[English] 日本語
Yorodumi
- PDB-2l4h: The Solution Structure of Calcium Bound CIB1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l4h
TitleThe Solution Structure of Calcium Bound CIB1
ComponentsCalcium and integrin-binding protein 1
KeywordsMETAL BINDING PROTEIN / Calcium and Integrin Binding protein 1
Function / homology
Function and homology information


calcium-dependent protein kinase inhibitor activity / thrombopoietin-mediated signaling pathway / endomitotic cell cycle / positive regulation of male germ cell proliferation / filopodium tip / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of microtubule depolymerization / protein serine/threonine kinase inhibitor activity / positive regulation of cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion ...calcium-dependent protein kinase inhibitor activity / thrombopoietin-mediated signaling pathway / endomitotic cell cycle / positive regulation of male germ cell proliferation / filopodium tip / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of microtubule depolymerization / protein serine/threonine kinase inhibitor activity / positive regulation of cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / platelet formation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of catalytic activity / regulation of cell division / spermatid development / positive regulation of protein targeting to membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of megakaryocyte differentiation / cytoplasmic microtubule organization / protein-membrane adaptor activity / positive regulation of substrate adhesion-dependent cell spreading / extrinsic apoptotic signaling pathway / cellular response to nerve growth factor stimulus / negative regulation of protein phosphorylation / cell periphery / response to ischemia / positive regulation of protein localization to plasma membrane / sarcolemma / positive regulation of protein serine/threonine kinase activity / cellular response to growth factor stimulus / ruffle membrane / small GTPase binding / double-strand break repair / negative regulation of neuron projection development / lamellipodium / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / growth cone / perikaryon / positive regulation of cell growth / angiogenesis / vesicle / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / cell adhesion / neuron projection / positive regulation of cell migration / positive regulation of protein phosphorylation / apical plasma membrane / cell division / axon / negative regulation of cell population proliferation / centrosome / neuronal cell body / apoptotic process / DNA damage response / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium and integrin-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHuang, H. / Vogel, H.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Solution Structures of Ca2+-CIB1 and Mg2+-CIB1 and Their Interactions with the Platelet Integrin {alpha}IIb Cytoplasmic Domain.
Authors: Huang, H. / Ishida, H. / Yamniuk, A.P. / Vogel, H.J.
History
DepositionOct 6, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calcium and integrin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5873
Polymers24,5071
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Calcium and integrin-binding protein 1 / CIB / Calcium- and integrin-binding protein / CIBP / Calmyrin / DNA-PKcs-interacting protein / ...CIB / Calcium- and integrin-binding protein / CIBP / Calmyrin / DNA-PKcs-interacting protein / Kinase-interacting protein / KIP / SNK-interacting protein 2-28 / SIP2-28


Mass: 24507.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIB1, CIB, KIP, PRKDCIP / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99828
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC IPAP
1213D HNCO type for CaCO and C'N RDC
1323D 1H-15N NOESY
1423D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N; U-2H] CIB1, 50 mM HEPES, 100 mM potassium chloride, 4 mM calcium cloride, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM I/L/V methyl 13C and 1H, [U,2H] CIB1, 50 mM HEPES, 100 mM potassium chloride, 4 mM calcium chloride, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCIB1[U-13C; U-15N; U-2H]1
50 mMHEPES1
100 mMpotassium chloride1
4 mMcalcium cloride1
10 mMDTT1
0.5 mMCIB1I/L/V methyl 13C and 1H, [U,2H]2
50 mMHEPES2
100 mMpotassium chloride2
4 mMcalcium chloride2
10 mMDTT2
Sample conditionsIonic strength: 200 / pH: 7.5 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 700 MHz

-
Processing

NMR softwareName: X-PLOR_NIH / Version: 2.18 / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: two steps: 1st step, 200K-20K; 2nd step, 20K-2K
NMR constraintsNOE constraints total: 1069 / NOE intraresidue total count: 80 / NOE long range total count: 118 / NOE medium range total count: 71 / NOE sequential total count: 167 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 174 / Protein psi angle constraints total count: 174
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 2.38 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11 / Maximum lower distance constraint violation: 1.8 Å / Maximum torsion angle constraint violation: 30 ° / Maximum upper distance constraint violation: 8 Å / Torsion angle constraint violation method: TALOS
NMR ensemble rmsDistance rms dev: 0.086 Å / Distance rms dev error: 0.005 Å

+
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