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- PDB-7aki: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-1]-NH2 -

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Basic information

Entry
Database: PDB / ID: 7aki
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-1]-NH2
ComponentsProtein enabled homolog
KeywordsCELL INVASION / proline-rich motif / Ena/VASP inhibitor / actin / protein-protein interaction
Function / homology
Function and homology information


actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / WW domain binding / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / cell junction ...actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / WW domain binding / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / cell junction / lamellipodium / actin binding / cytoskeleton / focal adhesion / synapse / plasma membrane / cytosol
Similarity search - Function
VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / PH-like domain superfamily
Similarity search - Domain/homology
NITRATE ION / Chem-RJQ / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsBarone, M. / Roske, Y.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research16GW0186K Germany
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells.
Authors: Barone, M. / Muller, M. / Chiha, S. / Ren, J. / Albat, D. / Soicke, A. / Dohmen, S. / Klein, M. / Bruns, J. / van Dinther, M. / Opitz, R. / Lindemann, P. / Beerbaum, M. / Motzny, K. / Roske, ...Authors: Barone, M. / Muller, M. / Chiha, S. / Ren, J. / Albat, D. / Soicke, A. / Dohmen, S. / Klein, M. / Bruns, J. / van Dinther, M. / Opitz, R. / Lindemann, P. / Beerbaum, M. / Motzny, K. / Roske, Y. / Schmieder, P. / Volkmer, R. / Nazare, M. / Heinemann, U. / Oschkinat, H. / Ten Dijke, P. / Schmalz, H.G. / Kuhne, R.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions.
Authors: Opitz, R. / Muller, M. / Reuter, C. / Barone, M. / Soicke, A. / Roske, Y. / Piotukh, K. / Huy, P. / Beerbaum, M. / Wiesner, B. / Beyermann, M. / Schmieder, P. / Freund, C. / Volkmer, R. / ...Authors: Opitz, R. / Muller, M. / Reuter, C. / Barone, M. / Soicke, A. / Roske, Y. / Piotukh, K. / Huy, P. / Beerbaum, M. / Wiesner, B. / Beyermann, M. / Schmieder, P. / Freund, C. / Volkmer, R. / Oschkinat, H. / Schmalz, H.G. / Kuhne, R.
History
DepositionOct 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Oct 26, 2022Group: Advisory / Database references
Category: citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0454
Polymers12,6281
Non-polymers1,4163
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint1 kcal/mol
Surface area6620 Å2
Unit cell
Length a, b, c (Å)34.700, 60.690, 89.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

21A-359-

HOH

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Components

#1: Protein Protein enabled homolog


Mass: 12628.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: M1A Q11A K21A are mutated for modelling as only the backbone was visible
Source: (gene. exp.) Homo sapiens (human) / Gene: ENAH, MENA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8N8S7
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-RJQ / (3~{S},7~{R},10~{R},13~{S})-4-[(3~{S},6~{R},8~{a}~{S})-1'-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8~{a}-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxamide


Mass: 677.190 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H41ClN6O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.84 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.541M ammonium sulfate, 564mM potassium bromide / Temp details: incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.36→44.53 Å / Num. obs: 20643 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 22.73 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.131 / Net I/σ(I): 11.48
Reflection shellResolution: 1.36→1.47 Å / Redundancy: 14.5 % / Num. unique obs: 4246 / CC1/2: 0.273 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N91

5n91


Resolution: 1.36→44.53 Å / SU ML: 0.2564 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.9997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236 1033 5.01 %
Rwork0.2012 19606 -
obs0.203 20639 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.8 Å2
Refinement stepCycle: LAST / Resolution: 1.36→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 100 62 1038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151112
X-RAY DIFFRACTIONf_angle_d1.64351539
X-RAY DIFFRACTIONf_chiral_restr0.0852160
X-RAY DIFFRACTIONf_plane_restr0.0075201
X-RAY DIFFRACTIONf_dihedral_angle_d14.7708462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.430.3991460.4482755X-RAY DIFFRACTION99.9
1.43-1.520.34741450.33892771X-RAY DIFFRACTION99.9
1.52-1.640.35871450.29052749X-RAY DIFFRACTION99.97
1.64-1.80.28411460.2232776X-RAY DIFFRACTION99.97
1.8-2.060.22121480.19152805X-RAY DIFFRACTION100
2.06-2.60.21561470.19792801X-RAY DIFFRACTION100
2.6-44.530.21791560.17592949X-RAY DIFFRACTION100
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)
11.70714934814-0.4175588369610.419541430311.563082318041.69339436442.292177798760.0267004599511-0.116614824666-0.1151252456360.268678434247-0.008758162232250.08210921302370.5091682750810.0710363088956-0.04981092360360.229469758067-0.007404013278190.01357896873510.1798963132980.01513805755430.20479020736910.079085118.110197164089.76539321368
25.48738559702-0.6215336566370.2267922884154.32801838492.931862914832.06246577289-0.13215829816-0.536669896350.488443564880.03135281081180.0593966502828-0.149565185897-0.254222879065-0.0989322560050.08019963258660.1841292287670.0281930114236-0.04625189292380.292709684312-0.04620630321980.23397375125714.631371569118.220216633219.3336452109
35.897047775543.380733167181.686633985695.868277127121.223463906693.58547448764-0.28971745473-0.194753105221-0.566200506354-0.2253108792140.143156438421-0.1408861694050.562086248055-0.1257788572360.1438713074530.2524497877010.02091686259020.04100456548870.186081643806-0.001064585217340.193946817258.611388141591.281734593739.10515051072
42.35117754303-0.911781319448-2.096691643424.108419137090.05704657097643.071565126210.296700987772-0.03420508541260.3704890196360.13077918754-0.180832602381-0.4424848625080.1965018866480.3879027882150.04193791805790.2419784377710.0278842900595-0.01089318100230.2858605723120.01544315311710.20413730131316.65017010476.1458748699413.0743062652
55.030162749211.44777291697-2.520911941033.5859182202-2.193723524866.25678770695-0.00990998454742-0.07034014707990.0306137277249-0.0279084563469-0.03802398961320.138854506525-0.0907890905066-0.199540758079-0.044503352360.09971255268510.010741795218-0.005029458696180.155048038091-0.03122984245310.150103192393.5165751368413.339533241913.1656133873
64.885696753944.06626691622-4.345091580144.37650138141-4.065916130414.07331560881-0.2915240647980.633245373733-0.431569419150.03406578037480.1336034750220.5154057324940.19437992253-0.8457716491930.07381552925860.29962171753-0.01480036776040.01971424143220.342295113293-0.0496859113520.3402916000290.390310276019.247578593043.7336703291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 63 )
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 93 )
6X-RAY DIFFRACTION6chain 'A' and (resid 94 through 111 )

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