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- PDB-7a0h: Structure of homodimeric actin capping protein alpha subunit from... -

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Basic information

Entry
Database: PDB / ID: 7a0h
TitleStructure of homodimeric actin capping protein alpha subunit from Plasmodium berghei
ComponentsF-actin-capping protein subunit alpha
KeywordsPROTEIN BINDING / capping protein / F-actin binding / asymmetric homodimer
Function / homology
Function and homology information


F-actin capping protein complex / barbed-end actin filament capping / actin binding
Similarity search - Function
F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit
Similarity search - Domain/homology
BROMIDE ION / F-actin-capping protein subunit alpha
Similarity search - Component
Biological speciesPlasmodium berghei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsBendes, A.A. / Kursula, P. / Kursula, I.
Funding support Finland, Norway, 2items
OrganizationGrant numberCountry
Academy of Finland Finland
Norwegian Research Council Norway
CitationJournal: Cell.Mol.Life Sci. / Year: 2022
Title: Structure and function of an atypical homodimeric actin capping protein from the malaria parasite.
Authors: Bendes, A.A. / Kursula, P. / Kursula, I.
History
DepositionAug 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-actin-capping protein subunit alpha
B: F-actin-capping protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,59429
Polymers68,2662
Non-polymers2,32827
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical SEC retention volume and calculated MW agrees with homodimer assembly, light scattering, SEC-SLS calculated MW agrees with homodimer assembly, SAXS, SEC-SAXS ...Evidence: gel filtration, Analytical SEC retention volume and calculated MW agrees with homodimer assembly, light scattering, SEC-SLS calculated MW agrees with homodimer assembly, SAXS, SEC-SAXS calculated MW, dimensions and ab initio shape agrees with homodimer assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-31 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.490, 35.168, 115.438
Angle α, β, γ (deg.)90.000, 104.437, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 103 or resid 109...
d_2ens_1(chain "B" and (resid 4 through 157 or resid 159...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUPROA3 - 102
d_12ens_1HISLYSA108 - 132
d_13ens_1VALLYSA155 - 156
d_14ens_1ALASERA158 - 164
d_15ens_1LYSCYSA169 - 177
d_16ens_1ASPASNA179 - 258
d_17ens_1VALLEUA260 - 285
d_21ens_1LEULYSB1 - 127
d_22ens_1ALACYSB129 - 144
d_23ens_1ASPASNB146 - 225
d_24ens_1VALLEUB227 - 252

NCS oper: (Code: givenMatrix: (0.878580748096, 0.115601889751, 0.46339192069), (-0.0300998949922, -0.954931985747, 0.295294596834), (0.476644380431, -0.273388195948, -0.835505253676)Vector: -32. ...NCS oper: (Code: given
Matrix: (0.878580748096, 0.115601889751, 0.46339192069), (-0.0300998949922, -0.954931985747, 0.295294596834), (0.476644380431, -0.273388195948, -0.835505253676)
Vector: -32.4217269091, -9.16700119604, 132.690857352)

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Components

#1: Protein F-actin-capping protein subunit alpha


Mass: 34132.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (strain Anka) (eukaryote)
Strain: Anka / Gene: PBANKA_1243100 / Plasmid: pNIC28-CH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A509AR49
#2: Chemical...
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.44 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 0.133 M triammonium-citrate, 10-12% (w/v) PEG 20k, 0.5 M NDSB-195

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.22→79.65 Å / Num. obs: 61855 / % possible obs: 99.24 % / Redundancy: 40.7 % / Biso Wilson estimate: 49.65 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2601 / Rpim(I) all: 0.03953 / Rrim(I) all: 0.2632 / Net I/σ(I): 10.62
Reflection shellResolution: 2.22→2.299 Å / Redundancy: 8.4 % / Rmerge(I) obs: 4.372 / Mean I/σ(I) obs: 0.45 / Num. unique obs: 6109 / CC1/2: 0.29 / CC star: 0.671 / Rpim(I) all: 1.571 / Rrim(I) all: 4.657 / % possible all: 95.57

