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- PDB-6mqk: Crystal Structure of GTPase Domain of Human Septin 12 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6mqk
TitleCrystal Structure of GTPase Domain of Human Septin 12 in complex with GDP
ComponentsSeptin-12
KeywordsSTRUCTURAL PROTEIN / cytoskeleton component septin GTPase spermatogenesis
Function / homology
Function and homology information


sperm annulus / septin complex / septin ring / cytoskeleton-dependent cytokinesis / cell division site / cleavage furrow / stress fiber / phosphatidylinositol binding / spindle / GDP binding ...sperm annulus / septin complex / septin ring / cytoskeleton-dependent cytokinesis / cell division site / cleavage furrow / stress fiber / phosphatidylinositol binding / spindle / GDP binding / microtubule cytoskeleton / protein localization / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / GTPase activity / GTP binding / perinuclear region of cytoplasm / protein homodimerization activity / identical protein binding / nucleus
Similarity search - Function
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-12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsCastro, D.K.S.V. / Pereira, H.M. / Brandao-Neto, J. / Ulian, A.P.U. / Garratt, R.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
Sao Paulo Research Foundation (FAPESP)2016/19734-2 Brazil
CitationJournal: Iucrj / Year: 2020
Title: A complete compendium of crystal structures for the human SEPT3 subgroup reveals functional plasticity at a specific septin interface.
Authors: Castro, D.K.S.D.V. / da Silva, S.M.O. / Pereira, H.D. / Macedo, J.N.A. / Leonardo, D.A. / Valadares, N.F. / Kumagai, P.S. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionOct 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Oct 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-12
B: Septin-12
C: Septin-12
D: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,25412
Polymers136,3844
Non-polymers1,8708
Water3,099172
1
A: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5643
Polymers34,0961
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5643
Polymers34,0961
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5643
Polymers34,0961
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5643
Polymers34,0961
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Septin-12
D: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1276
Polymers68,1922
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-40 kcal/mol
Surface area23400 Å2
MethodPISA
6
B: Septin-12
hetero molecules

C: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1276
Polymers68,1922
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5030 Å2
ΔGint-43 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.960, 69.250, 88.230
Angle α, β, γ (deg.)75.450, 89.460, 76.430
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Septin-12


Mass: 34096.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT12 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q8IYM1
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.98 Å3/Da / Density % sol: 37.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 M bicine/Trizma base pH 8.5, 30mM magnesium chloride, 30mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.19→45.59 Å / Num. obs: 52030 / % possible obs: 96.7 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.068 / Net I/σ(I): 6.9
Reflection shellResolution: 2.19→2.25 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3910 / CC1/2: 0.562 / Rpim(I) all: 0.607 / % possible all: 96.3

