihedral_angle_d12.4522447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.28580.3331170.29022611272898
2.2858-2.34760.30771400.2542631277198
2.3476-2.41670.28571750.24562593276898
2.4167-2.49470.25731370.22312634277198
2.4947-2.58380.26151470.20512648279599
2.5838-2.68720.2861230.20732602272599
2.6872-2.80950.24641530.22644279799
2.8095-2.95760.21761370.19392687282499
2.9576-3.14280.24011260.1942623274999
3.1428-3.38540.24941660.18552638280499
3.3854-3.72590.18691480.168526582806100
3.7259-4.26450.16491310.158626632794100
4.2645-5.37090.17641280.151926972825100
5.3709-40.62470.22221490.182686283599
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)
12.75610.77221.14994.7541.47291.7788-0.06050.01660.3130.15570.18260.1696-0.06670.172-0.12140.5002-0.16450.05670.42950.0110.440137.7553-1.275320.6235
21.35710.71080.52648.18620.99980.7682-0.18150.33560.0994-0.5080.4741-0.0105-0.23230.3273-0.3150.5336-0.21110.02380.5570.02320.400538.6972-5.01858.5027
33.6105-1.07611.49846.468-0.56992.97030.06150.2296-0.20930.09740.4668-1.1810.12320.6992-0.39430.5065-0.0458-0.12170.6908-0.24750.694951.0603-16.350713.1415
40.30810.80.3892.83761.58040.881-0.12510.15270.1054-0.85040.3756-0.3468-0.35480.3647-0.15910.7194-0.34710.02490.65870.0350.654644.28586.75310.1559
55.011-1.5258-2.8673.6831-1.40583.66640.14060.3904-0.38350.1210.1991-0.00830.43960.0747-0.33250.5798-0.0681-0.21630.3965-0.02890.405526.7423-35.9277.1114
64.9886-1.0607-0.9937.02821.19982.33250.04340.63380.3643-0.44680.1355-0.41150.04830.5975-0.24020.6877-0.1191-0.18340.7230.00310.489326.0366-30.6572-1.3165
74.25252.59670.59254.42241.19682.0622-0.07490.03320.2254-0.1320.21020.55840.42120.0043-0.14780.647-0.1567-0.13890.4260.16030.427514.9272-32.8566.8844
85.64062.6578-0.83493.3383-0.30660.1127-0.11240.33240.1761-0.09620.28720.36480.2120.0367-0.17820.6959-0.1383-0.11490.39190.09820.379716.8661-33.098213.2781
95.81941.74230.04483.52360.9621.08170.1503-0.52560.11910.67210.0625-0.00030.5770.0323-0.20770.8364-0.1047-0.18890.42060.05450.3829.4927-29.666222.8422
107.27821.0409-1.53683.4310.21582.77740.0582-0.0479-0.68760.38240.2332-0.78240.73070.3995-0.17940.77520.0554-0.31150.5416-0.11380.627936.6833-36.995715.5517
112.35453.52730.03247.02550.44444.44420.7603-0.35-0.97140.87120.032-0.9980.86660.4116-0.85330.92310.0602-0.27390.4448-0.06650.832138.2023-40.795614.8094
127.37592.5806-0.87692.95760.36422.93370.236-0.3484-0.15760.5518-0.2030.64630.5938-0.2111-0.12390.8631-0.2678-0.07550.47280.10790.58657.8933-41.424816.1832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 145 )A48 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 217 )A146 - 217
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 281 )A218 - 281
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 316 )A282 - 316
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 70 )B48 - 70
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 101 )B71 - 101
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 145 )B102 - 145
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 183 )B146 - 183
9X-RAY DIFFRACTION9chain 'B' and (resid 184 through 217 )B184 - 217
10X-RAY DIFFRACTION10chain 'B' and (resid 218 through 267 )B218 - 267
11X-RAY DIFFRACTION11chain 'B' and (resid 268 through 293 )B268 - 293
12X-RAY DIFFRACTION12chain 'B' and (resid 294 through 316 )B294 - 316

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