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- PDB-6mq9: Crystal Structure of GTPase Domain of Human Septin 12 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6mq9
TitleCrystal Structure of GTPase Domain of Human Septin 12 in complex with GMPPNP
ComponentsSeptin-12
KeywordsSTRUCTURAL PROTEIN / cytoskeleton component septin GTPase spermatogenesis
Function / homology
Function and homology information


sperm annulus / septin complex / cytoskeleton-dependent cytokinesis / septin ring / cell division site / cleavage furrow / stress fiber / phosphatidylinositol binding / spindle / GDP binding ...sperm annulus / septin complex / cytoskeleton-dependent cytokinesis / septin ring / cell division site / cleavage furrow / stress fiber / phosphatidylinositol binding / spindle / GDP binding / microtubule cytoskeleton / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Septin-12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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 9, 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)138,57012
Polymers136,3844
Non-polymers2,1868
Water14,286793
1
A: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6433
Polymers34,0961
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6433
Polymers34,0961
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6433
Polymers34,0961
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6433
Polymers34,0961
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Septin-12
D: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2856
Polymers68,1922
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-28 kcal/mol
Surface area22830 Å2
MethodPISA
6
B: Septin-12
hetero molecules

C: Septin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2856
Polymers68,1922
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5130 Å2
ΔGint-30 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.511, 70.340, 89.337
Angle α, β, γ (deg.)74.550, 87.840, 78.100
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): Roseta DE3 / References: UniProt: Q8IYM1
#2: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*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.: 793 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M bicine/Trizma base pH 8.5, 20mM of each: 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 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: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.86→46.91 Å / Num. obs: 88175 / % possible obs: 96.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 20.69 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.043 / Net I/σ(I): 5.7
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 2 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 13725 / CC1/2: 0.572 / Rpim(I) all: 0.592 / % possible all: 95.2

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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: 4Z51

