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- PDB-5nc2: ENAH EVH1 in complex with Ac-[2-Cl-F]-PPPPTEDEL-NH2 -

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Basic information

Entry
Database: PDB / ID: 5nc2
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-PPPPTEDEL-NH2
Components
  • Ac-[2-Cl-F]PPPPTEDEL-NH2
  • Protein enabled homolog
KeywordsCELL ADHESION / proline-rich motif / ActA / protein-protein interaction
Function / homology
Function and homology information


actin polymerization-dependent cell motility / WW domain binding / profilin 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 / WW domain binding / profilin 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
Virulence factor ActA / ActA Protein / 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) ...Virulence factor ActA / ActA Protein / 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
NITRATE ION / Actin assembly-inducing protein / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Listeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 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: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: 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
B: Protein enabled homolog
I: Ac-[2-Cl-F]PPPPTEDEL-NH2
J: Ac-[2-Cl-F]PPPPTEDEL-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,12411
Polymers27,6564
Non-polymers4687
Water3,279182
1
A: Protein enabled homolog
I: Ac-[2-Cl-F]PPPPTEDEL-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0485
Polymers13,8282
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-14 kcal/mol
Surface area6810 Å2
MethodPISA
2
B: Protein enabled homolog
J: Ac-[2-Cl-F]PPPPTEDEL-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0766
Polymers13,8282
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-3 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.781, 44.024, 34.667
Angle α, β, γ (deg.)90.00, 102.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein enabled homolog / ENAH EVH1


Mass: 12628.273 Da / Num. of mol.: 2
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(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q8N8S7
#2: Protein/peptide Ac-[2-Cl-F]PPPPTEDEL-NH2


Mass: 1199.716 Da / Num. of mol.: 2
Fragment: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by 2-chloro-L-Phe.
Source method: obtained synthetically
Details: As there is no monomer code for 2-chloro-L-phenylalanine, the acetylated 2-Cl-Phe was linked to a polymer
Source: (synth.) Listeria monocytogenes (bacteria) / References: UniProt: P33379*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2M ammonium sulfate, 500mM ammonium nitrate / Temp details: Incubator

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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: Nov 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.58→42.112 Å / Num. obs: 29131 / % possible obs: 96.8 % / Redundancy: 2.3 % / CC1/2: 0.998 / Rrim(I) all: 0.085 / Net I/σ(I): 10.23
Reflection shellResolution: 1.58→1.68 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.47 / Num. unique obs: 4618 / CC1/2: 0.605 / Rrim(I) all: 0.975 / % possible all: 95.7

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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: 5N9C

5n9c


Resolution: 1.58→42.1 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.62
RfactorNum. reflection% reflection
Rfree0.2451 1456 5 %
Rwork0.1989 --
obs0.2012 29120 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.58→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 29 182 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112047
X-RAY DIFFRACTIONf_angle_d1.1662781
X-RAY DIFFRACTIONf_dihedral_angle_d9.5961582
X-RAY DIFFRACTIONf_chiral_restr0.077284
X-RAY DIFFRACTIONf_plane_restr0.008378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.63620.36411410.3392686X-RAY DIFFRACTION95
1.6362-1.70170.36981440.29682751X-RAY DIFFRACTION98
1.7017-1.77910.27481450.24712754X-RAY DIFFRACTION97
1.7791-1.87290.291460.23292766X-RAY DIFFRACTION97
1.8729-1.99030.25131460.21412776X-RAY DIFFRACTION98
1.9903-2.14390.27871460.20162776X-RAY DIFFRACTION97
2.1439-2.35970.23151460.18962757X-RAY DIFFRACTION97
2.3597-2.70110.25651460.19482789X-RAY DIFFRACTION97
2.7011-3.40280.20771470.1752796X-RAY DIFFRACTION97
3.4028-42.10.21681490.17472813X-RAY DIFFRACTION95
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)
1-0.00110.0018-0.00790.00230.00960.00230.0463-0.0195-0.0173-0.01190.02890.0076-0.0080.034900.0542-0.0128-0.00390.06230.02760.060215.1919-26.591115.228
20.00040.0010.00010.0002-00.0009-0.0096-0.0087-0.00250.0059-0.01280.00070.0012-0.00600.1017-0.0772-0.04170.1085-0.00040.063125.9019-14.587317.7829
3-0.00120.00350.00420.0001-0.0012-0.00140.01530.0199-0.03160.0087-0.0580.03140.0019-0.0624-0-0.09120.0393-0.20910.05050.0774-0.22229.1829-26.848113.9009
40.00830.02320.00260.01510.00230.00310.02890.0182-0.0620.0422-0.0107-0.01250.0034-0.028600.0704-0.0080.00420.07130.00970.058216.6332-24.900612.5307
50.00210.0032-0.00110.0037-0.0040.0075-0.05540.02740.026-0.0395-0.0308-0.0150.0313-0.0504-00.0824-0.0218-0.0115-0.20330.11230.03218.5886-27.32318.2122
6-0.0013-0.004-0.0022-0.0001-0.00090.0008-0.00090.02820.0194-0.00510.02460.0164-0.00950.0321-00.04950.00250.0110.04090.0110.050613.8204-46.931726.4346
70.0007-0.0012-0.00040.00040.00090.0008-0.0098-0.0101-0.0047-0.0072-0.0162-0.0027-0.00360.0032-00.09460.04210.02560.03470.0310.050423.8414-58.966428.4247
800.0015-0.00110.00370.0034-0.0024-0.004-0.00460.0060.0024-0.016-0.02670.019-0.05800.064-0.00640.01170.09280.01930.095610.5942-45.112623.38
90.0015-0.00180.0009-0.0007-0.00210.0004-0.0044-0.00020.0043-0.0206-0.04160.02680.0029-0.0039-0-0.0361-0.00020.09880.12260.0225-0.04854.6594-47.65425.0281
100.0017-0.00090.0010.0015-0.00050.00160.03140.0129-0.0177-0.02470.00080.01880.0136-0.0053-00.11980.0090.02880.11020.00960.061912.4754-50.138319.5408
110.0033-0.00160.0029-0.0001-0.00740.0057-0.03-0.0132-0.02610.03740.0072-0.0394-0.0072-0.03500.0713-0.01440.01330.06370.02310.085114.2074-50.480736.5627
120.0034-0.00050.00140.0022-0.00020.0015-0.02170.0057-0.02810.06750.0089-0.0274-0.04440.0265-00.0838-0.00250.00860.03550.00970.053612.354-42.109433.6832
130.0013-0.00130.00390.0015-0.00530.0142-0.00120.0005-0.01160.0054-0.0029-0.00630.0032-0.001200.1427-0.04870.01410.2096-0.02230.151831.9888-22.413615.5259
140.00110.0003-0.0017-0.0006-0.00040.0033-0.0153-0.00980.0085-0.0089-0.0112-0.0064-0.0015-0.0039-00.10.00120.00810.18140.06050.208628.7181-51.740630.4376
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 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 111 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 17 )
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 28 )
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 40 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 63 )
11X-RAY DIFFRACTION11chain 'B' and (resid 64 through 85 )
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 111 )
13X-RAY DIFFRACTION13chain 'I' and (resid 2 through 8 )
14X-RAY DIFFRACTION14chain 'J' and (resid 2 through 10 )

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