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- PDB-6ui4: Crystal structure of phenamacril-bound F. graminearum myosin I -

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Basic information

Entry
Database: PDB / ID: 6ui4
TitleCrystal structure of phenamacril-bound F. graminearum myosin I
Components
  • Calmodulin
  • myosin I
KeywordsHYDROLASE / Myosin I / phenamcril / ATPase activity / fungicide / F. graminearum
Function / homology
Function and homology information


spindle pole body organization / central plaque of spindle pole body / actin cortical patch / myosin complex / cytoskeletal motor activity / enzyme regulator activity / actin binding / hydrolase activity / calcium ion binding / ATP binding / metal ion binding
Similarity search - Function
Fungal myosin-I, SH3 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin VI head, motor domain, U50 subdomain / : / Ca2+ insensitive EF hand / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 ...Fungal myosin-I, SH3 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin VI head, motor domain, U50 subdomain / : / Ca2+ insensitive EF hand / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / SH3 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / SH3-like domain superfamily / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ethyl (2Z)-3-amino-2-cyano-3-phenylprop-2-enoate / Myosin-1 / Myosin-1 / Calmodulin
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZhou, Y. / Zhou, X.E. / Gong, Y. / Zhu, Y. / Xu, H.E. / Zhou, M. / Melcher, K. / Zhang, F.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31871996 China
National Science Foundation (NSF, China)31730072 China
CitationJournal: Plos Pathog. / Year: 2020
Title: Structural basis of Fusarium myosin I inhibition by phenamacril.
Authors: Zhou, Y. / Zhou, X.E. / Gong, Y. / Zhu, Y. / Cao, X. / Brunzelle, J.S. / Xu, H.E. / Zhou, M. / Melcher, K. / Zhang, F.
History
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: myosin I
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4055
Polymers95,6422
Non-polymers7643
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-33 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.502, 100.311, 165.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein myosin I


Mass: 78760.062 Da / Num. of mol.: 1 / Fragment: Uniprot residues 44-735
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (fungus)
Strain: PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084 / Gene: FG01410.1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A098D3M4, UniProt: I1RCT2*PLUS
#2: Protein Calmodulin


Mass: 16881.463 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (fungus)
Strain: PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084 / Gene: FGRAMPH1_01T04571 / Production host: Escherichia coli (E. coli) / References: UniProt: I1RE19

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Non-polymers , 4 types, 29 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-Q8V / ethyl (2Z)-3-amino-2-cyano-3-phenylprop-2-enoate / phenamacril


Mass: 216.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M BIS-TRIS propanol, and 30% (w/v) polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 29620 / % possible obs: 99.8 % / Redundancy: 11.2 % / CC1/2: 0.996 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.66 Å / Num. unique obs: 3504 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BYF

