[English] 日本語
Yorodumi
- PDB-2kbt: Attachment of an NMR-invisible solubility enhancement tag (INSET)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kbt
TitleAttachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method
ComponentsProto-oncogene vav,Immunoglobulin G-binding protein G
KeywordsSIGNALING PROTEIN / sortase / protein ligation / GB1 / intein / INSET / solubility enhancement
Function / homology
Function and homology information


Azathioprine ADME / CD28 dependent Vav1 pathway / RAC2 GTPase cycle / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle ...Azathioprine ADME / CD28 dependent Vav1 pathway / RAC2 GTPase cycle / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle / RHOG GTPase cycle / VEGFR2 mediated vascular permeability / FCERI mediated Ca+2 mobilization / phosphorylation-dependent protein binding / G alpha (12/13) signalling events / PIP3 activates AKT signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / Regulation of actin dynamics for phagocytic cup formation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / IgG binding / regulation of cell size / positive regulation of natural killer cell mediated cytotoxicity / T cell differentiation / positive regulation of cell adhesion / phagocytosis / reactive oxygen species metabolic process / phosphotyrosine residue binding / T cell activation / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / integrin-mediated signaling pathway / cell-cell junction / cell migration / intracellular signal transduction / immune response / G protein-coupled receptor signaling pathway / extracellular region / metal ion binding / cytosol / cytoplasm
Similarity search - Function
VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / IgG-binding B ...VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / Calponin homology domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / YSIRK Gram-positive signal peptide / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / Proto-oncogene vav
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptococcus sp. 'group G' (bacteria)
MethodSOLUTION NMR / simulated annealing, distance geometry
Model detailslowest energy, model 1
AuthorsKumeta, H. / Kobashigawa, Y. / Ogura, K. / Inagaki, F.
CitationJournal: J.Biomol.Nmr / Year: 2009
Title: Attachment of an NMR-invisible solubility enhancement tag using a sortase-mediated protein ligation method
Authors: Kobashigawa, Y. / Kumeta, H. / Ogura, K. / Inagaki, F.
History
DepositionDec 7, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Apr 10, 2024Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proto-oncogene vav,Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)15,9741
Polymers15,9741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Antibody Proto-oncogene vav,Immunoglobulin G-binding protein G / p95vav / IgG-binding protein G


Mass: 15974.466 Da / Num. of mol.: 1
Fragment: SH3 2 domain of Proto-oncogene vav,UNP residues 228-282 of Immunoglobulin G-binding protein G
Source method: isolated from a genetically manipulated source
Details: A solubility-enhancement tag (SET) GB1, domain of immunoglobulin G-binding protein G (invisible GB1 tag), is non-labeled and attached to the C-terminal of 13C/15N-labeled Vav SH3 domain with protein ligation
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Streptococcus sp. 'group G' (bacteria)
Gene: Vav1, Vav, spg / Production host: Escherichia coli (E. coli) / References: UniProt: P27870, UniProt: P06654

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CO)CA
1513D HNCA
1613D HN(CA)HA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D (H)CCH-TOCSY
11012D 1H-13C HSQC (Arom)
11112D (Hb)Cb(CgCd)Hd
11212D (Hb)Cb(CgCdCe)He
11313D (H)CCH-TOCSY (Arom)
11413D 1H-15N NOESY
11513D 1H-13C NOESY
11613D 1H-13C NOESY (Arom)

-
Sample preparation

DetailsContents: 20 mM MES-1, 2 mM DTT-2, 150 mM NaCl-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMMES-11
2 mMDTT-21
150 mMNaCl-31
Sample conditionsIonic strength: 150 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY8001
Varian UnityVarianUNITY6002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
RNMRTK3Alan Stern, Jeff Hochprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddardrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

+
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