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

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Basic information

Entry
Database: PDB / ID: 6rcj
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-15]-OMe
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 / WW domain binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / lamellipodium ...actin polymerization-dependent cell motility / profilin binding / WW domain binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / lamellipodium / cell junction / 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-K0H / NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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)13,5395
Polymers12,6281
Non-polymers9104
Water2,072115
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Ena/VASP EVH1 are monomeric in SEC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint1 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.995, 141.524, 34.726
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-398-

HOH

21A-402-

HOH

31A-405-

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: S4A is 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-K0H / methyl 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]ethanoate


Mass: 694.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H44ClN5O7
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M ammonium sulfate, 240mM 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: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.35→42.012 Å / Num. obs: 24264 / % possible obs: 99.4 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rrim(I) all: 0.08 / Net I/σ(I): 13.69
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.21 / Num. unique obs: 3860 / CC1/2: 0.563 / % possible all: 99.5

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Processing

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

5n91


Resolution: 1.35→42.012 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.39
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 1214 5 %random
Rwork0.1713 ---
obs0.1728 24256 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→42.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 63 115 1046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021087
X-RAY DIFFRACTIONf_angle_d1.8771489
X-RAY DIFFRACTIONf_dihedral_angle_d15.178738
X-RAY DIFFRACTIONf_chiral_restr0.114151
X-RAY DIFFRACTIONf_plane_restr0.013199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3499-1.40390.35841330.33152508X-RAY DIFFRACTION99
1.4039-1.46780.27171330.28042532X-RAY DIFFRACTION99
1.4678-1.54520.26871320.21912516X-RAY DIFFRACTION100
1.5452-1.6420.21531340.20092539X-RAY DIFFRACTION100
1.642-1.76880.21891330.1812526X-RAY DIFFRACTION99
1.7688-1.94680.20711350.16472560X-RAY DIFFRACTION99
1.9468-2.22850.18391340.14992551X-RAY DIFFRACTION100
2.2285-2.80760.17531370.16542603X-RAY DIFFRACTION100
2.8076-42.03220.19321430.15462707X-RAY DIFFRACTION99
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)
10.0999-0.078-0.00320.0339-0.0240.2807-0.0225-0.09930.07190.02450.0534-0.06540.02930.03350.00010.13930.0256-0.02010.1156-0.01070.140955.751717.997311.6746
20.12490.09540.0130.1256-0.05390.0761-0.0347-0.05920.38980.0766-0.12710.0569-0.2528-0.0755-0.07230.17860.0791-0.02950.165-0.03240.213244.157129.052512.3978
30.53290.16130.04270.282-0.24990.26520.0177-0.0726-0.0890.1279-0.031-0.0620.2526-0.0579-0.06040.17240.0042-0.00940.1312-0.02380.136256.206612.799412.4616
40.1123-0.0969-0.02970.1207-0.01290.0333-0.1258-0.0459-0.07360.22270.12530.10520.1899-0.04770.00660.21640.01730.00020.2002-0.01720.141853.039316.763918.961
50.3896-0.32120.25850.7039-0.18240.70040.04010.08030.1086-0.029-0.16590.08640.0948-0.099-0.13990.1186-0.0105-0.01530.1533-0.02410.143852.159521.39161.8037
60.0818-0.05130.05750.2512-0.30550.3482-0.05140.09920.0543-0.0241-0.0652-0.0418-0.02580.0844-0.00740.12630.0016-0.01960.1663-0.02460.155260.610619.09894.2338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 63 )
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 85 )
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 111 )

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