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MQ9

6mq9


Resolution: 2.19→45.586 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.39
RfactorNum. reflection% reflection
Rfree0.2286 2542 4.89 %
Rwork0.1843 --
obs0.1865 52022 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.44 Å2 / Biso mean: 56.5932 Å2 / Biso min: 26.7 Å2
Refinement stepCycle: final / Resolution: 2.19→45.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8489 0 116 172 8777
Biso mean--36.49 49.13 -
Num. residues----1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058834
X-RAY DIFFRACTIONf_angle_d0.79812034
X-RAY DIFFRACTIONf_chiral_restr0.051363
X-RAY DIFFRACTIONf_plane_restr0.0041550
X-RAY DIFFRACTIONf_dihedral_angle_d17.9545320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.23210.34251410.29382808294996
2.2321-2.27770.3421500.27452657280796
2.2777-2.32720.30151420.27162759290196
2.3272-2.38140.32861410.26362708284996
2.3814-2.44090.30651150.25792751286696
2.4409-2.50690.321210.26042721284296
2.5069-2.58070.32071540.25332732288696
2.5807-2.6640.31261430.23332721286497
2.664-2.75920.28131370.22162795293297
2.7592-2.86960.28241470.22262740288797
2.8696-3.00020.28851560.21942758291498
3.0002-3.15830.26311170.20932843296098
3.1583-3.35620.23341600.18512775293598
3.3562-3.61520.23221370.17172768290598
3.6152-3.97880.18681480.15812757290597
3.9788-4.55410.18011450.13822730287597
4.5541-5.73590.16521450.14432769291497
5.7359-45.59570.1891430.15332688283195
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)
14.12432.16021.07757.95090.75336.866-0.1151-0.11150.2705-0.2378-0.0244-0.6652-0.311-0.01610.21710.27110.0440.06350.2901-0.00330.4083-47.4809-15.2813-0.6453
23.80261.6081-0.10815.20472.93594.53230.15430.1611-1.0309-0.88690.1564-0.97120.19670.6426-0.01390.41310.01760.14380.6012-0.02280.7294-44.537-19.1853-6.2303
34.57581.2226-3.0587.1723-6.27817.52960.4703-0.6492-0.08040.0693-0.3122-0.21940.01350.7905-0.12090.3661-0.12450.00920.4624-0.07030.5584-44.6692-14.48766.6416
46.89942.6893-2.43963.4488-0.48762.11280.3011-0.53370.6326-0.0657-0.0703-0.3461-0.33610.4444-0.22810.4069-0.05230.04960.3696-0.04810.4208-44.704-6.83455.5915
52.99860.7203-1.16912.81360.55624.87250.15370.13590.5957-0.06650.1650.0146-0.5091-0.1106-0.27480.35180.0167-0.01260.36150.04830.4165-61.213-7.98650.397
68.14415.56881.6167.53832.80513.90330.14120.22250.6317-0.20160.146-0.2426-0.35380.3482-0.27210.41730.02590.14450.3108-0.01580.4217-51.4607-6.8611-2.797
76.2392.6029-1.15512.7585-0.03165.2223-0.35410.23380.1954-0.30670.1131-0.1226-0.23270.19580.23320.47770.0082-0.05120.29850.01270.3448-68.9374-24.4371-39.7745
88.71822.60517.20820.81252.12495.9823-0.00340.5203-0.6528-0.13660.1682-0.37860.16080.5622-0.16020.68080.07780.04930.3966-0.02390.4927-64.667-29.2241-43.8848
93.5671.7903-2.05534.9617-0.56593.67960.20420.0406-0.09920.0249-0.2471-0.3032-0.2439-0.17780.07810.33190.0285-0.05090.36250.01940.3384-63.7351-18.7267-31.2498
106.54875.46470.45765.7723-0.00562.0518-0.35190.3785-0.0214-0.12460.193-0.1713-0.0601-0.04710.14010.3650.016-0.04490.28320.04990.3546-69.2759-15.6863-31.9914
115.63823.7916-1.00037.2056-2.07540.71010.19050.26470.49580.52370.00880.2549-0.0704-0.0658-0.13960.34330.0317-0.01360.3353-0.01730.3112-79.6801-21.8509-35.6993
126.53055.06073.2544.01922.83144.4362-0.27510.40930.4751-0.19080.2571.3176-0.16350.161-0.0210.5388-0.0192-0.03950.42030.04820.5527-90.3153-19.2099-35.0444
134.9405-2.20043.22358.090.932.9152-0.02390.19342.2343-0.5380.3827-0.3266-1.0552-0.4478-0.37260.61430.050.08930.48470.03350.9307-79.5156-6.086-35.9153
142.8973-1.0767-0.57757.14491.84272.26620.10480.47160.2325-0.2693-0.1936-0.08680.0809-0.28250.11570.4296-0.0249-0.05220.64320.06280.3039-80.7075-23.5868-48.0412
156.70226.69594.11158.58534.37374.3394-0.35060.37620.2202-0.49520.2360.1803-0.2230.09880.08580.29270.05050.06720.29910.05990.263-72.1119-15.4937-41.3974
