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- PDB-7c2h: Crystal Structure of the Thorarchaeota 2DGel3/rabbit actin complex -

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Basic information

Entry
Database: PDB / ID: 7c2h
TitleCrystal Structure of the Thorarchaeota 2DGel3/rabbit actin complex
Components
  • 2DGel3
  • Actin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / actin regulator
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Gelsolin-like domain-containing protein / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Candidatus Thorarchaeota archaeon SMTZ1-83 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.352 Å
AuthorsRobinson, R.C. / Akil, C.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H00476 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea
Authors: Akil, C. / Tran, L.T. / Orhant-Prioux, M. / Baskaran, Y. / Manser, E. / Blanchoin, L. / Robinson, R.C.
History
DepositionMay 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
G: 2DGel3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9039
Polymers65,1562
Non-polymers7487
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-91 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.915, 98.644, 62.448
Angle α, β, γ (deg.)90.000, 94.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli) / References: UniProt: P68135
#2: Protein 2DGel3


Mass: 23045.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Skeletal muscle
Source: (gene. exp.) Candidatus Thorarchaeota archaeon SMTZ1-83 (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A135VDL7
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 47.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M CHES pH 9.5 20% w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.352→40 Å / Num. obs: 23279 / % possible obs: 93.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 42.16 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.055 / Rrim(I) all: 0.146 / Χ2: 1.063 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.36-2.445.50.58419760.8620.2630.6430.66281.4
2.44-2.545.90.48621950.8830.2110.5310.67788.7
2.54-2.666.10.39223470.9530.1680.4280.70993.8
2.66-2.86.70.46424240.8590.1990.5060.74698.3
2.8-2.977.10.41324710.9610.1710.4480.85699.8
2.97-3.27.40.29324730.9840.1170.3161.027100
3.2-3.527.60.21325020.9910.0840.2291.273100
3.52-4.035.90.17318680.9690.0750.1891.62775.7
4.03-5.087.40.08124990.9970.0320.0871.48899.7
5.08-407.20.05225240.9980.0210.0571.36999.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C2G

7c2g


Resolution: 2.352→31.206 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.74
RfactorNum. reflection% reflection
Rfree0.2377 1041 4.49 %
Rwork0.2021 --
obs0.2037 23203 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.34 Å2 / Biso mean: 58.3657 Å2 / Biso min: 26.16 Å2
Refinement stepCycle: final / Resolution: 2.352→31.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4389 0 37 124 4550
Biso mean--39.06 50.98 -
Num. residues----553
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3523-2.47620.34181260.2962256275
2.4762-2.63130.27181680.2745309391
2.6313-2.83430.31681480.2563334698
2.8343-3.11930.28251400.24683446100
3.1193-3.57020.23091490.21583421100
3.5702-4.49590.22441350.1746284583
4.4959-31.2060.20311750.16133449100
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)
14.36540.8451-0.88193.5105-0.47513.3014-0.15140.2635-0.6823-0.82260.15350.10180.77850.15990.03970.6544-0.0833-0.02280.4649-0.08120.461114.6022-23.29269.2477
21.39710.20220.31652.6228-0.59362.5189-0.03720.47360.0068-0.97510.0794-0.18380.32760.2203-0.02770.5092-0.03230.06030.4419-0.04450.39417.9742-12.09927.8412
31.63370.68190.486.3457-0.75831.2307-0.06040.0129-0.16590.01340.1173-0.4275-0.01760.1997-0.05950.20080.02160.01350.3474-0.06290.315722.766-10.124529.2902
42.6644-0.4763-0.81292.86421.43362.79320.0040.99050.4339-1.3803-0.1413-0.1244-0.31130.17240.20870.8829-0.1055-0.11370.68450.10050.518410.295-5.1722-1.28
53.3961-0.26730.03214.96120.723.1167-0.03120.59450.4745-1.14940.24010.9597-0.3624-0.3654-0.20940.5439-0.0361-0.18110.42750.11530.55785.434713.538411.0543
65.36741.497-2.44056.3936-0.97063.87540.22760.25080.6973-0.3791-0.0740.5135-0.427-0.0374-0.02940.4781-0.0182-0.1230.41090.01540.580610.48419.883517.1979
70.60222.15371.04238.50834.51892.8662-0.1558-0.01860.261-0.1047-0.16231.63130.127-0.61270.56120.5575-0.0859-0.06410.60230.07720.8115-5.1429-3.17415.4281
84.267-1.17090.7796.5683-2.20246.1996-0.25010.7228-0.7483-0.7319-0.0823-0.22240.8790.13270.02690.4662-0.07230.14030.4338-0.05320.652-1.6977-31.466615.087
94.3763.10661.29446.61621.37945.2962-0.45490.2201-0.6888-1.04390.3029-0.65091.23560.20890.44561.1014-0.02730.22680.6310.03230.73061.1571-37.315215.4819
101.35110.4790.65653.1281-0.3884.0471-0.0390.0291-0.265-0.19120.08970.55670.3839-0.0869-0.02640.325-0.00650.01050.41010.10170.64940.1702-32.031323.6656
114.82981.574-0.84351.1699-0.54491.14910.0319-0.01930.26140.01750.2671.2181-0.1796-0.821-0.28650.48240.0322-0.02320.66370.08080.8168-8.6733-27.503424.2715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 78 )A6 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 196 )A79 - 196
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 334 )A197 - 334
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 372 )A335 - 372
5X-RAY DIFFRACTION5chain 'G' and (resid 2 through 64 )G2 - 64
6X-RAY DIFFRACTION6chain 'G' and (resid 65 through 92 )G65 - 92
7X-RAY DIFFRACTION7chain 'G' and (resid 93 through 106 )G93 - 106
8X-RAY DIFFRACTION8chain 'G' and (resid 107 through 117 )G107 - 117
9X-RAY DIFFRACTION9chain 'G' and (resid 118 through 133 )G118 - 133
10X-RAY DIFFRACTION10chain 'G' and (resid 134 through 174 )G134 - 174
11X-RAY DIFFRACTION11chain 'G' and (resid 175 through 198 )G175 - 198

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