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- PDB-7c2g: Crystal Structure of the Thorarchaeota 2DGel/rabbit actin complex -

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Basic information

Entry
Database: PDB / ID: 7c2g
TitleCrystal Structure of the Thorarchaeota 2DGel/rabbit actin complex
Components
  • 2DGel3
  • Actin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / actin regulator
Function / homology
Function and homology information


actin filament severing / barbed-end actin filament capping / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly ...actin filament severing / barbed-end actin filament capping / 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 / phosphatidylinositol-4,5-bisphosphate 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: 1.71 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)66,03410
Polymers65,2472
Non-polymers7888
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-100 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.854, 101.343, 55.765
Angle α, β, γ (deg.)90.000, 96.620, 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: 23136.734 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: A0A135VHY8
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / 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.: 557 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris pH 5.5 0.2 M magnesium chloride hexahydrate 25% w/v polyethylene glycol 3350

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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: 1.7→20 Å / Num. obs: 60879 / % possible obs: 98 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.16 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Χ2: 0.923 / Net I/σ(I): 12 / Num. measured all: 403297
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.50.91428930.6320.4551.0260.64492.5
1.73-1.765.10.81629340.7360.3810.9040.66796.2
1.76-1.795.60.7630230.7790.3390.8350.69696.2
1.79-1.836.10.65429880.8380.2840.7150.75297.1
1.83-1.876.40.58730090.880.2480.6380.79297.4
1.87-1.916.70.51130400.9230.2130.5540.84597.8
1.91-1.966.90.40630040.9390.1670.4390.90497.7
1.96-2.027.10.33930280.9580.1380.3660.98197.9
2.02-2.077.10.27230450.9670.1110.2941.02298.4
2.07-2.147.10.23330280.9740.0950.2511.08298.1
2.14-2.227.10.18730490.9810.0770.2021.08298.4
2.22-2.3170.15530620.9850.0650.1691.10698.5
2.31-2.4170.12630630.9880.0530.1361.03698.6
2.41-2.5470.10430610.9880.0440.1131.01998.9
2.54-2.770.08530640.9930.0360.0930.96999.1
2.7-2.96.90.07431210.9940.0310.0810.90299.3
2.9-3.26.90.06530730.9950.0270.0710.84299.5
3.2-3.666.90.05631060.9970.0240.0610.74699.7
3.66-4.66.90.06631220.9910.0270.0720.80899.7
4.6-206.90.08831660.9850.0360.0951.24199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBT

3hbt


Resolution: 1.71→19.862 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.61
RfactorNum. reflection% reflection
Rfree0.2027 2802 4.82 %
Rwork0.1686 --
obs0.1703 58175 92.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.01 Å2 / Biso mean: 25.4049 Å2 / Biso min: 3.8 Å2
Refinement stepCycle: final / Resolution: 1.71→19.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4436 0 38 557 5031
Biso mean--15.57 34.55 -
Num. residues----557
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7105-1.740.2644770.2241135446
1.74-1.77160.29931020.2197207869
1.7716-1.80560.22741170.2006233777
1.8056-1.84250.2321360.2068251486
1.8425-1.88250.25491320.2087277593
1.8825-1.92620.24261500.2286296
1.9262-1.97440.25941410.1821291298
1.9744-2.02770.20741550.1735292098
2.0277-2.08730.19151450.1691290198
2.0873-2.15460.22761400.1669296998
2.1546-2.23150.21571460.1706294599
2.2315-2.32070.2061550.1704294198
2.3207-2.42620.20581470.1728293699
2.4262-2.55380.22491520.1718294999
2.5538-2.71350.24361470.1692296199
2.7135-2.92240.19761570.173298899
2.9224-3.21540.20821360.1662980100
3.2154-3.67810.17781590.14743003100
3.6781-4.62430.14721620.13612997100
4.6243-19.8620.19021460.17283051100
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)
11.70080.2097-0.11210.89530.19131.65070.12370.05930.6435-0.34840.07760.229-0.471-0.2440.47480.16720.0377-0.01530.0790.07650.145455.316227.579313.0005
20.6087-0.1732-0.08440.72690.2420.4734-0.04270.08320.0674-0.16950.02030.2148-0.0665-0.2016-0.01190.10410.0049-0.04170.14770.03570.120250.592615.018816.3527
30.6550.4276-0.22821.4941-0.05690.71720.0042-0.08690.00330.0824-0.0042-0.08090.01050.0425-0.00490.04550.01110.00230.09940.00190.082572.791214.054227.8531
41.074-0.3439-0.50220.55660.00980.4816-0.07170.0788-0.2607-0.3005-0.05810.44770.1758-0.3417-0.39940.1309-0.0766-0.07210.1911-0.02210.234647.02296.657210.7448
50.87960.02330.05740.5403-0.04441.28720.09090.1189-0.3954-0.6116-0.003-0.29840.5293-0.06410.23990.3326-0.05680.11870.0917-0.05470.090662.5345-10.41057.6877
60.4639-0.0583-0.13760.6856-0.49590.4512-0.13650.46070.1662-0.76830.26410.1027-0.1052-0.13810.01750.4921-0.16940.01520.22250.07440.183369.455434.63931.5802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 68 )A5 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 165 )A69 - 165
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 334 )A166 - 334
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 372 )A335 - 372
5X-RAY DIFFRACTION5chain 'G' and (resid 2 through 106 )G2 - 106
6X-RAY DIFFRACTION6chain 'G' and (resid 107 through 197 )G107 - 197

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