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- PDB-6rcf: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-15]-OH -

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Basic information

Entry
Database: PDB / ID: 6rcf
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-15]-OH
ComponentsProtein enabled homolog
KeywordsCELL ADHESION / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-K0K / NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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. / Mueller, 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. / Mueller, 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. / Kuehne, R.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 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 1.4Feb 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 1.5Oct 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 1.6Jan 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)13,3703
Polymers12,6281
Non-polymers7422
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Ena/VASP EVH1 domains run as monomers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint1 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.384, 141.461, 34.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-432-

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
Source: (gene. exp.) Homo sapiens (human) / Gene: ENAH, MENA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q8N8S7
#2: Chemical ChemComp-K0K / 2-[(3~{a}~{R},6~{R},8~{a}~{S})-1-[(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-6-ethyl-8-oxidanylidene-3,3~{a},6,8~{a}-tetrahydro-2~{H}-pyrrolo[2,3-c]azepin-7-yl]ethanoic acid


Mass: 680.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H42ClN5O7
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.27M ammonium sulfate, 1000mM ammonium nitrate / Temp details: incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→41.477 Å / Num. obs: 42538 / % possible obs: 96.5 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rrim(I) all: 0.093 / Net I/σ(I): 9.43
Reflection shellResolution: 1.1→1.17 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.55 / Num. unique obs: 6649 / CC1/2: 0.278 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N91

5n91


Resolution: 1.1→41.477 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 2125 5 %0.05
Rwork0.1652 ---
obs0.167 42513 96.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→41.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 52 132 1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191046
X-RAY DIFFRACTIONf_angle_d1.6911429
X-RAY DIFFRACTIONf_dihedral_angle_d16.214630
X-RAY DIFFRACTIONf_chiral_restr0.121148
X-RAY DIFFRACTIONf_plane_restr0.014192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0999-1.12550.4421360.40132580X-RAY DIFFRACTION94
1.1255-1.15360.37611390.36362640X-RAY DIFFRACTION95
1.1536-1.18480.40951370.32732616X-RAY DIFFRACTION95
1.1848-1.21970.32051360.31722565X-RAY DIFFRACTION94
1.2197-1.2590.33741390.31642654X-RAY DIFFRACTION96
1.259-1.3040.27731380.26632650X-RAY DIFFRACTION96
1.304-1.35620.27281410.23012678X-RAY DIFFRACTION97
1.3562-1.4180.25071410.1962682X-RAY DIFFRACTION97
1.418-1.49270.23681410.17512667X-RAY DIFFRACTION96
1.4927-1.58630.19511430.14122713X-RAY DIFFRACTION97
1.5863-1.70870.18331440.12672749X-RAY DIFFRACTION99
1.7087-1.88070.18061450.12522753X-RAY DIFFRACTION98
1.8807-2.15280.16251450.12092746X-RAY DIFFRACTION97
2.1528-2.71230.1711470.15022800X-RAY DIFFRACTION98
2.7123-41.50670.18871530.16222895X-RAY DIFFRACTION97

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