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- PDB-4m63: Crystal Structure of a Filament-Like Actin Trimer Bound to the Ba... -

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Basic information

Entry
Database: PDB / ID: 4m63
TitleCrystal Structure of a Filament-Like Actin Trimer Bound to the Bacterial Effector VopL
Components
  • Actin-5C
  • T3SS2 effector VopL nucleation of actin polymerization
KeywordsACTIN-BINDING PROTEIN / actin nucleator / actin nucleation / HYDROLASE / WASP Homology 2 domain / VopL C-terminal domain / cytoskeleton / ATP-binding protein
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / VEGFA-VEGFR2 Pathway / ovarian fusome organization / Platelet degranulation ...Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / VEGFA-VEGFR2 Pathway / ovarian fusome organization / Platelet degranulation / MAP2K and MAPK activation / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / DNA Damage Recognition in GG-NER / Clathrin-mediated endocytosis / sperm individualization / UCH proteinases / maintenance of protein location in cell / brahma complex / tube formation / Ino80 complex / mitotic cytokinesis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / hydrolase activity / chromatin remodeling / ATP binding / cytoplasm
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1210 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1210 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Four Helix Bundle (Hemerythrin (Met), subunit A) / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Actin-5C
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.748 Å
AuthorsTomchick, D.R. / Zahm, J.A. / Rosen, M.K.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2013
Title: The Bacterial Effector VopL Organizes Actin into Filament-like Structures.
Authors: Zahm, J.A. / Padrick, S.B. / Chen, Z. / Pak, C.W. / Yunus, A.A. / Henry, L. / Tomchick, D.R. / Chen, Z. / Rosen, M.K.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Mechanism of actin filament nucleation by the bacterial effector VopL.
Authors: Yu, B. / Cheng, H.C. / Brautigam, C.A. / Tomchick, D.R. / Rosen, M.K.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: T3SS2 effector VopL nucleation of actin polymerization
B: T3SS2 effector VopL nucleation of actin polymerization
C: Actin-5C
D: Actin-5C
E: Actin-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,70011
Polymers179,0585
Non-polymers1,6426
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)287.759, 66.084, 103.160
Angle α, β, γ (deg.)90.000, 94.010, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a VopL dimer bound to an actin trimer. There is 1 biological unit in the asymmetric unit.

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Components

#1: Protein T3SS2 effector VopL nucleation of actin polymerization


Mass: 26816.123 Da / Num. of mol.: 2 / Fragment: VopL C-terminal domain residues 247-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: BB22OP / Gene: VopL, VPBB_A1249 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1R / References: UniProt: L0I5A1
#2: Protein Actin-5C


Mass: 41808.750 Da / Num. of mol.: 3 / Mutation: D286A, V287A, D288A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: 5C-actin, Act5C, CG4027 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10987, EC: 3.6.1.3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M MMT buffer, 20% (w/v) PEG 1500, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.748→44.59 Å / Num. all: 49991 / Num. obs: 49991 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 75.35 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.268 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.748-2.8013.30.7381.524091.25999.2
2.801-2.853.40.6624781.15299.2
2.85-2.93.60.62624531.15100
2.9-2.963.70.59224861.199100
2.96-3.033.70.45725181.247100
3.03-3.13.70.36924801.275100
3.1-3.173.80.27724631.363100
3.17-3.263.70.23325051.369100
3.26-3.363.80.18724741.424100
3.36-3.463.70.14225291.408100
3.46-3.593.70.11324861.323100
3.59-3.733.70.08924611.246100
3.73-3.93.70.07525291.259100
3.9-4.113.70.06325121.12100
4.11-4.363.70.05624941.07100
4.36-4.73.70.05625311.313100
4.7-5.173.70.06125031.23100
5.17-5.923.60.05525341.30899.9
5.92-7.463.50.03925471.38599.9
7.46-503.50.03125991.24298.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SEO, 3EL2

