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- PDB-3dwl: Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp... -

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Basic information

Entry
Database: PDB / ID: 3dwl
TitleCrystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit
Components
  • (Actin-related protein 2/3 complex subunit ...) x 5
  • Actin-related protein 3
KeywordsSTRUCTURAL PROTEIN / PROPELLOR / Actin-binding / ATP-binding / Cytoskeleton / Nucleotide-binding / WD repeat
Function / homology
Function and homology information


Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Clathrin-mediated endocytosis / actin cortical patch organization / Neutrophil degranulation / cell cortex of cell tip / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / actin cortical patch ...Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Clathrin-mediated endocytosis / actin cortical patch organization / Neutrophil degranulation / cell cortex of cell tip / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / actin cortical patch / cell tip / regulation of actin filament polymerization / mating projection tip / cortical actin cytoskeleton organization / establishment or maintenance of cell polarity / cell division site / mitotic cytokinesis / actin filament polymerization / structural constituent of cytoskeleton / endocytosis / actin filament binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #160 / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily ...Arc Repressor Mutant, subunit A - #160 / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 16 kDa subunit (p16-Arc) / ARP2/3 complex 20 kDa subunit (ARPC4) / Yope Regulator; Chain: A, / Arc Repressor Mutant, subunit A / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / YVTN repeat-like/Quinoprotein amine dehydrogenase / ATPase, nucleotide binding domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Actin / Actin family / Actin / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / ATPase, nucleotide binding domain / Alpha Horseshoe / Nucleotidyltransferase; domain 5 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 1 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.78 Å
AuthorsNolen, B.J. / Pollard, T.D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure and biochemical properties of fission yeast arp2/3 complex lacking the arp2 subunit.
Authors: Nolen, B.J. / Pollard, T.D.
History
DepositionJul 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-related protein 3
C: Actin-related protein 2/3 complex subunit 1
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5
B: Actin-related protein 3
H: Actin-related protein 2/3 complex subunit 1
I: Actin-related protein 2/3 complex subunit 2
J: Actin-related protein 2/3 complex subunit 3
K: Actin-related protein 2/3 complex subunit 4
L: Actin-related protein 2/3 complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,05714
Polymers365,04312
Non-polymers1,0142
Water00
1
A: Actin-related protein 3
C: Actin-related protein 2/3 complex subunit 1
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,0297
Polymers182,5216
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-65 kcal/mol
Surface area54020 Å2
MethodPISA
2
B: Actin-related protein 3
H: Actin-related protein 2/3 complex subunit 1
I: Actin-related protein 2/3 complex subunit 2
J: Actin-related protein 2/3 complex subunit 3
K: Actin-related protein 2/3 complex subunit 4
L: Actin-related protein 2/3 complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,0297
Polymers182,5216
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-66 kcal/mol
Surface area53970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.967, 218.967, 315.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22H
13D
23I
14E
24J
15F
25K
16G
26L

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILEAA3 - 4223 - 422
21SERSERILEILEBG3 - 4223 - 422
12ALAALALEULEUCB2 - 3772 - 377
22ALAALALEULEUHH2 - 3772 - 377
13METMETGLUGLUDC1 - 3031 - 303
23METMETGLUGLUII1 - 3031 - 303
14ILEILELYSLYSED44 - 17244 - 172
24ILEILELYSLYSJJ44 - 17244 - 172
15ASNASNPHEPHEFE3 - 1683 - 168
25ASNASNPHEPHEKK3 - 1683 - 168
16VALVALARGARGGF32 - 14932 - 149
26VALVALARGARGLL32 - 14932 - 149

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Actin-related protein 2/3 complex subunit ... , 5 types, 10 molecules CHDIEJFKGL

#2: Protein Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex 41 kDa subunit / p41-ARC


Mass: 41643.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: TM011 / References: UniProt: P78774
#3: Protein Actin-related protein 2/3 complex subunit 2 / Arp2/3 complex 34 kDa subunit / p34-ARC


Mass: 37025.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: TM011 / References: UniProt: O14241
#4: Protein Actin-related protein 2/3 complex subunit 3 / Arp2/3 complex 21 kDa subunit / p21-ARC


Mass: 19865.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: TM011 / References: UniProt: Q9Y7J4
#5: Protein Actin-related protein 2/3 complex subunit 4 / Arp2/3 complex 20 kDa / p20-ARC


Mass: 19637.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: TM011 / References: UniProt: Q92352
#6: Protein Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 16 kDa subunit / p16-ARC


Mass: 16922.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: TM011 / References: UniProt: Q10316

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Protein / Non-polymers , 2 types, 4 molecules AB

#1: Protein Actin-related protein 3 / Actin-like protein 3


Mass: 47427.137 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: TM011 / References: UniProt: P32390
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 5.17 Å3/Da / Density % sol: 76.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 750 mM ammonium sulfate 50 mM sodium citrate 7 % glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 21, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.78→29 Å / Num. all: 73308 / Num. obs: 72502 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.198 / Net I/σ(I): 9.5
Reflection shellResolution: 3.775→3.872 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.495 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1k8k

