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- PDB-7c2f: Crystal Structure of the Thorarchaeota ProGel/rabbit actin complex -

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Basic information

Entry
Database: PDB / ID: 7c2f
TitleCrystal Structure of the Thorarchaeota ProGel/rabbit actin complex
Components
  • Actin, alpha skeletal muscle
  • Gelsolin-like domain-containing protein
KeywordsSTRUCTURAL PROTEIN / actin regulator
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / 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 / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / 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: 2.03 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
B: Gelsolin-like domain-containing protein
C: Actin, alpha skeletal muscle
D: Gelsolin-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,89010
Polymers105,0364
Non-polymers1,8546
Water10,215567
1
A: Actin, alpha skeletal muscle
B: Gelsolin-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4455
Polymers52,5182
Non-polymers9273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Actin, alpha skeletal muscle
D: Gelsolin-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4455
Polymers52,5182
Non-polymers9273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.427, 108.626, 167.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 32 or resid 34...
21(chain C and (resid 5 through 32 or resid 34...
12(chain B and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))
22(chain D and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 32 or resid 34...A5 - 32
121(chain A and (resid 5 through 32 or resid 34...A34 - 41
131(chain A and (resid 5 through 32 or resid 34...A51 - 59
141(chain A and (resid 5 through 32 or resid 34...A5 - 374
151(chain A and (resid 5 through 32 or resid 34...A5 - 374
161(chain A and (resid 5 through 32 or resid 34...A5 - 374
171(chain A and (resid 5 through 32 or resid 34...A298 - 374
181(chain A and (resid 5 through 32 or resid 34...A1376 - 1379
211(chain C and (resid 5 through 32 or resid 34...C5 - 32
221(chain C and (resid 5 through 32 or resid 34...C34 - 59
231(chain C and (resid 5 through 32 or resid 34...C5 - 374
241(chain C and (resid 5 through 32 or resid 34...C5 - 374
251(chain C and (resid 5 through 32 or resid 34...C142 - 2
261(chain C and (resid 5 through 32 or resid 34...C298 - 374
271(chain C and (resid 5 through 32 or resid 34...C1 - 374
281(chain C and (resid 5 through 32 or resid 34...C1376 - 1379
112(chain B and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))B1 - 49
122(chain B and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))B51 - 53
132(chain B and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))B55 - 88
212(chain D and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))D1 - 49
222(chain D and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))D51 - 53
232(chain D and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))D55 - 88

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 41875.633 Da / Num. of mol.: 2
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 Gelsolin-like domain-containing protein


Mass: 10642.312 Da / Num. of mol.: 2
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: A0A135VMT5

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Non-polymers , 4 types, 573 molecules

#3: Chemical ChemComp-LAB / LATRUNCULIN B / Latrunculin


Mass: 395.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO5S / Comment: toxin*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M MES pH 6.0 0.2 M magnesium chloride hexahydrate 20% w/v polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→91.14 Å / Num. obs: 68445 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.048 / Rrim(I) all: 0.125 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1 / Resolution: 2.03→2.08 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
6.60.7942830.8930.3270.85693
5.70.0467670.9990.0210.05198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBT

3hbt


Resolution: 2.03→48.59 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 3407 5 %RANDOM
Rwork0.199 64785 --
obs0.2006 68192 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.79 Å2 / Biso mean: 55.0174 Å2 / Biso min: 14.07 Å2
Refinement stepCycle: final / Resolution: 2.03→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7064 0 184 567 7815
Biso mean--28.44 43.1 -
Num. residues----899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3432X-RAY DIFFRACTION5.92TORSIONAL
12C3432X-RAY DIFFRACTION5.92TORSIONAL
21B825X-RAY DIFFRACTION5.92TORSIONAL
22D825X-RAY DIFFRACTION5.92TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.060.29611220.28032429255189
2.06-2.090.31251230.270826402763100
2.09-2.120.29291800.25426882868100
2.12-2.160.2491400.249426382778100
2.16-2.190.26971260.244627052831100
2.19-2.230.2531530.243826622815100
2.23-2.280.29771560.239426482804100
2.28-2.320.24481290.230826882817100
2.32-2.370.24721290.221627082837100
2.37-2.430.24791580.22426542812100
2.43-2.490.26531400.211526852825100
2.49-2.560.23621340.210626922826100
2.56-2.630.24081300.207527252855100
2.63-2.720.25081300.207727122842100
2.72-2.810.21841580.209926912849100
2.81-2.930.27761310.209627272858100
2.93-3.060.21531560.19926912847100
3.06-3.220.22241490.196727292878100
3.22-3.420.2141320.193127392871100
3.42-3.690.21551640.191227072871100
3.69-4.060.22231430.169227532896100
4.06-4.640.18961360.15262762289899
4.64-5.850.21341470.165728072954100
5.85-48.590.21891410.19672905304698
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)
11.33220.28110.26093.5440.46331.8585-0.00480.0778-0.1617-0.43750.1083-0.42830.12030.2552-0.04640.1963-0.02990.05660.2462-0.00190.226646.621718.0561.6129
21.5666-0.37171.00331.1316-0.38632.3706-0.1525-0.120.05960.04040.0945-0.0352-0.12780.04630.06110.0944-0.0299-0.00020.2480.00230.2850.535435.172980.6943
31.01030.00780.20812.62980.0121.0293-0.07830.03570.0858-0.3870.06230.247-0.1186-0.0970.0310.1886-0.0226-0.07410.26560.02360.251235.985438.629165.6765
42.87990.80240.32850.22540.09880.6025-0.06481.09960.4678-1.32940.236-0.0813-1.07290.2455-0.18231.2286-0.1474-0.02590.73210.0050.409640.929618.415342.8871
53.46190.8194-0.33741.07681.52922.97530.2292-0.2585-0.46840.5825-0.24790.01420.8515-0.29570.00591.0642-0.3876-0.05971.2125-0.1480.682811.993434.698247.7875
60.055-0.07290.0020.0954-0.0030.0007-0.147-0.43330.44630.0105-0.0070.2794-0.3459-0.16940.1730.7243-0.05370.02131.5109-0.03931.32826.183142.321651.4739
71.3244-0.26380.14963.4148-0.89873.5055-0.0502-1.20860.2610.2792-0.15620.6438-0.5168-1.34030.22720.5478-0.007-0.12651.1532-0.07020.503214.924243.284250.3701
80.7783-0.1187-0.55750.29440.45750.91450.2813-1.0126-0.29910.19810.06270.00420.3255-0.318-0.32880.4946-0.1219-0.14080.93160.00490.434219.335839.806755.0639
91.8915-0.59180.96842.0944-1.24973.29040.5313-0.4451-0.6422-0.05110.01540.27160.9092-0.7611-0.51010.6585-0.119-0.09420.52460.0690.442322.097932.779648.0556
101.1405-0.2910.02610.988-0.10062.53460.1499-0.58640.32440.4784-0.21620.0129-0.4015-0.09270.10540.5060.041-0.12580.6784-0.13110.407422.073345.939749.0414
111.1442-1.50150.74252.3587-0.8531.97010.1261-0.03910.1877-0.01090.15930.7199-0.423-0.71-0.28050.82630.3712-0.27720.9299-0.34151.01413.901451.853653.7354
123.4083-0.6333-0.22492.8575-0.03142.76770.1258-0.0261-0.59250.2618-0.05250.38940.6886-0.2756-0.08590.639-0.04160.06740.25220.0120.36799.214413.839418.1032
131.26390.20450.30931.87220.73682.1688-0.1316-0.1187-0.04630.35540.03630.0060.3230.00740.08660.29470.04520.02750.1736-0.00790.193815.514532.330216.1985
142.0858-0.2411-0.22280.4856-0.87531.79330.23880.3771-0.52180.0562-0.2981-0.05720.29090.43310.03161.08760.213-0.12481.36350.06130.703746.875435.19236.1154
151.5609-0.2392-0.64611.2540.47532.21250.2860.36980.1297-0.26560.0089-0.0038-0.1649-0.1493-0.26510.85730.0257-0.07851.87620.16961.292452.413242.714332.0055
161.80790.7210.24632.23910.52534.51650.50151.4320.1052-0.4751-0.382-0.4805-0.87081.151-0.06450.79850.0313-0.00371.38280.14950.553944.116143.592333.3844
174.11610.1395-0.69042.08590.62823.82850.26631.2109-0.7389-0.2134-0.3471-0.23450.74131.10320.0650.73240.2439-0.10190.95240.00550.596138.037635.802731.2021
182.8735-0.2119-0.5972.18260.18422.3545-0.18750.1541-0.28660.0163-0.2421-0.0755-0.56420.43410.44250.5466-0.1209-0.08910.48350.05320.333337.671742.037446.1071
190.4351-0.2248-0.37811.79690.06854.0772-0.2290.79350.6642-0.2834-0.085-0.6754-1.12361.10910.27540.8897-0.1846-0.05461.08620.35560.572540.054148.924529.7111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 165 )A5 - 165
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 273 )A166 - 273
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 354 )A274 - 354
4X-RAY DIFFRACTION4chain 'A' and (resid 355 through 374 )A355 - 374
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 14 )B1 - 14
6X-RAY DIFFRACTION6chain 'B' and (resid 15 through 22 )B15 - 22
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 37 )B23 - 37
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 48 )B38 - 48
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 65 )B49 - 65
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 80 )B66 - 80
11X-RAY DIFFRACTION11chain 'B' and (resid 81 through 88 )B81 - 88
12X-RAY DIFFRACTION12chain 'C' and (resid 5 through 97 )C5 - 97
13X-RAY DIFFRACTION13chain 'C' and (resid 98 through 374 )C98 - 374
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 14 )D1 - 14
15X-RAY DIFFRACTION15chain 'D' and (resid 15 through 22 )D15 - 22
16X-RAY DIFFRACTION16chain 'D' and (resid 23 through 37 )D23 - 37
17X-RAY DIFFRACTION17chain 'D' and (resid 38 through 61 )D38 - 61
18X-RAY DIFFRACTION18chain 'D' and (resid 62 through 69 )D62 - 69
19X-RAY DIFFRACTION19chain 'D' and (resid 70 through 88 )D70 - 90

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