3seo

3el2


Resolution: 2.748→44.592 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 33.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 2484 4.97 %RANDOM
Rwork0.2191 ---
obs0.2216 49937 98.08 %-
all-49937 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 305.97 Å2 / Biso mean: 101.9627 Å2 / Biso min: 37.7 Å2
Refine analyzeLuzzati sigma a obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.748→44.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11864 0 96 0 11960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412201
X-RAY DIFFRACTIONf_angle_d0.65616515
X-RAY DIFFRACTIONf_chiral_restr0.0371836
X-RAY DIFFRACTIONf_plane_restr0.0032116
X-RAY DIFFRACTIONf_dihedral_angle_d11.3024534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.748-2.80070.4052980.38351839193769
2.8007-2.85780.38141350.34452654278999
2.8578-2.920.38841390.336326242763100
2.92-2.98790.42661370.321826722809100
2.9879-3.06260.36181420.297826812823100
3.0626-3.14540.3061350.281626792814100
3.1454-3.23790.35371460.291426372783100
3.2379-3.34240.34571390.286526542793100
3.3424-3.46180.33671440.260126792823100
3.4618-3.60030.32751290.24926962825100
3.6003-3.76410.31500.231926402790100
3.7641-3.96250.31291400.213827062846100
3.9625-4.21050.23251330.196926902823100
4.2105-4.53530.24031440.175326822826100
4.5353-4.99120.2041440.175526922836100
4.9912-5.71220.2341400.19527132853100
5.7122-7.19190.26871490.22527372886100
7.1919-44.59780.22321400.17942778291899
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)
10.1565-0.1002-0.17730.23450.00090.2655-0.24451.0348-0.10620.07310.4858-0.0718-0.34160.30430.00160.851-0.3658-0.17371.41630.06870.613625.09785.1543-48.3435
20.73-0.06380.18770.5336-0.47020.6413-0.17110.1554-0.2534-0.17050.1141-0.10850.5315-0.4324-00.8663-0.1847-0.01580.5467-0.00730.570225.935-21.8379-24.5332
30.177-0.16660.02940.2699-0.24170.1934-0.0076-0.08170.1531-0.0422-0.00250.0202-0.06970.1632-00.7771-0.1056-0.02721.1277-0.00580.618515.418-0.4833-41.3302
40.0794-0.00130.0077-0.00470.00690.0371-0.1898-0.0819-0.0387-0.15-0.7643-0.0828-1.0795-0.3543-0.00090.99020.0138-0.2011.4117-0.04610.679311.774617.6595-38.2993
50.3140.057-0.2996-0.1706-0.1780.626-0.1161-0.0093-0.11480.10590.05720.1629-0.1449-0.403-00.7052-0.0515-0.06770.65130.01650.720312.344525.50221.6419
60.213-0.133-0.16460.46470.38140.27770.0657-0.08570.1822-0.0308-0.1175-0.1740.13940.157200.6524-0.07610.04910.43630.02980.473225.845518.648418.6263
70.4727-0.64840.20560.77020.51620.5864-0.36090.2773-0.008-0.10840.03420.0782-0.3973-0.1811-0.00010.8737-0.0753-0.12970.96110.01350.793510.794422.3894-18.1406
80.18850.0955-0.24170.25010.07440.6433-0.04010.19040.0815-0.003-0.2226-0.0869-0.1880.1485-00.5233-0.0578-0.05510.57190.10910.602345.0428-2.7502-27.3021
90.8165-0.36860.53110.9426-0.81820.62280.11730.0518-0.29760.0142-0.4611-0.2411-0.14280.6255-0.00060.61340.04270.00050.6590.1210.570152.5338-9.9403-18.0538
101.57330.3475-0.15321.72040.35040.62960.31030.34220.010.6249-0.42270.83340.07370.3714-0.07780.8833-0.19140.1030.4209-0.08320.640539.60619.0088-13.949
110.6725-0.09790.62573.2923-0.49652.64990.5049-0.29640.75891.2515-1.19721.0189-0.42471.1233-1.29941.2607-0.41540.3212-0.0103-0.37580.800438.645417.9996-8.1592
121.1904-0.53440.97450.2144-0.39860.82080.23310.09810.08420.7042-0.4650.0075-0.1580.5216-0.08691.079-0.43660.06990.613-0.10940.625150.038413.9751-3.079
130.075-0.0328-0.09820.07450.09850.24590.115-0.3933-0.08190.3961-0.056-0.33640.08970.506300.8320.0396-0.14780.82090.20910.610959.3488-12.2755-9.8601
140.1087-0.08690.0876-0.0109-0.07690.05890.18540.2256-0.20430.0964-0.3278-0.42180.0766-0.3103-00.643-0.25190.1240.6494-0.03720.61479.8621-7.764818.3342
150.0108-0.01580.09280.0304-0.05790.07230.10061.02650.00960.12090.05490.35230.0418-0.2268-0.00010.7524-0.0341-0.08730.9906-0.00620.619511.64974.01063.0647
160.2824-0.3981-0.50620.50630.42240.794-0.0862-0.01040.13610.1492-0.04630.11990.1072-0.2973-00.5721-0.11460.03230.5910.02330.611114.3647-2.379624.6781
171.41330.2461-0.11440.66670.36150.58290.08390.04080.182-0.08410.0442-0.13580.29880.1061-00.69580.02320.01950.42670.01140.557930.6774-14.54077.4515
180.6426-0.4308-0.24680.4950.66770.6304-0.2082-0.1549-0.2510.24140.2524-0.11670.84560.473400.82080.1281-0.09920.71010.03670.585735.7283-18.062221.2505
190.10.02440.0250.03310.08260.05680.10750.4952-0.27190.1817-0.39610.17170.4678-0.1174-0.00010.9724-0.17890.11090.58410.05160.662916.3117-17.63124.5066
200.0728-0.0017-0.1326-0.0019-0.01910.25150.1-0.74160.19090.9317-0.02550.1034-0.1551-0.350301.0163-0.16280.25371.0343-0.05630.7138.52550.428738.1437
210.8578-0.15780.39650.81070.45470.49130.26860.67110.0201-0.532-0.12040.30851.45580.96480.03220.67230.45730.05931.10250.06690.500764.1311-0.374137.5487
220.67830.02590.64351.0836-0.32271.8950.0691-0.02560.0211-0.1648-0.0649-0.08220.4066-0.034-00.3594-0.02540.03010.49760.04620.475143.08728.903546.6154
23-0.0128-0.0513-0.05730.1281-0.06210.0280.1288-0.1571-0.06660.1676-0.1351-0.52471.00271.1219-0.00031.13530.5153-0.19031.4960.04721.095276.1032-3.27350.5111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 247 through 279 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 280 through 396 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 455 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 474 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 247 through 321 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 322 through 382 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 383 through 475 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 78 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 79 through 145 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 146 through 216 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 217 through 319 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 320 through 337 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 338 through 374 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 5 through 37 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 38 through 68 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 69 through 165 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 166 through 246 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 247 through 328 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 329 through 348 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 349 through 374 )D0
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 145 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 146 through 346 )E0
23X-RAY DIFFRACTION23chain 'E' and (resid 347 through 374 )E0

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