1k8k


Resolution: 3.78→29 Å / Cor.coef. Fo:Fc: 0.807 / Cor.coef. Fo:Fc free: 0.789 / SU B: 89.208 / SU ML: 0.611 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.673 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.34367 3847 5 %RANDOM
Rwork0.3237 ---
obs0.32469 72502 98.94 %-
all-73308 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 3.78→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18643 0 62 0 18705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02219089
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.92526106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15252563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88423.878735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.758152406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8991584
X-RAY DIFFRACTIONr_chiral_restr0.0690.23083
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214676
X-RAY DIFFRACTIONr_nbd_refined0.2150.28172
X-RAY DIFFRACTIONr_nbtor_refined0.3050.213045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2556
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.23
X-RAY DIFFRACTIONr_mcbond_it0.4331.513206
X-RAY DIFFRACTIONr_mcangle_it0.797220300
X-RAY DIFFRACTIONr_scbond_it0.84536712
X-RAY DIFFRACTIONr_scangle_it1.5054.55806
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2556tight positional0.020.05
2C2261tight positional0.010.05
3D2029tight positional0.020.05
4E398tight positional0.010.05
5F1293tight positional0.020.05
6G791tight positional0.020.05
1A2556tight thermal0.020.5
2C2261tight thermal0.090.5
3D2029tight thermal0.020.5
4E398tight thermal0.020.5
5F1293tight thermal0.030.5
6G791tight thermal0.020.5
LS refinement shellResolution: 3.775→3.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 254 -
Rwork0.36 4843 -
obs--92.1 %
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)
12.8469-1.7594-0.82092.37370.30752.9797-0.0604-0.1347-0.14360.28370.08210.2489-0.1289-0.8065-0.0217-0.49540.06070.01710.1789-0.0103-0.368354.042-86.807-6.68
24.92731.2239-0.71441.5894-0.12231.40650.25640.02170.4643-0.0873-0.08040.3288-0.1982-0.1605-0.176-0.30080.1365-0.0129-0.1215-0.0258-0.242534.808-106.239-73.534
32.6721-0.51190.89313.2302-1.12484.11910.0964-0.511-0.5946-0.0012-0.0160.56580.3697-0.4696-0.0804-0.4299-0.05630.0358-0.15040.1758-0.09442.564-142.441-41.278
42.36960.1591.02341.03410.28211.6583-0.07670.03510.1422-0.03830.1908-0.08520.06390.1549-0.1141-0.45150.0137-0.0151-0.10540.0089-0.369588.151-86.72-12.266
53.12710.7704-0.20260.1898-0.04990.01310.46260.38270.8329-0.7804-1.2750.5474-0.61970.17540.81240.45381.0380.14521.54470.01940.578919.508-60.916-10.419
63.22693.80341.96427.58883.56191.69610.0632-0.36-0.08240.2850.0344-0.0550.03390.1723-0.0976-0.48380.17170.004-0.08880.0497-0.437271.094-120-32.4
716.0577-4.6582-3.01455.68822.05193.6496-0.1022-0.0615-0.6051-0.12830.367-0.34450.7995-0.2247-0.2648-0.29360.0679-0.0575-0.3538-0.0581-0.453781.427-140.123-49.637
82.6054-0.37760.212.20760.01255.74940.43340.34940.4586-0.1881-0.0620.3988-2.0459-1.6488-0.37140.72911.04890.33760.61920.19070.048243.788-50.165-39.19
91.82680.093-0.16051.87081.62553.5362-0.03260.02150.0399-0.28710.1595-0.3672-0.22670.2859-0.1268-0.21830.16380.0648-0.20970.0115-0.218967.732-107.754-87.091
106.504-1.0485-5.77182.7233-0.00345.46350.3297-0.5654-0.66490.21420.33280.13410.3469-0.3244-0.6626-0.3934-0.0998-0.10760.65330.51750.36812.859-128.145-52.733
111.3328-0.9789-1.87286.0726.13736.86750.26990.34310.3061-0.51170.2242-0.3235-0.6211-0.3364-0.4941-0.14420.17640.15010.05660.0671-0.254665.613-75.01-60.575
1214.79643.1929-5.44533.9725-2.517210.73850.3355-0.52220.63080.3349-0.3332-1.1347-1.84891.4494-0.00230.4023-0.23620.29050.1767-0.22860.047482.985-54.999-51.148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 4223 - 422
2X-RAY DIFFRACTION2BG4 - 4224 - 422
3X-RAY DIFFRACTION3CB6 - 3756 - 375
4X-RAY DIFFRACTION4DC1 - 3011 - 301
5X-RAY DIFFRACTION5ED44 - 17244 - 172
6X-RAY DIFFRACTION6FE3 - 1683 - 168
7X-RAY DIFFRACTION7GF32 - 14832 - 148
8X-RAY DIFFRACTION8HH13 - 36913 - 369
9X-RAY DIFFRACTION9II1 - 3001 - 300
10X-RAY DIFFRACTION10JJ44 - 17244 - 172
11X-RAY DIFFRACTION11KK3 - 1683 - 168
12X-RAY DIFFRACTION12LL38 - 14838 - 148

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