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- PDB-7a5m: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-17]-OMe -

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Basic information

Entry
Database: PDB / ID: 7a5m
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-17]-OMe
Components
  • Ac-[2-Cl-F]-[ProM-2]-[ProM-17]-OMe
  • Protein enabled homolog
KeywordsCELL INVASION / proline-rich motif / 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 / 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
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: 0.78 Å
AuthorsBarone, M. / 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. / Muller, 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. / Muller, 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. / Kuhne, R.
History
DepositionAug 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 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 2.0Aug 16, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_src_syn / pdbx_poly_seq_scheme / struct_conn / struct_ref_seq
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.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _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_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
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.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 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: Ac-[2-Cl-F]-[ProM-2]-[ProM-17]-OMe
C: Ac-[2-Cl-F]-[ProM-2]-[ProM-17]-OMe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1034
Polymers14,0413
Non-polymers621
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Runs as monomer on a size exclusion column.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-0 kcal/mol
Surface area6740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.150, 61.360, 88.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-431-

HOH

31A-433-

HOH

41B-101-

HOH

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Components

#1: Protein Protein enabled homolog


Mass: 12628.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENAH, MENA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N8S7
#2: Protein/peptide Ac-[2-Cl-F]-[ProM-2]-[ProM-17]-OMe


Mass: 706.271 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.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 1.91 Å3/Da / Density % sol: 35.51 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.90M ammonium sulfate, 360mM ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 0.78→30.68 Å / Num. obs: 106735 / % possible obs: 97.7 % / Redundancy: 19 % / Biso Wilson estimate: 9.26 Å2 / CC1/2: 1 / Rrim(I) all: 0.051 / Net I/σ(I): 23.08
Reflection shellResolution: 0.78→0.85 Å / Redundancy: 16 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 23284 / CC1/2: 0.539 / Rrim(I) all: 2.81 / % possible all: 94.7

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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: 0.78→17.97 Å / SU ML: 0.1062 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 16.961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.14 10302 5 %random
Rwork0.1192 195866 --
obs0.1202 106735 97.39 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.86 Å2
Refinement stepCycle: LAST / Resolution: 0.78→17.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 106 166 1155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02171488
X-RAY DIFFRACTIONf_angle_d2.37652073
X-RAY DIFFRACTIONf_chiral_restr0.3114211
X-RAY DIFFRACTIONf_plane_restr0.0156274
X-RAY DIFFRACTIONf_dihedral_angle_d18.6091702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.78-0.790.39633330.38496280X-RAY DIFFRACTION93.31
0.79-0.80.363320.37876277X-RAY DIFFRACTION93.39
0.8-0.810.48353150.47355918X-RAY DIFFRACTION89.06
0.81-0.820.37043330.37086365X-RAY DIFFRACTION94.19
0.82-0.830.34853370.36066287X-RAY DIFFRACTION94.55
0.83-0.840.32553380.30396417X-RAY DIFFRACTION94.89
0.84-0.850.26373300.2726322X-RAY DIFFRACTION95.16
0.85-0.860.28813390.2526442X-RAY DIFFRACTION95.63
0.86-0.880.22063350.2146433X-RAY DIFFRACTION95.88
0.88-0.890.21913460.19666473X-RAY DIFFRACTION96.63
0.89-0.910.1963420.18426540X-RAY DIFFRACTION97.19
0.91-0.920.18153450.16736523X-RAY DIFFRACTION97.27
0.92-0.940.16163420.15336469X-RAY DIFFRACTION97.59
0.94-0.960.1723460.14746572X-RAY DIFFRACTION97.79
0.96-0.980.15493430.13116621X-RAY DIFFRACTION98.06
0.98-1.010.12683480.12086579X-RAY DIFFRACTION98.28
1.01-1.030.12133500.10746571X-RAY DIFFRACTION98.41
1.03-1.060.1293430.09826607X-RAY DIFFRACTION98.65
1.06-1.090.10383480.09046619X-RAY DIFFRACTION98.89
1.09-1.120.1223440.08676658X-RAY DIFFRACTION99.04
1.12-1.170.08613480.08236645X-RAY DIFFRACTION99.3
1.17-1.210.10443540.08456699X-RAY DIFFRACTION99.46
1.21-1.270.10193500.09056668X-RAY DIFFRACTION99.57
1.27-1.330.12763470.09536676X-RAY DIFFRACTION99.7
1.33-1.420.10493520.09456722X-RAY DIFFRACTION99.86
1.42-1.530.11483510.09776682X-RAY DIFFRACTION99.97
1.53-1.680.12193550.09976723X-RAY DIFFRACTION99.97
1.68-1.920.11453550.1126660X-RAY DIFFRACTION100
1.92-2.420.14443460.11356702X-RAY DIFFRACTION100
2.42-17.970.15353550.12336716X-RAY DIFFRACTION99.9

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