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- PDB-2l4i: The Solution Structure of Magnesium bound CIB1 -

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Basic information

Entry
Database: PDB / ID: 2l4i
TitleThe Solution Structure of Magnesium bound CIB1
ComponentsCalcium and integrin-binding protein 1
KeywordsMETAL BINDING PROTEIN / calcium and integrin binding protein 1 / magnesium / integrin
Function / homology
Function and homology information


positive regulation of male germ cell proliferation / calcium-dependent protein kinase inhibitor activity / endomitotic cell cycle / positive regulation of catalytic activity / filopodium tip / thrombopoietin-mediated signaling pathway / negative regulation of microtubule depolymerization / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of cell adhesion mediated by integrin / positive regulation of cell migration involved in sprouting angiogenesis ...positive regulation of male germ cell proliferation / calcium-dependent protein kinase inhibitor activity / endomitotic cell cycle / positive regulation of catalytic activity / filopodium tip / thrombopoietin-mediated signaling pathway / negative regulation of microtubule depolymerization / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of cell adhesion mediated by integrin / positive regulation of cell migration involved in sprouting angiogenesis / platelet formation / positive regulation of cell-matrix adhesion / negative regulation of protein phosphorylation / regulation of cell division / positive regulation of protein serine/threonine kinase activity / spermatid development / positive regulation of protein targeting to membrane / protein serine/threonine kinase inhibitor activity / negative regulation of megakaryocyte differentiation / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / cytoplasmic microtubule organization / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to ischemia / cell periphery / positive regulation of protein localization to plasma membrane / cellular response to nerve growth factor stimulus / : / sarcolemma / small GTPase binding / cellular response to growth factor stimulus / ruffle membrane / positive regulation of protein phosphorylation / cellular response to tumor necrosis factor / double-strand break repair / lamellipodium / regulation of cell population proliferation / negative regulation of neuron projection development / growth cone / positive regulation of cell growth / angiogenesis / perikaryon / vesicle / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / cell adhesion / neuron projection / nuclear body / positive regulation of cell migration / apical plasma membrane / axon / negative regulation of cell population proliferation / cell division / neuronal cell body / positive regulation of cell population proliferation / apoptotic process / calcium ion binding / DNA damage response / centrosome / negative regulation of apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / extracellular exosome / nucleoplasm / nucleus / membrane / 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 ...: / 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, torsion angle dynamics
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
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,5322
Polymers24,5071
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

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

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM MAGNESIUM ION, 100 mM potassium chloride, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM I/L/V methyl labeled [U, 2H] CIB1, 5 mM MAGNESIUM ION, 100 mM potassium 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
5 mMMAGNESIUM ION1
100 mMpotassium chloride1
10 mMDTT1
0.5 mMCIB1I/L/V methyl labeled [U, 2H]2
5 mMMAGNESIUM ION2
100 mMpotassium chloride2
10 mMDTT2
Sample conditionsIonic strength: 200 / pH: 7.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: Because the backbone resonances of residues 158-191 are largely missing, only residues 8-157 of Mg2+-CIB1 are presented in this entry. Simulated annealing was done in two steps, 1st step, ...Details: Because the backbone resonances of residues 158-191 are largely missing, only residues 8-157 of Mg2+-CIB1 are presented in this entry. Simulated annealing was done in two steps, 1st step, 200k-20k; 2nd step, 20K-2K, refer to J Biomol NMR. 2000 Nov;18(3):217-27. (Chou and Bax)
NMR constraintsNOE constraints total: 1007 / NOE intraresidue total count: 63 / NOE long range total count: 97 / NOE medium range total count: 109 / NOE sequential total count: 164 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 147 / Protein psi angle constraints total count: 146
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 1.6 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 1.8 Å / Maximum torsion angle constraint violation: 30 ° / Maximum upper distance constraint violation: 8 Å
NMR ensemble rmsDistance rms dev: 0.077 Å / Distance rms dev error: 0.005 Å

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