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- PDB-5n91: ENAH EVH1 in complex with Ac-[2-Cl-F]-PPPP-OH -

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Basic information

Entry
Database: PDB / ID: 5n91
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-PPPP-OH
Components
  • Ac-[2-Cl-F]-PPPP-OH
  • Protein 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 / 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
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
NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.citation_id / _citation_author.name
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 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
E: Ac-[2-Cl-F]-PPPP-OH
F: Ac-[2-Cl-F]-PPPP-OH
G: Ac-[2-Cl-F]-PPPP-OH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3479
Polymers27,0995
Non-polymers2484
Water3,171176
1
A: Protein enabled homolog
F: Ac-[2-Cl-F]-PPPP-OH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3664
Polymers13,2422
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-5 kcal/mol
Surface area6830 Å2
MethodPISA
2
B: Protein enabled homolog
E: Ac-[2-Cl-F]-PPPP-OH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3664
Polymers13,2422
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-3 kcal/mol
Surface area6650 Å2
MethodPISA
3
G: Ac-[2-Cl-F]-PPPP-OH


  • defined by author&software
  • 614 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6141
Polymers6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-1 kcal/mol
Surface area850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.910, 43.365, 43.652
Angle α, β, γ (deg.)61.15, 84.25, 84.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein enabled homolog


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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8N8S7
#2: Protein/peptide Ac-[2-Cl-F]-PPPP-OH


Mass: 614.131 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-NO3 / NITRATE ION


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M ammonium sulfate, 350mM 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 2M / Detector: PIXEL / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.49→38.2 Å / Num. obs: 33987 / % possible obs: 93 % / Redundancy: 2.7 % / Rrim(I) all: 0.055 / Net I/σ(I): 1.58
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 2.7 % / Num. unique obs: 5476 / CC1/2: 0.595 / Rrim(I) all: 0.965 / % possible all: 92.6

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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: 4MY6

4my6


Resolution: 1.49→38.164 Å / Cross valid method: FREE R-VALUE / σ(F): 5.5 / Phase error: 29.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1839 5.41 %Random
Rwork0.1796 ---
obs0.183 33987 93.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→38.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 16 176 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062033
X-RAY DIFFRACTIONf_angle_d1.2092770
X-RAY DIFFRACTIONf_dihedral_angle_d13.337929
X-RAY DIFFRACTIONf_chiral_restr0.066285
X-RAY DIFFRACTIONf_plane_restr0.004364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4902-1.5340.35481420.33682694X-RAY DIFFRACTION88
1.534-1.58360.34351420.31662689X-RAY DIFFRACTION88
1.5836-1.64020.28351370.28312612X-RAY DIFFRACTION88
1.6402-1.70580.26371400.28792646X-RAY DIFFRACTION86
1.7058-1.78350.29461420.25192697X-RAY DIFFRACTION90
1.7835-1.87750.24451430.23742734X-RAY DIFFRACTION89
1.8775-1.99510.2131390.20892637X-RAY DIFFRACTION88
1.9951-2.14910.21261420.18962703X-RAY DIFFRACTION89
2.1491-2.36540.20321430.18882701X-RAY DIFFRACTION90
2.3654-2.70760.19811420.1792712X-RAY DIFFRACTION89
2.7076-3.41090.18961450.16072745X-RAY DIFFRACTION91
3.4109-37.93030.1541430.12832711X-RAY DIFFRACTION90
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)
11.2803-0.1491-0.10310.14510.20930.89920.0183-0.0090.2162-0.1708-0.0526-0.06-0.08980.01980.20810.0751-0.0027-0.010.15980.05980.20661.683837.6095-8.564
23.2522-2.43830.26172.3556-0.93761.06310.1040.0822-0.6115-0.0420.00860.40880.1641-0.1655-0.14940.1269-0.0041-0.01440.17780.08830.28912.199219.7095-4.4966
32.77060.91650.33622.7640.66751.95770.0088-0.0620.42810.03330.0706-0.0933-0.1874-0.0747-0.04530.08890.01370.01640.15910.03120.21831.977941.0785-7.3262
45.0824-0.7105-1.1720.12950.4112.29290.072-0.0069-0.30220.0162-0.03180.150.0678-0.33620.0440.08810.0016-0.00060.26070.06870.3039-11.188135.1361-9.4824
51.77130.02280.27120.5423-0.06230.66320.0820.04020.1441-0.0367-0.0231-0.1689-0.03240.088-0.06950.07460.00170.00270.17150.05870.19569.660433.5371-8.6925
62.3226-0.11440.53582.298-0.67691.49840.03270.06080.13020.006-0.0711-0.1081-0.02450.06040.01250.08570.0130.01060.20640.07680.1639.370634.477-11.7918
72.29350.0438-0.02291.4776-0.15281.2481-0.09590.13630.0789-0.02670.0538-0.01910.0760.130.01550.0850.0139-0.01770.21460.07160.1598-9.451922.16594.1597
82.3468-0.4196-0.64751.52290.07841.3354-0.0523-0.30890.31470.2160.0816-0.0527-0.06860.0731-0.13340.0990.0263-0.00380.22610.03140.1966-9.371128.449714.2702
90.8413-0.00380.49041.948-0.33420.3693-0.1321-0.06910.02870.04640.1747-0.324-0.06390.20330.05070.09420.0055-0.00260.31510.02870.2172-2.934326.67718.8865
103.2563-2.13050.24917.58591.06151.76520.046-0.2180.04090.1807-0.07990.07130.0867-0.36030.03930.0995-0.00240.00690.32330.0950.1806-21.199521.20478.772
111.8588-0.29950.1641.2721-0.39381.62510.0425-0.17960.0012-0.00320.09780.07680.0602-0.1915-0.03480.10510.0262-0.00010.2730.08820.1699-16.754121.389910.5757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 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 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 111 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 28 )
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 52 )
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 76 )
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 111 )

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