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Processing

Software
NameVersionClassification
PHENIXdev-3928refinement
PHENIX1.13-2998model building
HKL2Map0.4c-betaphasing
xia20.5.582data scaling
DIALS1.10.4data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.22→74.2 Å / SU ML: 0.3746 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2568 3062 4.99 %
Rwork0.2069 58357 -
obs0.2095 61419 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.81 Å2
Refinement stepCycle: LAST / Resolution: 2.22→74.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 46 149 4607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01594558
X-RAY DIFFRACTIONf_angle_d1.47446173
X-RAY DIFFRACTIONf_chiral_restr0.0774702
X-RAY DIFFRACTIONf_plane_restr0.0102773
X-RAY DIFFRACTIONf_dihedral_angle_d13.79131702
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.89391335778 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.250.42841160.41962419X-RAY DIFFRACTION91.88
2.25-2.290.39581250.40712628X-RAY DIFFRACTION98.39
2.29-2.330.42721590.36192749X-RAY DIFFRACTION99.73
2.33-2.370.34961330.33612633X-RAY DIFFRACTION99.6
2.37-2.420.34961410.31012607X-RAY DIFFRACTION99.89
2.42-2.470.33091220.28872722X-RAY DIFFRACTION99.68
2.47-2.520.38451230.29472703X-RAY DIFFRACTION99.51
2.52-2.580.30231390.25882568X-RAY DIFFRACTION99.23
2.58-2.650.31641520.25292705X-RAY DIFFRACTION99.2
2.65-2.720.22881160.22452728X-RAY DIFFRACTION99.03
2.72-2.80.2951110.21482626X-RAY DIFFRACTION99.74
2.8-2.890.271550.1992669X-RAY DIFFRACTION99.19
2.89-2.990.27241150.22082653X-RAY DIFFRACTION99.53
2.99-3.110.28571860.2242611X-RAY DIFFRACTION99.89
3.11-3.250.26141380.20892702X-RAY DIFFRACTION99.89
3.25-3.420.26691490.17882630X-RAY DIFFRACTION99.86
3.42-3.640.24561620.18712680X-RAY DIFFRACTION99.68
3.64-3.920.24721380.17562688X-RAY DIFFRACTION100
3.92-4.310.23541560.17742641X-RAY DIFFRACTION99.89
4.31-4.940.18071450.15262666X-RAY DIFFRACTION99.96
4.94-6.220.26541330.19592659X-RAY DIFFRACTION99.93
6.22-74.20.22981480.19572670X-RAY DIFFRACTION99.68
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)
13.73061834287-0.271905110439-1.478817411930.952768042339-0.2003856123972.41932333542-0.0630819007632-0.1913871566970.0306350721739-0.0408425372226-0.0109404680043-0.3640928838890.002701395060160.6161675251140.06396928154470.360772085562-0.0236614088796-0.05688768388180.4905105146420.02899475354890.64305015608743.66378486723.72089051057105.51648392
21.40795307413-2.60471846182-2.917310050254.632836843725.222003852425.653870095170.1204967642940.659277492005-0.580054241307-0.339014448342-0.1452229866920.2704423199690.35145830088-0.389758930224-0.1325745213370.866944395236-0.0003294298967970.01609509441410.804866275418-0.12755936920.74273668542623.869991089-14.631009045491.7532523584
32.53443627742-0.212456303694-1.644212968641.129493051690.6263522255225.81726124532-0.0938044789940.1741128078030.0089696946136-0.105908805160.0400141869265-0.108837125249-0.05825117902980.004070018199850.02742243523580.318970912852-0.0216428875974-0.04785733900670.3165783563050.03892409760160.49063524322726.1062185557.7282628716799.6742022524
42.71620806495-1.398278243650.6443626578770.830678475874-0.2217602057080.2515696730220.03181785075090.966167207088-0.1517371217660.150634107487-0.379167438013-0.06016154602680.323709768745-0.3076994435390.26988237081.805502276250.01422849413150.4717801680111.43959961090.1603388918931.0264234387857.2867278348.5388851400780.1876019596
51.489176584810.2412716202311.299758896771.81870135824-0.09072309912293.80609673264-0.7764938424130.3353609562770.353213096218-0.1004845139910.15128058015-0.858886650308-0.04258853940491.05670136860.5078934009941.32134639604-0.2492789156330.3225742524212.28140461705-0.0004568222042781.1781941867757.099222635517.092043544864.6067521872
60.513277366186-0.363996381748-0.7929001434941.12261122842-0.5839528087071.79202699702-0.3187959682781.06303969974-0.0391906358122-0.776413967029-0.0581980105043-0.558159278865-0.01563078730370.6474403881770.2578495697731.41653777509-0.3985633848850.1924497616681.971041324360.1351971802980.75891685433146.254340913919.666917209755.5896795036
70.530114590548-0.05740678427760.6986395956451.821628131020.2478750779816.18524303316-0.5113032772521.41611180304-0.0584563531253-1.319297676810.420332807882-0.05583657645640.444282281207-0.0663309388453-0.01444080039631.0857965837-0.2948291160710.02728000756021.34777241553-0.01538950595880.47621219212132.55534269488.6219008878463.3044911777
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 131 )AA2 - 1311 - 130
22chain 'A' and (resid 132 through 153 )AA132 - 153131 - 152
33chain 'A' and (resid 154 through 286 )AA154 - 286153 - 285
44chain 'B' and (resid 4 through 34 )BB4 - 341 - 31
55chain 'B' and (resid 35 through 86 )BB35 - 8632 - 83
66chain 'B' and (resid 87 through 205 )BB87 - 20584 - 171
77chain 'B' and (resid 206 through 289 )BB206 - 289172 - 255

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