[English] 日本語
Yorodumi
- PDB-5nc7: ENAH EVH1 in complex with Ac-WPPPPTEDEL-NH2 -

+
Open data


ID or keywords:

Loading...

-
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


actin polymerization-dependent cell motility / profilin binding / WW domain 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 / profilin binding / WW domain 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more