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- PDB-5mw1: cryoEM structure of crenactin double helical filament at 3.8A res... -

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Basic information

Entry
Database: PDB / ID: 5mw1
TitlecryoEM structure of crenactin double helical filament at 3.8A resolution
ComponentsActin/actin family protein
KeywordsSTRUCTURAL PROTEIN / actin / bacterial cytoskeleton
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoskeleton / hydrolase activity / ATP binding / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #570 / ATPase, nucleotide binding domain / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Crenactin
Similarity search - Component
Biological speciesPyrobaculum calidifontis (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsIzore, T. / Lowe, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105184326 United Kingdom
Wellcome Trust095514/Z/11/Z United Kingdom
CitationJournal: Elife / Year: 2016
Title: Crenactin forms actin-like double helical filaments regulated by arcadin-2.
Authors: Thierry Izoré / Danguole Kureisaite-Ciziene / Stephen H McLaughlin / Jan Löwe /
Abstract: The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of ...The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of crenactin and actin are similar, although their filament architectures were suggested to be different. Here we report that crenactin forms double helical filaments that show exceptional similarity to eukaryotic F-actin. With cryo-electron microscopy and helical reconstruction we solved the structure of the crenactin filament to 3.8 Å resolution. When forming double filaments, the 'hydrophobic plug' loop in crenactin rearranges. Arcadin-2, also encoded by the arcade gene cluster, binds tightly with its C-terminus to the hydrophobic groove of crenactin. Binding is reminiscent of eukaryotic actin modulators such as cofilin and thymosin β4 and arcadin-2 is a depolymeriser of crenactin filaments. Our work further supports the theory of shared ancestry of Eukaryotes and Crenarchaea.
History
DepositionJan 17, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 8, 2017ID: 5LY4
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
B: Actin/actin family protein
A: Actin/actin family protein
C: Actin/actin family protein
D: Actin/actin family protein
E: Actin/actin family protein
F: Actin/actin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,11612
Polymers290,5536
Non-polymers2,5636
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14B
24E
15B
25F
16A
26C
17A
27D
18A
28E
19A
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B5 - 430
2111A5 - 430

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.950378, -0.311096, -0.001097), (0.311097, -0.950378, -0.000391), (-0.000921, -0.000713, 0.999999)424.60175, 307.7085, -25.31679
3given(1), (1), (1)
4given(0.805643, -0.592402, -0.000197), (0.592402, 0.805643, 0.000311), (-2.6E-5, -0.000367, 1)147.6833, -74.74139, 51.36035
5given(1), (1), (1)
6given(-0.950263, 0.31145, -0.000538), (-0.31145, -0.950263, 0.000127), (-0.000472, 0.000289, 1)307.60364, 424.37506, 25.67918
7given(1), (1), (1)
8given(-0.580378, 0.814345, -0.001835), (-0.814347, -0.580376, 0.001455), (0.00012, 0.002339, 0.999997)144.01476, 449.08545, 76.4254
9given(1), (1), (1)
10given(0.803289, 0.595586, 0.002233), (-0.595569, 0.803286, -0.005353), (-0.004982, 0.00297, 0.999983)-75.29544, 150.04695, -50.80272
11given(1), (1), (1)
12given(-0.581371, 0.813638, -0.000637), (-0.813638, -0.581371, -0.000948), (-0.001142, -3.2E-5, 0.999999)144.12766, 449.56555, 77.13061
13given(1), (1), (1)
14given(0.806218, -0.591618, -0.00037), (0.591618, 0.806218, -0.000667), (0.000693, 0.000318, 1)147.44005, -74.51614, 51.0787
15given(1), (1), (1)
16given(0.298238, -0.954491, 0.001275), (0.954491, 0.298236, -0.001525), (0.001075, 0.001672, 0.999998)310.55182, -47.14471, 101.99478
17given(1), (1), (1)
18given(-0.948703, -0.316135, -0.004709), (0.31612, -0.948712, 0.00368), (-0.00563, 0.002002, 0.999982)426.06677, 305.3721, -24.87563
19given(1), (1), (1)
20given(-0.950076, -0.31202, -0.000384), (0.31202, -0.950076, 5.4E-5), (-0.000382, -6.8E-5, 1)424.51669, 307.38196, -25.55724
21given(1), (1), (1)
22given(-0.949998, 0.312255, -0.000642), (-0.312256, -0.949996, 0.001892), (-1.9E-5, 0.001998, 0.999998)307.35968, 424.18137, 25.22887
23given(1), (1), (1)
24given(0.294348, 0.955697, -0.001398), (-0.955684, 0.294335, -0.006003), (-0.005325, 0.003103, 0.999981)-46.4736, 313.22964, -102.04918
25given(1), (1), (1)
26given(0.80514, -0.593085, 0.000819), (0.593085, 0.805138, -0.001665), (0.000329, 0.001826, 0.999998)147.73236, -74.41641, 50.83745
27given(1), (1), (1)
28given(-0.577843, -0.816148, -0.000926), (0.81613, -0.577837, 0.006071), (-0.00549, 0.002752, 0.999981)449.33008, 141.40787, -76.31077
29given(1), (1), (1)
30given(0.018788, -0.999818, 0.003183), (0.999797, 0.018811, 0.007264), (-0.007322, 0.003046, 0.999969)370.7886, -5.33688, -127.2605

