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- PDB-6p8v: Structure of E. coli MS115-1 HORMA:CdnC:Trip13 complex -

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Basic information

Entry
Database: PDB / ID: 6p8v
TitleStructure of E. coli MS115-1 HORMA:CdnC:Trip13 complex
Components
  • ATPase, AAA family
  • E. coli MS115-1 CdnC
  • E. coli MS115-1 HORMA
KeywordsPROTEIN BINDING / ATPase / Remodeller / HORMA domain / TRIP13 / Pch2
Function / homology
Function and homology information


2'-5'-oligoadenylate synthetase activity / diadenylate cyclase / diadenylate cyclase activity / nucleotide metabolic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / double-stranded RNA binding / microtubule cytoskeleton / defense response to virus / ATP hydrolysis activity / ATP binding ...2'-5'-oligoadenylate synthetase activity / diadenylate cyclase / diadenylate cyclase activity / nucleotide metabolic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / double-stranded RNA binding / microtubule cytoskeleton / defense response to virus / ATP hydrolysis activity / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
Bacterial HORMA domain 1 / Bacterial HORMA domain family 1 / : / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / : / Nucleotidyltransferase superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities ...Bacterial HORMA domain 1 / Bacterial HORMA domain family 1 / : / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / : / Nucleotidyltransferase superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Bacterial HORMA domain-containing protein / Cyclic AMP-AMP-AMP synthase / CD-NTase-associated protein 7 / CD-NTase-associated protein 6
Similarity search - Component
Biological speciesEscherichia coli MS 115-1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsYe, Q. / Corbett, K.D.
CitationJournal: Mol.Cell / Year: 2020
Title: HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity.
Authors: Ye, Q. / Lau, R.K. / Mathews, I.T. / Birkholz, E.A. / Watrous, J.D. / Azimi, C.S. / Pogliano, J. / Jain, M. / Corbett, K.D.
History
DepositionJun 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Structure summary / Category: citation / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase, AAA family
B: ATPase, AAA family
C: ATPase, AAA family
D: ATPase, AAA family
E: ATPase, AAA family
F: ATPase, AAA family
G: E. coli MS115-1 CdnC
H: E. coli MS115-1 HORMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,28014
Polymers263,7208
Non-polymers2,5606
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32700 Å2
ΔGint-75 kcal/mol
Surface area93940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.789, 138.516, 100.212
Angle α, β, γ (deg.)90.00, 98.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ATPase, AAA family


Mass: 34636.684 Da / Num. of mol.: 6 / Mutation: E159Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli MS 115-1 (bacteria) / Gene: HMPREF9540_01760 / Production host: Escherichia coli (E. coli) / References: UniProt: D7Y2H4
#2: Protein E. coli MS115-1 CdnC


Mass: 36451.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli MS 115-1 (bacteria) / Gene: HMPREF9540_01758 / Production host: Escherichia coli (E. coli) / References: UniProt: D7Y2H2
#3: Protein E. coli MS115-1 HORMA


Mass: 19447.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BHS87_27760, CG706_08820 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X1LKT4, UniProt: D7Y2H3*PLUS
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M MOPS pH 7.0, 0.2 M MgCl2, and 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.64→99.19 Å / Num. obs: 70640 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.091 / Rrim(I) all: 0.17 / Net I/σ(I): 7.2
Reflection shellResolution: 2.64→2.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.186 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4550 / CC1/2: 0.292 / Rpim(I) all: 0.783 / Rrim(I) all: 1.426 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P80

