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- PDB-5ncp: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-12]-OH -

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Basic information

Entry
Database: PDB / ID: 5ncp
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-12]-OH
ComponentsProtein enabled homolog
KeywordsCELL ADHESION / proline-rich motif / Ena/VASP inhibitor / actin / protein-protein interaction
Function / homology
Function and homology information


postsynaptic cytoskeleton organization / actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / WW domain binding / Generation of second messenger molecules / axon guidance / filopodium / GABA-ergic synapse ...postsynaptic cytoskeleton organization / actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / WW domain binding / Generation of second messenger molecules / axon guidance / filopodium / GABA-ergic synapse / SH3 domain binding / lamellipodium / actin binding / cytoskeleton / postsynapse / focal adhesion / 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-EG5 / NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBarone, M. / Roske, Y.
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
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: 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.title / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 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)13,5275
Polymers12,6281
Non-polymers8984
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Tetramerization of Ena/VASP is mediated by EVH2 domain (Bachmann1999)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-12 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.141, 141.367, 34.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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 / Plasmid: pGEX-4T-1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8N8S7
#2: Chemical ChemComp-EG5 / (3~{S},7~{R},10~{R},13~{R})-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-carboxylic acid


Mass: 678.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40ClN5O7
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 42.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.7M ammonium sulfate, 180mM ammonium nitrate / Temp details: plate hotel

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.65→42.135 Å / Num. obs: 13548 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC1/2: 0.997 / Rrim(I) all: 0.2 / Net I/σ(I): 9.14
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 0.97 / Num. unique obs: 2144 / CC1/2: 0.433 / Rrim(I) all: 2.106 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NCG

5ncg


Resolution: 1.65→42.135 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.36
RfactorNum. reflection% reflection
Rfree0.2083 677 5 %
Rwork0.1845 --
obs0.1856 13543 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→42.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 0 61 78 1002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009987
X-RAY DIFFRACTIONf_angle_d1.2681347
X-RAY DIFFRACTIONf_dihedral_angle_d16.34654
X-RAY DIFFRACTIONf_chiral_restr0.061140
X-RAY DIFFRACTIONf_plane_restr0.007177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6497-1.7770.34811320.31522509X-RAY DIFFRACTION100
1.777-1.95590.28851320.25442529X-RAY DIFFRACTION100
1.9559-2.23890.21171350.19162555X-RAY DIFFRACTION100
2.2389-2.82070.20631350.17662572X-RAY DIFFRACTION100
2.8207-42.14850.17561430.15622701X-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)
18.0908-2.66741.24780.8126-0.45452.891-0.1418-0.17730.00980.03880.12530.06250.04260.11770.08460.1232-0.02640.02080.10140.0080.135455.497719.285411.6686
28.1793-5.18094.43724.8665-5.84988.1469-0.0712-0.130.22130.34520.06460.5123-0.4444-0.3718-0.05540.21440.05770.00060.1991-0.0790.263944.07729.166111.9776
33.10270.87030.25336.69536.4978.5272-0.0144-0.0356-0.21760.3802-0.09550.01510.6294-0.13790.10260.1471-0.00660.00270.11930.0090.128156.474612.503312.1652
42.91960.7514.93148.10470.53988.7602-0.2246-0.0711-0.28740.36940.2334-0.0131-0.01590.1730.04770.16810.00590.02650.2841-0.02980.186252.811816.31718.1604
58.81326.40615.28444.65335.11328.22430.09990.222-0.1539-0.1127-0.0921-0.42130.11720.07850.14890.14490.04720.00070.1654-0.00580.154655.903521.38650.0434
64.82945.50434.62227.30954.48834.60430.2270.31850.38870.2853-0.24840.53260.3812-0.1957-0.08330.1728-0.0245-0.0210.2612-0.0430.268148.755621.77154.3879
75.65470.12240.94966.68243.65315.65060.0030.3513-0.1362-0.08870.0868-0.2350.08810.2941-0.09210.11770.0076-0.00350.1340.04250.085260.758519.13364.2479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 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 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 85 )
7X-RAY DIFFRACTION7chain 'A' and (resid 86 through 111 )

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