[English] 日本語
Yorodumi
- PDB-2kr9: Kalirin DH1 NMR structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kr9
TitleKalirin DH1 NMR structure
ComponentsKalirin
KeywordsTRANSFERASE / Dbl-family GEF / Rho GTPase GEF / Cytoskeleton / Disulfide bond / Guanine-nucleotide releasing factor / Immunoglobulin domain / Kinase
Function / homology
Function and homology information


RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / MAPK6/MAPK4 signaling / RAC1 GTPase cycle / maternal process involved in parturition / RHOA GTPase cycle / modification of postsynaptic actin cytoskeleton / regulation of dendrite development / NMDA selective glutamate receptor signaling pathway ...RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / MAPK6/MAPK4 signaling / RAC1 GTPase cycle / maternal process involved in parturition / RHOA GTPase cycle / modification of postsynaptic actin cytoskeleton / regulation of dendrite development / NMDA selective glutamate receptor signaling pathway / negative regulation of growth hormone secretion / positive regulation of dendritic spine morphogenesis / EPHB-mediated forward signaling / regulation of modification of postsynaptic actin cytoskeleton / habituation / maternal behavior / G alpha (q) signalling events / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / extrinsic component of membrane / neuromuscular junction development / social behavior / lactation / axonogenesis / adult locomotory behavior / guanyl-nucleotide exchange factor activity / axon guidance / memory / presynapse / nervous system development / postsynaptic density / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain ...Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / 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. / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Fibronectin type III domain / SH3 domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, matrix relaxation
Model detailsLowest total energy, model 121
AuthorsGorbatyuk, V.Y. / Schiller, M.R. / Hoch, J.C.
CitationJournal: To be Published
Title: The solution NMR structure of the first Dbl domain of RhoGEF Kalirin.
Authors: Gorbatyuk, V.Y. / Schiller, M.R. / Hoch, J.C.
History
DepositionDec 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kalirin


Theoretical massNumber of molelcules
Total (without water)21,9951
Polymers21,9951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100Total energy
RepresentativeModel #1lowest total energy

-
Components

#1: Protein Kalirin / / Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine kinase with Dbl- ...Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine kinase with Dbl- and pleckstrin homology domain / PAM COOH-terminal interactor protein 10 / P-CIP10


Mass: 21995.221 Da / Num. of mol.: 1 / Fragment: DH 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kalrn, Duo, Hapip / Organ: brain / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P97924, non-specific serine/threonine protein kinase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: N-terminal Kalirin DBL-homology domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1223D 1H-15N NOESY
131aroChsqc (H[C[caro]])
1422D 1H-15N HSQC/HMQC
1513D 1H-13C NOESY
1612D 1H-13C HSQC/HMQC
1714dCNnoesy (H[C] H[N].NOESY)
1812D 1H-15N HSQC/HMQC
1913D CBCA(CO)NH
11013D HN(CA)CB
11113D HNCO
11213D HN(CA)CO
11313D HNCA
11413D C(CO)NH
11513D (H)CCH-COSY
11613D (H)CCH-TOCSY
11713D HBHA(CO)NH
11823D HNHA
11923D NhsqcnoesyNhsqc

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] KalDH1, 50.0 mM Hepes, 90% H2O/10% D2O90% H2O/10% D2O
20.56 mM [U-100% 15N] KalDH1, 50.00 mM Hepes, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMKalDH1-1[U-100% 13C; U-100% 15N]1
50.0 mMHepes-21
0.56 mMKalDH1-3[U-100% 15N]2
50.00 mMHepes-42
Sample conditionsIonic strength: 0.05 / pH: 6.80 / Pressure: 1.00 atm / Temperature: 298.15 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityInovaVarianUnityInova6001
Varian UnityInovaVarianUnityInova5002

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Nilges M., et alstructure solution
CcpNmr Analysis1CCPNdata analysis
CcpNmr Analysis2.1CCPNdata analysis
CYANA2.1P. Guntertgeometry optimization
DANGLE1.1CCPNprocessing
NMRDrawF. Delaglio, et aldata analysis
NMRDrawF. Delaglio, et alprocessing
NMRPipeF. Delaglio, et alprocessing
SparkyT. D. Goddard and D. G. Knellerchemical shift assignment
SparkyT. D. Goddard and D. G. Knellerdata analysis
ARIA2.2Nilges M., et alrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, matrix relaxation
Software ordinal: 1
NMR representativeSelection criteria: lowest total energy
NMR ensembleConformer selection criteria: Total energy / Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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