6p80


Resolution: 2.64→88.876 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 33.4
RfactorNum. reflection% reflection
Rfree0.2709 3478 4.93 %
Rwork0.2331 --
obs0.235 70547 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.64→88.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17660 0 156 0 17816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418152
X-RAY DIFFRACTIONf_angle_d0.66224668
X-RAY DIFFRACTIONf_dihedral_angle_d13.46111094
X-RAY DIFFRACTIONf_chiral_restr0.042821
X-RAY DIFFRACTIONf_plane_restr0.0053213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.67620.42041240.3712642X-RAY DIFFRACTION99
2.6762-2.71440.37041420.36072746X-RAY DIFFRACTION99
2.7144-2.75490.41021300.34652617X-RAY DIFFRACTION99
2.7549-2.7980.38151350.3472730X-RAY DIFFRACTION100
2.798-2.84390.37751430.32392639X-RAY DIFFRACTION99
2.8439-2.89290.36491520.33532725X-RAY DIFFRACTION100
2.8929-2.94550.34551220.30042684X-RAY DIFFRACTION100
2.9455-3.00220.37381310.3012696X-RAY DIFFRACTION99
3.0022-3.06340.37221480.30112670X-RAY DIFFRACTION100
3.0634-3.13010.34461570.29732666X-RAY DIFFRACTION99
3.1301-3.20290.34221500.28292686X-RAY DIFFRACTION100
3.2029-3.2830.3521410.28212667X-RAY DIFFRACTION99
3.283-3.37170.30051490.26152667X-RAY DIFFRACTION99
3.3717-3.4710.30151430.25852688X-RAY DIFFRACTION99
3.471-3.5830.32571330.25092686X-RAY DIFFRACTION99
3.583-3.71110.27271370.24282679X-RAY DIFFRACTION99
3.7111-3.85960.28031610.23282621X-RAY DIFFRACTION98
3.8596-4.03530.26111270.2182644X-RAY DIFFRACTION98
4.0353-4.2480.2241270.20682676X-RAY DIFFRACTION99
4.248-4.51420.22931410.18712686X-RAY DIFFRACTION99
4.5142-4.86270.21631260.17822697X-RAY DIFFRACTION99
4.8627-5.3520.22381440.18752701X-RAY DIFFRACTION99
5.352-6.12630.24281220.24052721X-RAY DIFFRACTION99
6.1263-7.71780.23831450.2182709X-RAY DIFFRACTION99
7.7178-88.92630.19531480.17492726X-RAY DIFFRACTION98
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)
10.7731-0.1712-0.27421.1978-0.11193.9119-0.00520.10950.0293-0.1868-0.02210.0636-0.0689-0.2215-00.53890.0028-0.03990.5147-0.02980.5521-18.8654-41.3682-21.1099
22.5277-0.81960.49142.2830.25811.32830.0003-0.1288-0.1362-0.01430.08320.33460.0337-0.271300.6559-0.04560.01180.74160.09510.6283-30.6601-0.490333.8231
30.90440.46640.58412.5508-0.34431.6029-0.11820.0240.2923-0.0565-0.11530.2935-0.3988-0.1023-0.00030.67680.03220.02580.63340.00660.6016-7.789319.168547.172
40.85160.0820.19352.48020.62162.7905-0.0511-0.0952-0.1760.1826-0.03550.28790.0455-0.151800.51060.00370.0380.52120.03480.5382-5.2706-4.097252.6895
51.82831.4967-0.261.96790.10030.7781-0.1155-0.15930.10640.59890.0312-0.2941-0.12850.3059-00.6317-0.004-0.11670.68250.01610.625327.9576-0.552351.3593
61.96980.02051.14132.3884-0.29171.80150.0612-0.2718-0.19320.3838-0.0965-0.16640.2482-0.070900.67190.00360.00970.59170.01320.598619.6468-21.565843.2734
72.57630.0215-0.31241.57560.44082.02850.16290.12670.1636-0.10590.2122-0.56090.07140.45040.00010.68020.0546-0.09060.7906-0.11950.922143.2485-21.797719.8552
81.9739-0.6755-1.16071.93511.22772.3549-0.1105-0.1089-0.04970.0390.0705-0.20060.18580.117100.6268-0.0121-0.0460.5510.01940.618922.2863-31.109113.0952
92.9846-0.1957-0.10941.7874-1.44963.14940.21490.23530.3279-0.1156-0.0392-0.2537-0.70830.22240.00010.82190.02270.12580.6075-0.04170.628824.7434-20.2829-17.7954
103.13080.2387-0.82053.2498-0.5541.5867-0.24060.5347-0.51560.02090.23530.2130.354-0.30840.00010.9542-0.0469-0.00251.0533-0.12440.9709-33.1316-6.415-8.6798
112.5440.46680.34332.30870.14313.4285-0.02330.03970.2083-0.2661-0.00050.0482-0.4059-0.1338-00.55950.00280.03840.50720.00970.56622.0606-21.3084-7.5257
121.8782-0.21870.11611.4055-0.49541.3149-0.40190.12890.52120.0537-0.0531-0.1222-0.6031-0.5374-0.00031.03360.04750.01910.80670.05090.6322-12.63547.6363-19.2229
130.4990.88170.14322.42340.45021.307-0.0219-0.2635-0.10580.6135-0.0563-0.01560.68660.0280.00010.94060.02170.05880.61820.02890.6293-20.5828-51.898520.4503
141.5949-0.1332-0.23681.868-0.2482.33390.06010.02930.3619-0.245-0.0028-0.3371-0.3352-0.09610.00020.7871-0.00220.02620.65860.070.7617-31.201518.255914.9064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND RESID 2:321 )G2 - 321
2X-RAY DIFFRACTION2( CHAIN A AND RESID 3:223 )A3 - 223
3X-RAY DIFFRACTION3( CHAIN A AND RESID 224:308 )A224 - 308
4X-RAY DIFFRACTION4( CHAIN B AND RESID 3:223 )B3 - 223
5X-RAY DIFFRACTION5( CHAIN B AND RESID 224:308 )B224 - 308
6X-RAY DIFFRACTION6( CHAIN C AND RESID 3:223 )C3 - 223
7X-RAY DIFFRACTION7( CHAIN C AND RESID 224:309 )C224 - 309
8X-RAY DIFFRACTION8( CHAIN D AND RESID 3:223 )D3 - 223
9X-RAY DIFFRACTION9( CHAIN D AND RESID 224:309 )D224 - 309
10X-RAY DIFFRACTION10( CHAIN F AND RESID 6:223 )F6 - 223
11X-RAY DIFFRACTION11( CHAIN E AND RESID 5:223 )E5 - 223
12X-RAY DIFFRACTION12( CHAIN E AND RESID 224:307 )E224 - 307
13X-RAY DIFFRACTION13( CHAIN H AND RESID 0:172 )H0 - 172
14X-RAY DIFFRACTION14( CHAIN F AND RESID 224:307 )F224 - 307

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