4z51


Resolution: 1.86→46.91 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.26
RfactorNum. reflection% reflection
Rfree0.233 4223 4.85 %
Rwork0.1921 --
obs0.1941 86997 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.79 Å2 / Biso mean: 32.2296 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 1.86→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8551 0 132 793 9476
Biso mean--20.17 38.56 -
Num. residues----1057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028900
X-RAY DIFFRACTIONf_angle_d0.57112121
X-RAY DIFFRACTIONf_chiral_restr0.0441363
X-RAY DIFFRACTIONf_plane_restr0.0031559
X-RAY DIFFRACTIONf_dihedral_angle_d18.4145373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8598-1.88090.43021220.35852461258385
1.8809-1.9030.39941330.35272729286291
1.903-1.92620.38041180.3242630274892
1.9262-1.95060.31891300.30752665279592
1.9506-1.97630.3681570.29562692284993
1.9763-2.00340.3121410.28672688282993
2.0034-2.0320.31331520.28092711286394
2.032-2.06230.31731300.25642768289893
2.0623-2.09450.30941410.26062679282094
2.0945-2.12890.29131480.24932730287894
2.1289-2.16560.2721260.23272760288694
2.1656-2.2050.26871500.22122727287795
2.205-2.24740.25771310.21672773290495
2.2474-2.29320.2391490.212741289095
2.2932-2.34310.27931620.2042753291595
2.3431-2.39760.29181330.19512746287994
2.3976-2.45760.23231320.20462780291296
2.4576-2.5240.26921470.19882745289295
2.524-2.59830.23621530.19032731288495
2.5983-2.68210.23951350.19422793292896
2.6821-2.7780.26911260.18732860298697
2.778-2.88920.26511510.18242809296098
2.8892-3.02070.22961240.1822853297797
3.0207-3.17990.19741490.17142842299198
3.1799-3.37910.17991510.16692837298898
3.3791-3.63990.17471600.15622838299898
3.6399-4.0060.17911390.14482857299698
4.006-4.58520.16071440.14212862300699
4.5852-5.77520.1931300.15392883301398
5.7752-46.9250.20761590.16752831299098
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)
12.30010.88381.36362.2683-0.25014.70110.08090.1326-0.2987-0.25720.0559-0.3110.0690.0586-0.04470.08770.08490.01380.15360.04260.2542-48.5471-16.7309-5.3677
22.21921.2202-0.19652.6665-1.24343.08440.2813-0.2139-0.3655-0.0553-0.1411-0.33840.20030.0746-0.13570.12490.0279-0.03110.19530.06320.3542-43.8394-16.7182.0777
32.53062.3189-0.95362.0461-0.85460.32720.1892-0.2636-0.11340.1281-0.2343-0.21130.02290.08580.00920.12870.0011-0.00880.21630.06620.2501-41.7207-6.03425.3557
43.27761.7317-1.11874.0428-0.66391.60850.1837-0.07760.35190.20350.00970.3913-0.2382-0.1069-0.1710.12350.03330.00190.16320.02970.1393-59.9862-6.06557.2509
51.5291.5380.53275.74651.05882.36020.03360.2250.38750.058-0.03080.1607-0.1691-0.09820.0350.06060.02880.00270.21120.06060.1823-60.8726-5.2502-1.9336
61.55791.49480.74576.19811.89411.9967-0.0060.0295-0.0361-0.11990.0312-0.01840.0982-0.1679-0.05230.08510.03040.00310.174-0.0010.1142-61.0471-19.6263-8.3024
77.41012.75511.12876.3691.28945.74960.1167-0.51120.7310.1163-0.131-0.3697-0.320.2760.12340.13640.00820.07920.1722-0.01090.3714-39.63393.94082.2599
81.70781.18660.04762.53220.43841.7143-0.20510.2451-0.3437-0.5470.1077-0.45160.28680.21570.03370.29960.03310.09680.1719-0.0360.2528-68.1077-25.4286-37.9919
93.26622.12960.86473.2891-0.12841.6341-0.15060.1201-0.0434-0.2511-0.0204-0.4445-0.01920.43670.23980.16170.0420.04250.21120.03010.2268-57.0564-9.9749-33.1875
101.58460.3283-0.32743.13250.04041.74520.02990.00920.6544-0.0440.05040.8453-0.0656-0.2702-0.02960.15770.02580.00150.1632-0.02570.3718-83.2691-17.8653-30.9432
112.30480.6245-0.51090.749-0.45661.7804-0.2551.03910.445-0.75630.22170.27750.32-0.6469-0.04990.4102-0.0799-0.10620.43490.0540.3187-81.7581-23.123-45.9148
123.45412.91360.63715.06130.40081.7203-0.37180.26850.2394-0.68150.24010.42090.1044-0.15130.09410.2471-0.00660.00980.17650.01180.1232-73.527-15.4477-39.9712
134.03570.7073-0.93614.4212-2.10365.3006-0.0444-0.01570.1079-0.01530.2460.5356-0.2031-0.3414-0.15340.15070.05780.00550.0939-0.04420.2122-48.2004-42.6407-19.4843
141.3873-0.0471-1.70692.1741-0.48143.56450.00460.21890.201-0.25580.17160.8247-0.0786-0.6607-0.14420.25390.031-0.0710.30930.05850.4786-56.1792-43.1912-21.2092
152.23950.8826-0.97013.0601-1.05182.75860.2483-0.29820.18220.5694-0.09670.5613-0.30410.0931-0.13590.29470.00060.09560.185-0.06990.2453-45.3386-40.8855-8.3815
