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- PDB-5nc7: ENAH EVH1 in complex with Ac-WPPPPTEDEL-NH2 -

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Basic information

Entry
Database: PDB / ID: 5nc7
TitleENAH EVH1 in complex with Ac-WPPPPTEDEL-NH2
Components
  • ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
  • Protein enabled homolog
KeywordsCELL ADHESION / proline-rich motif / ActA / 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
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
Actin assembly-inducing protein / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Listeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Protein enabled homolog
D: Protein enabled homolog
K: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
I: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
J: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
L: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
Z: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
X: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
Y: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
W: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization


Theoretical massNumber of molelcules
Total (without water)60,14812
Polymers60,14812
Non-polymers00
Water724
1
D: Protein enabled homolog
L: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
Z: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization


Theoretical massNumber of molelcules
Total (without water)15,0373
Polymers15,0373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein enabled homolog
I: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
W: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization


Theoretical massNumber of molelcules
Total (without water)15,0373
Polymers15,0373
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Protein enabled homolog
J: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
X: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization


Theoretical massNumber of molelcules
Total (without water)15,0373
Polymers15,0373
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Protein enabled homolog
K: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization
Y: ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization


Theoretical massNumber of molelcules
Total (without water)15,0373
Polymers15,0373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.960, 34.430, 110.990
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein enabled homolog


Mass: 12628.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: S2A, L68A, and R84A are mutated for modelling as only the backbone was visible
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: Protein/peptide
ActA-derived 10-mer Ac-FPPPPTEDEL-NH2 with acetylated (Ac) and amidated (NH2) termini. Phe is substitued by Trp to increase affinity for crystallization


Mass: 1204.307 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: Termini not resolved in electrostatic binding site (chains W-Z)
Source: (synth.) Listeria monocytogenes (bacteria) / References: UniProt: P33379*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Merged data set of crystals grown in 2.2M ammonium sulfate, 200mM lithium chloride and 2.2M ammonium sulfate, 200mM sodium nitrate
Temp details: plate hotel

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918410, 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
20.9184091
ReflectionResolution: 2.7→48.3445 Å / Num. obs: 20211 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.989 / Rrim(I) all: 0.23 / Net I/σ(I): 8.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 2039 / CC1/2: 0.587 / Rrim(I) all: 1.534 / % 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: 5N9C

5n9c


Resolution: 2.7→48.337 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7
RfactorNum. reflection% reflection
Rfree0.272 1011 5 %
Rwork0.2093 --
obs0.2123 20204 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3985 0 0 4 3989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094099
X-RAY DIFFRACTIONf_angle_d1.1025583
X-RAY DIFFRACTIONf_dihedral_angle_d8.7662418
X-RAY DIFFRACTIONf_chiral_restr0.058580
X-RAY DIFFRACTIONf_plane_restr0.008748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84230.38081430.31342712X-RAY DIFFRACTION100
2.8423-3.02040.43861400.28342659X-RAY DIFFRACTION100
3.0204-3.25360.29121430.24652726X-RAY DIFFRACTION100
3.2536-3.58090.30831430.22332708X-RAY DIFFRACTION100
3.5809-4.09880.25681450.18622754X-RAY DIFFRACTION100
4.0988-5.16310.1991450.16032750X-RAY DIFFRACTION100
5.1631-48.34450.25571520.20542884X-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)
10.0042-0.0074-0.00370.0055-0.00020.00120.04270.02990.0127-0.00290.01810.0201-0.00260.022700.1123-0.02670.0326-0.0690.03720.1349-35.84669.039336.227
2-0.0013-0.00430.00630.00140.00020.00110.04580.0375-0.0175-0.0126-0.0134-0.0225-0.0141-0.0279-00.0832-0.0164-0.0168-0.2849-0.03730.0568-58.240126.021636.0776
30.00740.0008-0.00180-0.00080.0038-0.04960.01540.00050.00690.01530.01490.0122-0.001700.16810.03820.04210.37670.0310.1652-13.66674.989717.7948
40.0089-0.00060.0013-0.0012-0.00060.0048-0.03380.0098-0.00880.00310.0187-0.0053-0.00970.0041-00.18940.0196-0.05610.4064-0.04190.2041-80.376830.119217.834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 111)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 111)
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 111)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 111)

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