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

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Basic information

Entry
Database: PDB / ID: 6xxr
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-PPPPTEDEA-NH2
Components
  • Ac-[2-Cl-F]-PPPPTEDEA-NH2
  • Protein enabled homolog
KeywordsCELL ADHESION / proline-rich motif / ActA / 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 / PH-like domain superfamily
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: 1.48 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 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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: Advisory / Database references
Category: citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Mar 15, 2023Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Polymer sequence / 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 / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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
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
F: Ac-[2-Cl-F]-PPPPTEDEA-NH2
G: Ac-[2-Cl-F]-PPPPTEDEA-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9979
Polymers26,6874
Non-polymers3105
Water93752
1
A: Protein enabled homolog
G: Ac-[2-Cl-F]-PPPPTEDEA-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5305
Polymers13,3442
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-1 kcal/mol
Surface area6970 Å2
MethodPISA
2
B: Protein enabled homolog
F: Ac-[2-Cl-F]-PPPPTEDEA-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4684
Polymers13,3442
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-5 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.740, 43.190, 44.010
Angle α, β, γ (deg.)61.038, 84.196, 84.210
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
11SERSERALAALA(chain 'A' and (resid 5 through 13 or resid 15...AA5 - 127 - 14
12VALVALTRPTRP(chain 'A' and (resid 5 through 13 or resid 15...AA15 - 2317 - 25
13ALAALATHRTHR(chain 'A' and (resid 5 through 13 or resid 15...AA26 - 4528 - 47
14VALVALVALVAL(chain 'A' and (resid 5 through 13 or resid 15...AA48 - 4950 - 51
15LYSLYSILEILE(chain 'A' and (resid 5 through 13 or resid 15...AA52 - 6054 - 62
16ALAALAALAALA(chain 'A' and (resid 5 through 13 or resid 15...AA63 - 10765 - 109
27SERSERALAALA(chain 'B' and (resid 5 through 13 or resid 15...BB5 - 127 - 14
28VALVALTRPTRP(chain 'B' and (resid 5 through 13 or resid 15...BB15 - 2317 - 25
29ALAALATHRTHR(chain 'B' and (resid 5 through 13 or resid 15...BB26 - 4528 - 47
210VALVALVALVAL(chain 'B' and (resid 5 through 13 or resid 15...BB48 - 4950 - 51
211LYSLYSILEILE(chain 'B' and (resid 5 through 13 or resid 15...BB52 - 6054 - 62
212ALAALAALAALA(chain 'B' and (resid 5 through 13 or resid 15...BB63 - 10765 - 109

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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 E109A 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 Ac-[2-Cl-F]-PPPPTEDEA-NH2


Mass: 715.235 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.932M AmSO4 291mM NaNO3

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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: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.48→38.44 Å / Num. obs: 35565 / % possible obs: 95.7 % / Redundancy: 3.1 % / CC1/2: 0.984 / Rrim(I) all: 0.221 / Net I/σ(I): 3.86
Reflection shellResolution: 1.48→1.59 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.58 / Num. unique obs: 18406 / CC1/2: 0.376 / % possible all: 93.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NCG

5ncg


Resolution: 1.48→38.44 Å / Cross valid method: FREE R-VALUE / σ(F): 2.47 / Phase error: 44.4207
RfactorNum. reflection% reflection
Rfree0.2688 1857 5.23 %
Rwork0.2464 --
obs0.2551 35515 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.24 Å2
Refinement stepCycle: LAST / Resolution: 1.48→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 119 52 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0241919
X-RAY DIFFRACTIONf_angle_d1.66522604
X-RAY DIFFRACTIONf_chiral_restr0.1001271
X-RAY DIFFRACTIONf_plane_restr0.0108342
X-RAY DIFFRACTIONf_dihedral_angle_d13.9817433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.46491290.44692443X-RAY DIFFRACTION86.51
1.52-1.560.41161350.38842549X-RAY DIFFRACTION89.75
1.56-1.620.35771360.35592592X-RAY DIFFRACTION90.85
1.62-1.670.34711370.34122597X-RAY DIFFRACTION91.06
1.67-1.740.33451370.3242611X-RAY DIFFRACTION91.33
1.74-1.820.33021380.31852610X-RAY DIFFRACTION91.39
1.82-1.920.34451360.32572585X-RAY DIFFRACTION90.64
1.92-2.040.33021350.30682582X-RAY DIFFRACTION90.72
2.04-2.190.30641390.28222639X-RAY DIFFRACTION92.76
2.19-2.410.29441380.28342625X-RAY DIFFRACTION92.3
2.41-2.760.28221390.26022624X-RAY DIFFRACTION91.62
2.76-3.480.23721380.22742636X-RAY DIFFRACTION92.59
3.48-38.440.19191400.18392645X-RAY DIFFRACTION92.61
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)
10.529609674281-0.009999477370790.2384469531450.829421470659-0.06021796607450.6226239526770.01853001900180.02018919270970.06829062152270.0165779592466-0.00586185784669-0.0301929843769-0.0300864656736-0.008948723670140.04953171259330.1249664452520.0205956825176-0.004549053430880.3014542252520.1714077563920.21716942013810.05826729140.129679519342-13.9509376562
20.641673142176-0.3229163934910.183059197291.05138164620.4248555906411.54057110710.00952319982681-0.03369585011090.0488355924046-0.0003145280722150.016773115138-0.0105571274053-0.0163963213072-0.0713357459471-0.02312818450210.105764863940.00959947456461-0.01110237339480.2929245852650.1744429978850.22010180036627.6360957793-11.32555963344.70567386845
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 4 through 111)

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