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Components

#1: Protein
Actin/actin family protein


Mass: 48425.484 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Gene: Pcal_1635 / Production host: Escherichia coli (E. coli) / References: UniProt: A3MWN5
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: crenactin double helical filaments / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pyrobaculum calidifontis (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0151 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -161.9 ° / Axial rise/subunit: 25.6 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 470396 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
RefinementResolution: 3.8→214.4 Å / Cor.coef. Fo:Fc: 0.825 / SU B: 31.405 / SU ML: 0.422 / ESU R: 0.868
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.26403 --
obs0.26403 108620 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 105.169 Å2
Baniso -1Baniso -2Baniso -3
1-4.15 Å20.55 Å2-0.09 Å2
2--2.32 Å2-0.05 Å2
3----6.47 Å2
Refinement stepCycle: 1 / Total: 20358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0160.01920790
ELECTRON MICROSCOPYr_bond_other_d0.0040.0220178
ELECTRON MICROSCOPYr_angle_refined_deg1.4531.98328296
ELECTRON MICROSCOPYr_angle_other_deg1.069346296
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.92152550
ELECTRON MICROSCOPYr_dihedral_angle_2_deg22.32422.922924
ELECTRON MICROSCOPYr_dihedral_angle_3_deg9.214153498
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.72915204
ELECTRON MICROSCOPYr_chiral_restr0.0830.23204
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.02123160
ELECTRON MICROSCOPYr_gen_planes_other0.0030.024638
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it16.9717.79910218
ELECTRON MICROSCOPYr_mcbond_other16.9627.79910217
ELECTRON MICROSCOPYr_mcangle_it25.74111.73512762
ELECTRON MICROSCOPYr_mcangle_other25.7411.73612763
ELECTRON MICROSCOPYr_scbond_it32.21212.25610572
ELECTRON MICROSCOPYr_scbond_other32.21112.25610573
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other52.50116.69615535
ELECTRON MICROSCOPYr_long_range_B_refined59.31491899
ELECTRON MICROSCOPYr_long_range_B_other59.31491900
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 3366 / Refine-ID: ELECTRON MICROSCOPY

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1BTIGHT POSITIONAL0.020.11
1BTIGHT POSITIONAL0.020.11
1BTIGHT POSITIONAL0.030.11
1BTIGHT POSITIONAL0.020.11
1BTIGHT POSITIONAL0.030.11
1BTIGHT POSITIONAL0.030.11
1BTIGHT THERMAL8.191.12
2BTIGHT THERMAL8.051.12
3BTIGHT THERMAL7.361.12
4BTIGHT THERMAL9.461.12
5BTIGHT THERMAL13.271.12
6ATIGHT THERMAL9.521.12
7ATIGHT THERMAL8.651.12
8ATIGHT THERMAL10.861.12
9ATIGHT THERMAL12.161.12
10CTIGHT THERMAL7.281.12
11CTIGHT THERMAL7.931.12
12CTIGHT THERMAL13.621.12
13DTIGHT THERMAL8.681.12
14DTIGHT THERMAL13.541.12
15ETIGHT THERMAL14.281.12
LS refinement shellResolution: 3.8→3.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.655 8080 -
Rfree-0 -
obs--100 %

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