[English] 日本語
Yorodumi
- PDB-6rd2: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-1]-TEDEL-NH2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rd2
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-1]-TEDEL-NH2
Components
  • Protein enabled homolog
  • THR-GLU-ASP-GLU-NLW
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 / GABA-ergic synapse / filopodium ...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 / GABA-ergic synapse / filopodium / 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 / 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
Chem-K1N / NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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. / 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
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 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 / Derived calculations / Category: citation_author / database_2 / struct_conn
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI ..._citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jan 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
B: Protein enabled homolog
A: Protein enabled homolog
C: THR-GLU-ASP-GLU-NLW
D: THR-GLU-ASP-GLU-NLW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,71819
Polymers26,4664
Non-polymers2,25315
Water3,729207
1
B: Protein enabled homolog
C: THR-GLU-ASP-GLU-NLW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,37510
Polymers13,2332
Non-polymers1,1428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein enabled homolog
D: THR-GLU-ASP-GLU-NLW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3439
Polymers13,2332
Non-polymers1,1107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.390, 44.000, 34.830
Angle α, β, γ (deg.)90.00, 102.17, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules BACD

#1: Protein Protein enabled homolog


Mass: 12628.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: R84A is 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 THR-GLU-ASP-GLU-NLW


Mass: 604.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 222 molecules

#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K1N / (3~{S},7~{R},10~{R},13~{S})-4-[(3~{S},6~{R},8~{a}~{S})-1'-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8~{a}-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid


Mass: 678.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H40ClN5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.41M ammonium sulfate, 1000mM ammonium nitrate / Temp details: incubator

-
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 6M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1→42.106 Å / Num. obs: 118323 / % possible obs: 99.9 % / Redundancy: 14.6 % / CC1/2: 0.998 / Rrim(I) all: 0.239 / Net I/σ(I): 5.26
Reflection shellResolution: 1→1.06 Å / Redundancy: 13.1 % / Num. unique obs: 18886 / CC1/2: 0.144 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ND0

5nd0


Resolution: 1→42.106 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.51
RfactorNum. reflection% reflectionSelection details
Rfree0.224 5812 5 %random
Rwork0.1977 ---
obs0.199 116220 98.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1→42.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 152 207 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162154
X-RAY DIFFRACTIONf_angle_d1.582935
X-RAY DIFFRACTIONf_dihedral_angle_d11.9311730
X-RAY DIFFRACTIONf_chiral_restr0.111304
X-RAY DIFFRACTIONf_plane_restr0.011397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9999-1.01130.60481280.56282390X-RAY DIFFRACTION65
1.0113-1.02320.57261830.53833456X-RAY DIFFRACTION91
1.0232-1.03570.60181730.52523300X-RAY DIFFRACTION90
1.0357-1.04880.5191960.52923722X-RAY DIFFRACTION99
1.0488-1.06260.53811970.51743742X-RAY DIFFRACTION100
1.0626-1.07710.52851960.51573726X-RAY DIFFRACTION100
1.0771-1.09250.45041970.46243737X-RAY DIFFRACTION100
1.0925-1.10880.42881960.39393717X-RAY DIFFRACTION100
1.1088-1.12620.38551980.36663759X-RAY DIFFRACTION100
1.1262-1.14460.36221950.34263709X-RAY DIFFRACTION100
1.1446-1.16440.36511980.32553753X-RAY DIFFRACTION100
1.1644-1.18550.30551950.30793716X-RAY DIFFRACTION100
1.1855-1.20830.33841950.28563717X-RAY DIFFRACTION100
1.2083-1.2330.32041970.2753738X-RAY DIFFRACTION100
1.233-1.25980.34441970.26583745X-RAY DIFFRACTION100
1.2598-1.28910.28731980.24113758X-RAY DIFFRACTION100
1.2891-1.32140.27811950.22333693X-RAY DIFFRACTION100
1.3214-1.35710.25141970.20813764X-RAY DIFFRACTION100
1.3571-1.3970.2571970.1983757X-RAY DIFFRACTION100
1.397-1.44210.2331970.18863732X-RAY DIFFRACTION100
1.4421-1.49370.24661970.1773741X-RAY DIFFRACTION100
1.4937-1.55350.22871970.1623771X-RAY DIFFRACTION100
1.5535-1.62420.19521970.15463736X-RAY DIFFRACTION100
1.6242-1.70980.18231980.15373757X-RAY DIFFRACTION100
1.7098-1.8170.1951980.15873765X-RAY DIFFRACTION100
1.817-1.95720.20931980.16373759X-RAY DIFFRACTION100
1.9572-2.15420.15761990.15363796X-RAY DIFFRACTION100
2.1542-2.46590.19371980.16763765X-RAY DIFFRACTION100
2.4659-3.10660.19952010.17423816X-RAY DIFFRACTION100
3.1066-42.14290.18692040.17963871X-RAY DIFFRACTION100

+
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