164.93622.1928-1.73077.7341-3.9482.81260.0277-0.13520.3051-0.0501-0.04990.4026-0.0186-0.38680.08650.4207-0.01820.02250.3806-0.07350.3382-49.597-41.631-21.8282
171.0427-0.8332-2.76818.0942-0.61069.5803-0.3666-0.18440.3868-0.06080.10211.5924-0.0999-0.49220.38530.6217-0.02940.05040.708-0.05480.7287-55.9941-40.9074-24.7393
187.83215.76031.96937.74451.98826.0933-0.0609-0.40250.4465-0.05940.12890.4778-0.5552-0.1637-0.09510.44630.10420.08650.40210.00460.3666-47.6124-37.3384-16.0632
192.0611-0.0695-0.26373.714-0.34927.75440.0942-0.29620.00560.6059-0.14680.56940.4101-0.76940.03660.4649-0.07630.12010.5212-0.09350.4225-52.2262-46.1449-2.2765
203.24480.8173-1.35323.617-1.88664.6962-0.1472-0.2458-0.2404-0.024-0.0571-0.19580.28650.20040.21670.4061-0.02170.0180.293-0.03730.3339-33.4731-46.0848-21.8418
218.2999-4.68865.45517.9851-4.70927.5642-0.60350.0484-0.27520.13090.45580.07850.1222-0.60690.09580.4158-0.10070.15640.3846-0.09430.2336-45.4826-50.4598-32.2354
221.1470.50380.02834.0333-3.17133.0492-0.04320.2843-0.2117-0.37290.36080.31410.5922-0.4092-0.37540.4416-0.090.03890.3796-0.07540.4035-46.6986-51.5745-25.7518
234.8846-4.5445-4.6346.48454.22144.4181-0.371-0.92990.63671.62010.5167-0.38761.7030.19330.02920.7879-0.00380.00920.5907-0.05520.4046-43.239-48.23684.9806
245.96341.81110.517.5534-0.68368.8005-0.06210.17950.15180.08420.09880.77380.0664-0.95680.02190.2930.04420.06320.4095-0.02010.3963-75.0141-30.859721.6458
250.51560.094-0.6791.5373-1.49027.04570.0542-0.08180.15290.2318-0.00910.0568-0.1688-0.068-0.07060.3453-0.04520.00970.3316-0.05690.3405-65.3448-30.198929.5029
267.23470.7892-0.64613.57680.63886.211-0.4682-0.4342-0.8698-0.01030.0478-0.33921.17870.16920.27590.57660.02760.08890.3784-0.01420.4436-57.1872-44.218717.6494
270.69970.30081.07672.406-0.79817.4581-0.00660.003-0.007-0.2155-0.00890.27140.5059-0.4811-0.02440.2363-0.0370.03180.4055-0.0220.4043-70.5419-37.128620.212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 70 )A48 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 100 )A71 - 100
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 126 )A101 - 126
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 200 )A127 - 200
5X-RAY DIFFRACTION5chain 'A' and (resid 201 through 267 )A201 - 267
6X-RAY DIFFRACTION6chain 'A' and (resid 268 through 314 )A268 - 314
7X-RAY DIFFRACTION7chain 'B' and (resid 47 through 70 )B47 - 70
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 99 )B71 - 99
9X-RAY DIFFRACTION9chain 'B' and (resid 100 through 144 )B100 - 144
10X-RAY DIFFRACTION10chain 'B' and (resid 145 through 184 )B145 - 184
11X-RAY DIFFRACTION11chain 'B' and (resid 185 through 200 )B185 - 200
12X-RAY DIFFRACTION12chain 'B' and (resid 201 through 217 )B201 - 217
13X-RAY DIFFRACTION13chain 'B' and (resid 218 through 231 )B218 - 231
14X-RAY DIFFRACTION14chain 'B' and (resid 232 through 268 )B232 - 268
15X-RAY DIFFRACTION15chain 'B' and (resid 269 through 317 )B269 - 317
16X-RAY DIFFRACTION16chain 'C' and (resid 48 through 71 )C48 - 71
17X-RAY DIFFRACTION17chain 'C' and (resid 72 through 92 )C72 - 92
18X-RAY DIFFRACTION18chain 'C' and (resid 93 through 126 )C93 - 126
19X-RAY DIFFRACTION19chain 'C' and (resid 127 through 159 )C127 - 159
20X-RAY DIFFRACTION20chain 'C' and (resid 160 through 231 )C160 - 231
21X-RAY DIFFRACTION21chain 'C' and (resid 232 through 268 )C232 - 268
22X-RAY DIFFRACTION22chain 'C' and (resid 269 through 305 )C269 - 305
23X-RAY DIFFRACTION23chain 'C' and (resid 306 through 319 )C306 - 319
24X-RAY DIFFRACTION24chain 'D' and (resid 48 through 84 )D48 - 84
25X-RAY DIFFRACTION25chain 'D' and (resid 85 through 200 )D85 - 200
26X-RAY DIFFRACTION26chain 'D' and (resid 201 through 244 )D201 - 244
27X-RAY DIFFRACTION27chain 'D' and (resid 245 through 317 )D245 - 317

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