[English] 日本語
Yorodumi
- PDB-2l81: Solution NMR Structure of the serine-rich domain of hEF1 (Enhance... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l81
TitleSolution NMR Structure of the serine-rich domain of hEF1 (Enhancer of filamentation 1) from Homo sapiens, Northeast Structural Genomics Consortium Target HR5554A
ComponentsEnhancer of filamentation 1
KeywordsCELL ADHESION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


positive regulation of lymphocyte chemotaxis / positive regulation of immunological synapse formation / lymphocyte migration into lymphoid organs / cilium disassembly / positive regulation of osteoclast differentiation / positive regulation of protein localization / actin filament bundle assembly / immunological synapse / positive regulation of protein tyrosine kinase activity / positive regulation of dendritic spine maintenance ...positive regulation of lymphocyte chemotaxis / positive regulation of immunological synapse formation / lymphocyte migration into lymphoid organs / cilium disassembly / positive regulation of osteoclast differentiation / positive regulation of protein localization / actin filament bundle assembly / immunological synapse / positive regulation of protein tyrosine kinase activity / positive regulation of dendritic spine maintenance / positive regulation of substrate adhesion-dependent cell spreading / cytoskeleton organization / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of cell migration / protein tyrosine kinase binding / ciliary basal body / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / mitotic spindle / spindle pole / spindle / cell migration / lamellipodium / cell cortex / basolateral plasma membrane / learning or memory / cell adhesion / positive regulation of cell migration / cell cycle / cell division / focal adhesion / Golgi apparatus / signal transduction / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine-rich domain / Enhancer of filamentation 1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / Variant SH3 domain / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Serine-rich domain / Enhancer of filamentation 1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / Variant SH3 domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Enhancer of filamentation 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Xiao, R. / Huang, Y.J. / Patel, D. / Ciccosanti, C.T. / Acton, T.B. / Tong, S. / Everett, J.T. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR5554A
Authors: Liu, G. / Xiao, R. / Huang, Y.J. / Patel, D. / Ciccosanti, C. / Tong, S. / Acton, T.B. / Everett, J.T. / Montelione, G.T.
History
DepositionDec 31, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enhancer of filamentation 1


Theoretical massNumber of molelcules
Total (without water)20,2381
Polymers20,2381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Enhancer of filamentation 1 / hEF1 / CRK-associated substrate-related protein / CAS-L / CasL / Cas scaffolding protein family ...hEF1 / CRK-associated substrate-related protein / CAS-L / CasL / Cas scaffolding protein family member 2 / Neural precursor cell expressed developmentally down-regulated protein 9 / NEDD-9 / Renal carcinoma antigen NY-REN-12 / p105 / Enhancer of filamentation 1 p55


Mass: 20238.178 Da / Num. of mol.: 1 / Fragment: sequence database residues 399-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD9, CASL, CASS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14511

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: hEF1, also named CRK-associated substrate-related protein CAS-L CasL Cas scaffolding protein family member 2 Neural precursor cell expressed developmentally down-regulated protein 9 NEDD-9 ...Details: hEF1, also named CRK-associated substrate-related protein CAS-L CasL Cas scaffolding protein family member 2 Neural precursor cell expressed developmentally down-regulated protein 9 NEDD-9 Renal carcinoma antigen NY-REN-12 p105Contains Enhancer of filamentation 1)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.56 mM [U-100% 13C; U-100% 15N] HR5554A, 95% H2O/5% D2O95% H2O/5% D2O
20.56 mM [U-5% 13C; U-100% 15N] HR5554A, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.56 mMHR5554A-1[U-100% 13C; U-100% 15N]1
0.56 mMHR5554A-2[U-5% 13C; U-100% 15N]2
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
CYANArefinement
CNSrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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