[English] 日本語
Yorodumi
- PDB-2lnw: Identification and structural basis for a novel interaction betwe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lnw
TitleIdentification and structural basis for a novel interaction between Vav2 and Arap3
Components
  • Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
  • Guanine nucleotide exchange factor VAV2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


phosphatidylinositol-3,4-bisphosphate binding / Azathioprine ADME / regulation of small GTPase mediated signal transduction / lamellipodium assembly / Fc-gamma receptor signaling pathway involved in phagocytosis / epidermal growth factor receptor binding / NRAGE signals death through JNK / small GTPase-mediated signal transduction / regulation of cell size / regulation of GTPase activity ...phosphatidylinositol-3,4-bisphosphate binding / Azathioprine ADME / regulation of small GTPase mediated signal transduction / lamellipodium assembly / Fc-gamma receptor signaling pathway involved in phagocytosis / epidermal growth factor receptor binding / NRAGE signals death through JNK / small GTPase-mediated signal transduction / regulation of cell size / regulation of GTPase activity / RHOB GTPase cycle / RHOC GTPase cycle / Fc-epsilon receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / vesicle-mediated transport / GPVI-mediated activation cascade / cytoskeleton organization / ruffle / phosphotyrosine residue binding / RAC1 GTPase cycle / FCERI mediated Ca+2 mobilization / VEGFR2 mediated vascular permeability / guanyl-nucleotide exchange factor activity / Signal transduction by L1 / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / platelet activation / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / G alpha (12/13) signalling events / cell migration / cellular response to xenobiotic stimulus / DAP12 signaling / lamellipodium / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
VAV2 protein, second SH3 domain / VAV2 protein, first SH3 domain / VAV2, SH2 domain / ARAP, RhoGAP domain / : / Vav, PH domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Arf GTPase activating protein / ArfGAP domain superfamily ...VAV2 protein, second SH3 domain / VAV2 protein, first SH3 domain / VAV2, SH2 domain / ARAP, RhoGAP domain / : / Vav, PH domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Ras-associating (RA) domain / SOS1/NGEF-like PH domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Variant SH3 domain / Calponin homology domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Rho GTPase activation protein / 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. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / SH2 domain / SHC Adaptor Protein / 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 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Guanine nucleotide exchange factor VAV2 / Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Zhang, J. / Wu, J. / Shi, Y.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Identification and structural basis for a novel interaction between Vav2 and Arap3.
Authors: Wu, B. / Wang, F. / Zhang, J. / Zhang, Z. / Qin, L. / Peng, J. / Li, F. / Liu, J. / Lu, G. / Gong, Q. / Yao, X. / Wu, J. / Shi, Y.
History
DepositionJan 5, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine nucleotide exchange factor VAV2
B: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)15,7592
Polymers15,7592
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Guanine nucleotide exchange factor VAV2 / VAV-2


Mass: 14628.519 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 659-771
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52735
#2: Protein/peptide Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 / Centaurin-delta-3 / Cnt-d3


Mass: 1130.052 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1404-1412 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WWN8
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HCACO
1613D HBHA(CO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D H(CCO)NH
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11223D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] entity_1-1, 3 mM entity_2-2, 5 mM potassium phosphate-3, 20 mM sodium phosphate-4, 5 mM DTT-5, 2 mM EDTA-6, 75 mM sodium chloride-7, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] entity_1-8, 3 mM entity_2-9, 5 mM potassium phosphate-10, 75 mM sodium chloride-11, 5 mM DTT-12, 2 mM EDTA-13, 20 mM sodium phosphate-14, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 13C; U-100% 15N]1
3 mMentity_2-21
5 mMpotassium phosphate-31
20 mMsodium phosphate-41
5 mMDTT-51
2 mMEDTA-61
75 mMsodium chloride-71
1 mMentity_1-8[U-100% 13C; U-100% 15N]2
3 mMentity_2-92
5 mMpotassium phosphate-102
75 mMsodium chloride-112
5 mMDTT-122
2 mMEDTA-132
20 mMsodium phosphate-142
Sample conditionsIonic strength: 120 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readchemical shift calculation
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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