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- PDB-6xvt: ENAH EVH1 in complex with Ac-[2-Cl-F]-PPPPTEDDL-NH2 -

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Basic information

Entry
Database: PDB / ID: 6xvt
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-PPPPTEDDL-NH2
Components
  • ACY-SC1-SC2-SC3-SC4-SC5-NME
  • Protein enabled homolog
KeywordsCELL ADHESION / proline-rich motif / ActA / 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 / SH3 domain binding ...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 / SH3 domain binding / GABA-ergic synapse / 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
NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBarone, M. / Le Cong, K. / 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
DepositionJan 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 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: Database references / Category: citation_author / database_2
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Jul 19, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_ncs_dom_lim / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / 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 3.1Feb 7, 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
G: ACY-SC1-SC2-SC3-SC4-SC5-NME
H: ACY-SC1-SC2-SC3-SC4-SC5-NME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,91710
Polymers26,5114
Non-polymers4066
Water2,522140
1
A: Protein enabled homolog
G: ACY-SC1-SC2-SC3-SC4-SC5-NME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4144
Polymers13,2552
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-19 kcal/mol
Surface area6740 Å2
MethodPISA
2
B: Protein enabled homolog
H: ACY-SC1-SC2-SC3-SC4-SC5-NME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5036
Polymers13,2552
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-3 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.650, 44.280, 43.160
Angle α, β, γ (deg.)60.849, 84.037, 84.005
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLNGLN(chain 'A' and (resid 3 or resid 5 through 9...AA5 - 87 - 10
12ALAALAALAALA(chain 'A' and (resid 3 or resid 5 through 9...AA11 - 1213 - 14
13VALVALTYRTYR(chain 'A' and (resid 3 or resid 5 through 9...AA15 - 1617 - 18
14ALAALAALAALA(chain 'A' and (resid 3 or resid 5 through 9...AA1921
15LYSLYSGLYGLY(chain 'A' and (resid 3 or resid 5 through 9...AA22 - 2724 - 29
16THRTHRVALVAL(chain 'A' and (resid 3 or resid 5 through 9...AA30 - 4932 - 51
17ILEILEILEILE(chain 'A' and (resid 3 or resid 5 through 9...AA53 - 6055 - 62
18ALAALAARGARG(chain 'A' and (resid 3 or resid 5 through 9...AA63 - 8465 - 86
19VALVALSERSER(chain 'A' and (resid 3 or resid 5 through 9...AA86 - 9388 - 95
110ASPASPPHEPHE(chain 'A' and (resid 3 or resid 5 through 9...AA96 - 10098 - 102
111METMETVALVAL(chain 'A' and (resid 3 or resid 5 through 9...AA105 - 110107 - 112
21SERSERGLNGLN(chain 'B' and (resid 3 or resid 5 through 9...BB5 - 87 - 10
22ALAALAALAALA(chain 'B' and (resid 3 or resid 5 through 9...BB11 - 1213 - 14
23VALVALTYRTYR(chain 'B' and (resid 3 or resid 5 through 9...BB15 - 1617 - 18
24ALAALAALAALA(chain 'B' and (resid 3 or resid 5 through 9...BB1921
25LYSLYSGLYGLY(chain 'B' and (resid 3 or resid 5 through 9...BB22 - 2724 - 29
26THRTHRVALVAL(chain 'B' and (resid 3 or resid 5 through 9...BB30 - 4932 - 51
27ILEILEILEILE(chain 'B' and (resid 3 or resid 5 through 9...BB53 - 6055 - 62
28ALAALAARGARG(chain 'B' and (resid 3 or resid 5 through 9...BB63 - 8465 - 86
29VALVALSERSER(chain 'B' and (resid 3 or resid 5 through 9...BB86 - 9388 - 95
210ASPASPPHEPHE(chain 'B' and (resid 3 or resid 5 through 9...BB96 - 10098 - 102
211METMETVALVAL(chain 'B' and (resid 3 or resid 5 through 9...BB105 - 110107 - 112

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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
Details: S0A, Q4A, E95A are 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: Protein/peptide ACY-SC1-SC2-SC3-SC4-SC5-NME


Mass: 627.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / 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.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 45.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.07M AmSO4, 300mM LiNO3 / 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 PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→38.6 Å / Num. obs: 42224 / % possible obs: 96 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.36 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.093 / Net I/σ(I): 9.48
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6456 / CC1/2: 0.479 / % possible all: 95.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NCG

5ncg


Resolution: 1.4→38.6 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 27.345 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 2110 5 %Random
Rwork0.2016 40099 --
obs0.203 42209 96.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.44 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 115 140 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922005
X-RAY DIFFRACTIONf_angle_d1.63152722
X-RAY DIFFRACTIONf_chiral_restr0.0961277
X-RAY DIFFRACTIONf_plane_restr0.0054362
X-RAY DIFFRACTIONf_dihedral_angle_d6.05581288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.37461400.38542673X-RAY DIFFRACTION95.68
1.43-1.470.33411390.33392642X-RAY DIFFRACTION95.37
1.47-1.510.36971400.31092659X-RAY DIFFRACTION95.59
1.51-1.550.30591350.27722565X-RAY DIFFRACTION93.01
1.55-1.60.28291410.25982666X-RAY DIFFRACTION96.23
1.6-1.660.28321410.24352689X-RAY DIFFRACTION96
1.66-1.730.25481410.22722668X-RAY DIFFRACTION96.3
1.73-1.80.27421410.21152673X-RAY DIFFRACTION96.44
1.8-1.90.2021400.19962676X-RAY DIFFRACTION96.6
1.9-2.020.20591410.18422673X-RAY DIFFRACTION95.75
2.02-2.170.22491420.18942706X-RAY DIFFRACTION98.07
2.17-2.390.21231420.18442716X-RAY DIFFRACTION98.15
2.39-2.740.23791420.18982686X-RAY DIFFRACTION96.82
2.74-3.450.22121430.1862710X-RAY DIFFRACTION97.37
3.45-38.60.19141420.17332697X-RAY DIFFRACTION97.16
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)
12.344353123130.240298394695-0.3372919857220.962858318842-0.04653394663632.56750275242-0.01006845964030.144729202411-0.124599973514-0.0005316691557130.0156458545223-0.0116441444091-0.00493998344681-0.063068141715-0.001086791208260.08991258365040.005013345301740.002767723608050.1295691741570.03823425290820.140220082771-9.282117508858.46360253952-4.43325618487
22.44899051882-0.297930056579-0.3970575511262.42605046259-1.160039017341.916445672370.04859573708380.15833649887-0.116959283527-0.0313019238932-0.0961252927727-0.006936154375210.003858932760830.03730021576730.0405456404810.1013812014230.01234493908970.005318606594370.1827201643860.04163778645690.131022505584-27.1426650358-2.7951973379814.2423892677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 111)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 111)

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