4byf


Resolution: 2.65→42.9056 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.58
RfactorNum. reflection% reflection
Rfree0.2437 2107 7.14 %
Rwork0.2111 --
obs0.2134 29509 99.77 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 343.36 Å2 / Biso mean: 92.5816 Å2 / Biso min: 43.97 Å2
Refinement stepCycle: final / Resolution: 2.65→42.9056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6382 0 48 26 6456
Biso mean--61.6 68.44 -
Num. residues----817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6501-2.71170.3591290.32561822100
2.7117-2.77950.3231350.3251767100
2.7795-2.85460.35791580.31881777100
2.8546-2.93860.32781510.28711783100
2.9386-3.03350.30071370.2611804100
3.0335-3.14180.28391350.25441823100
3.1418-3.26760.28371320.23351799100
3.2676-3.41620.29931480.22121785100
3.4162-3.59630.23951310.2222182799
3.5963-3.82150.23541230.21351836100
3.8215-4.11630.22111490.18291812100
4.1163-4.53010.20881240.17141870100
4.5301-5.18470.19421460.17391854100
5.1847-6.52850.24321350.2171899100
6.5285-42.9050.22541740.19541944100
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)
10.0865-0.03920.09580.32770.07140.1551-0.0020.01220.0773-0.00380.0483-0.1575-0.08130.0121-00.5408-0.0411-0.01570.5554-0.0210.601422.2783139.717219.2609
2-0.00090.0064-0.00490.01070.02160.00270.0869-0.00990.0961-0.15840.1345-0.01180.11260.104700.6421-0.01260.0220.61670.00880.703418.0096110.6129191.6817
30.0564-0.019-0.02830.11-0.00410.0334-0.05670.04320.00260.1318-0.0363-0.06990.182-0.118800.5734-0.0125-0.01220.543-0.01360.55538.5434129.5809223.5681
40.01270.0053-00.0269-0.02360.01110.06470.06770.0364-0.0477-0.03990.0580.0332-0.137400.5302-0.01870.01850.623-0.02550.6368-5.5489123.441210.7086
50.0012-0.0072-0.00250.00330.01250.0222-0.0602-0.0234-0.03950.0006-0.0245-0.12870.0308-0.065800.537-0.00120.02230.5507-0.03810.770417.2606113.5344205.5478
60.06360.01-0.02650.02440.00840.09310.05460.0706-0.1739-0.1442-0.0167-0.07030.07530.0028-00.73040.018-0.02920.5970.03670.599210.9798129.9463220.9204
70.04770.0582-0.00350.00570.00660.02050.0144-0.0426-0.00260.04140.0081-0.0414-0.0428-0.027500.6706-0.0399-0.08330.6474-0.00270.486313.6293144.9919252.8879
80.00040.00470.0007-0.00040.00490.00210.01840.0192-0.00220.02720.0346-0.02360.00620.0205-01.2141-0.1699-0.02981.1504-0.1431.074719.9049168.0954261.6835
90.00370.03250.01280.01580.0039-0.00970.114-0.07770.0362-0.0851-0.01480.026-0.1347-0.024201.0013-0.049-0.06930.8188-0.20790.969822.3818158.5672256.5231
10-0.0006-0.00060.0003-0.0001-0.00010.0001-0.0073-0.00750.00050.0054-0.0088-0.00390.00720.004901.5410.04940.02841.46130.04011.409638.8741135.2673264.7307
11-0.00030.00140.0005-0.0006-0.0026-0.0007-0.00790.01970.0169-0.0424-0.0101-0.0017-0.03770.013501.3029-0.0358-0.07981.44350.11591.323442.793145.1487258.7293
12-0.00010.00080.0009-0.0041-0.00150.00060.024-0.00670.00450.01440.0101-0.0349-0.03520.0178-01.4045-0.1296-0.06751.40720.06981.227747.4051153.1945262.5011
13-0.0012-0.00240.00150.0005-0.0018-0.0006-0.0132-0.00270.0096-0.011-0.0210.00980.03750.000601.3679-0.0691-0.20151.39420.14321.314244.3097144.3736271.7462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 307 )A37 - 307
2X-RAY DIFFRACTION2chain 'A' and (resid 308 through 362 )A308 - 362
3X-RAY DIFFRACTION3chain 'A' and (resid 363 through 476 )A363 - 476
4X-RAY DIFFRACTION4chain 'A' and (resid 477 through 530 )A477 - 530
5X-RAY DIFFRACTION5chain 'A' and (resid 531 through 561 )A531 - 561
6X-RAY DIFFRACTION6chain 'A' and (resid 562 through 615 )A562 - 615
7X-RAY DIFFRACTION7chain 'A' and (resid 616 through 728 )A616 - 728
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 39 )B9 - 39
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 92 )B40 - 92
10X-RAY DIFFRACTION10chain 'B' and (resid 93 through 98 )B93 - 98
11X-RAY DIFFRACTION11chain 'B' and (resid 99 through 111 )B99 - 111
12X-RAY DIFFRACTION12chain 'B' and (resid 112 through 130 )B112 - 130
13X-RAY DIFFRACTION13chain 'B' and (resid 131 through 146 )B131 - 146

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