161.10880.4118-0.46573.2682-1.10941.6659-0.0583-0.1007-0.1966-0.1478-0.1061-0.23360.11170.15250.10190.17610.01040.02930.1298-0.03170.179-36.2159-49.5924-18.0712
172.375-0.31090.94632.7217-0.94874.6527-0.29140.45810.0612-0.87510.34660.37240.3649-0.5418-0.01750.4264-0.1156-0.07640.2723-0.02750.2615-48.2512-47.1995-33.1095
187.9533-0.66051.25185.92721.23998.01710.1095-0.7594-0.02331.0416-0.0633-0.0994-0.01850.22730.02120.2612-0.02860.03290.18380.02790.179-42.5709-53.3752-1.1948
198.70623.9724-4.96963.7442-4.90797.0840.024-0.3859-0.09990.1151-0.3626-0.00410.00920.22390.20460.1599-0.011-0.00120.1656-0.01630.1661-67.8036-31.262526.6294
204.12233.10.90112.57991.33852.6660.0226-0.34880.03010.07340.22620.78820.0686-0.9231-0.01380.09070.0001-0.04570.39450.15510.4255-78.6728-31.008920.1972
211.3077-0.5342-1.24565-1.04575.0476-0.09560.21350.2059-0.20980.53580.9471-0.4357-0.8979-0.43380.27830.11160.03430.3810.03660.3541-75.2268-26.446626.8673
225.20152.9459-0.2394.3294-1.3074.50140.16910.0757-0.09730.366-0.093-0.0624-0.51210.3262-0.1070.2115-0.0381-0.02460.23770.02070.1712-63.6749-26.32327.7528
232.3285-0.0513-0.39354.1286-3.02285.68360.1038-0.05430.38110.4808-0.14090.2723-0.91020.33820.05380.3062-0.08430.03320.2447-0.00140.1479-64.0355-31.566941.5784
240.9277-0.2413-1.08580.4784-1.31496.8892-0.1163-0.08960.14550.30020.16940.31590.2465-0.6017-0.16640.2646-0.01690.09280.2327-0.01770.1947-72.4788-38.173146.4118
252.0904-0.25290.61761.8325-0.36730.2834-0.0207-0.03790.1295-0.001-0.3326-0.2428-0.00160.77230.14570.10550.0033-0.03580.35440.08430.1929-56.9942-31.994420.5872
267.096-3.87084.3999.1227-3.43013.90720.15330.1188-0.1359-0.906-0.3001-0.02960.6740.7623-0.0980.19290.1610.08170.40290.09610.235-54.1197-38.748311.2273
279.19030.6435-1.96410.2431.08168.5946-0.53860.0694-0.93040.1822-0.1744-0.24771.75070.65850.2670.42180.13570.00670.33930.08080.3532-58.0314-46.895922.674
284.3891-1.20940.95841.2479-1.52772.1585-0.12710.2332-0.3247-0.56450.45250.80170.3457-0.4084-0.26380.1555-0.0346-0.25650.32690.1450.3812-76.3115-31.74329.3431
291.3752-0.14641.80582.1985-1.95027.36330.12260.0411-0.0327-0.150.00780.18960.4510.0955-0.0870.07110.00670.00650.19220.03330.168-67.1734-39.561325.897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 81 )A48 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 126 )A86 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 184 )A127 - 184
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 231 )A185 - 231
5X-RAY DIFFRACTION5chain 'A' and (resid 232 through 254 )A232 - 254
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 294 )A255 - 294
7X-RAY DIFFRACTION7chain 'A' and (resid 295 through 316 )A295 - 316
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 126 )B47 - 126
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 159 )B127 - 159
10X-RAY DIFFRACTION10chain 'B' and (resid 160 through 231 )B160 - 231
11X-RAY DIFFRACTION11chain 'B' and (resid 232 through 267 )B232 - 267
12X-RAY DIFFRACTION12chain 'B' and (resid 268 through 317 )B268 - 317
13X-RAY DIFFRACTION13chain 'C' and (resid 48 through 70 )C48 - 70
14X-RAY DIFFRACTION14chain 'C' and (resid 71 through 101 )C71 - 101
15X-RAY DIFFRACTION15chain 'C' and (resid 102 through 144 )C102 - 144
16X-RAY DIFFRACTION16chain 'C' and (resid 145 through 244 )C145 - 244
17X-RAY DIFFRACTION17chain 'C' and (resid 245 through 294 )C245 - 294
18X-RAY DIFFRACTION18chain 'C' and (resid 295 through 317 )C295 - 317
19X-RAY DIFFRACTION19chain 'D' and (resid 48 through 61 )D48 - 61
20X-RAY DIFFRACTION20chain 'D' and (resid 62 through 85 )D62 - 85
21X-RAY DIFFRACTION21chain 'D' and (resid 86 through 101 )D86 - 101
22X-RAY DIFFRACTION22chain 'D' and (resid 102 through 126 )D102 - 126
23X-RAY DIFFRACTION23chain 'D' and (resid 127 through 144 )D127 - 144
24X-RAY DIFFRACTION24chain 'D' and (resid 145 through 159 )D145 - 159
25X-RAY DIFFRACTION25chain 'D' and (resid 160 through 200 )D160 - 200
26X-RAY DIFFRACTION26chain 'D' and (resid 201 through 217 )D201 - 217
27X-RAY DIFFRACTION27chain 'D' and (resid 218 through 244 )D218 - 244
28X-RAY DIFFRACTION28chain 'D' and (resid 245 through 268 )D245 - 268
29X-RAY DIFFRACTION29chain 'D' and (resid 269 through 317 )D269 - 317

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