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- PDB-2lm5: Solution structure of Ca2+-CIB1 in complex with the cytoplasmic d... -

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Basic information

Entry
Database: PDB / ID: 2lm5
TitleSolution structure of Ca2+-CIB1 in complex with the cytoplasmic domain of the integrin aIIb subunit
ComponentsCalcium and integrin-binding protein 1
KeywordsMETAL BINDING PROTEIN
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 / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of microtubule depolymerization / 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 / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of microtubule depolymerization / 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 / protein serine/threonine kinase inhibitor activity / spermatid development / positive regulation of protein targeting to membrane / 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 / positive regulation of NF-kappaB transcription factor activity / cellular response to nerve growth factor stimulus / sarcolemma / cellular response to growth factor stimulus / small GTPase binding / 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 / negative regulation of cell population proliferation / axon / 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
Model detailslowest energy, model 2
AuthorsHuang, H. / Vogel, H.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Structural basis for the activation of platelet integrin alphaIIb-beta3 by calcium- and integrin-binding protein 1.
Authors: Huang, H. / Vogel, H.J.
History
DepositionNov 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 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 / 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_database_status.status_code_nmr_data / _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_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
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 RDC 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99828
#2: Chemical ChemComp-CA / CALCIUM ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D HNCO
1313D HCACO
1413D HN(COCA)CB
1553D HNCO type RDC
1652D 1H-15N HSQC IPAP
1723D (H)CCH-TOCSY
1832D 1H-13C HSQC
1963D HNCO type RDC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-2H], I/L/V methyl [1H,13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O100% D2O
30.5 mM [U-10% 13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O100% D2O
40.5 mM [U-2H], I/L/V methyl [1H,13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O100% D2O
50.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 14 mg/mL pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
60.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 5 % C12E5/glycerol (0.96/1), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCIB1-1[U-13C; U-15N; U-2H]1
5 mMDTT-2[U-2H]1
2 mMCALCIUM ION-31
100 mMsodium chloride-41
50 mMHEPES-51
0.6 mMaIIb peptide-61
0.5 mMCIB1-7[U-13C; U-2H], I/L/V methyl [1H,13C]2
5 mMDTT-8[U-2H]2
2 mMCALCIUM ION-92
100 mMsodium chloride-102
50 mMHEPES-112
0.6 mMaIIb peptide-122
0.5 mMCIB1-13[U-10% 13C]3
5 mMDTT-14[U-2H]3
2 mMCALCIUM ION-153
100 mMsodium chloride-163
50 mMHEPES-173
0.6 mMaIIb peptide-183
0.5 mMCIB1-19[U-2H], I/L/V methyl [1H,13C]4
5 mMDTT-20[U-2H]4
2 mMCALCIUM ION-214
100 mMsodium chloride-224
50 mMHEPES-234
0.6 mMaIIb peptide-244
0.5 mMCIB1-25[U-13C; U-15N; U-2H]5
5 mMDTT-26[U-2H]5
2 mMCALCIUM ION-275
100 mMsodium chloride-285
50 mMHEPES-295
0.6 mMaIIb peptide-305
14 mg/mLpf1 phage-315
0.5 mMCIB1-32[U-13C; U-15N; U-2H]6
5 mMDTT-33[U-2H]6
2 mMCALCIUM ION-346
100 mMsodium chloride-356
50 mMHEPES-366
0.6 mMaIIb peptide-376
5 %C12E5/glycerol (0.96/1)-386
Sample conditionsIonic strength: 0.2 / pH: 7.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: two steps: 1st step, 200K->20K; 2nd step, 20K->2K. For the 1st step, use ca2+-CIB1 (PDB: 2L4H) as a template and for the 2nd step, use the lowest-energy str. from step1 as the template
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest RDC energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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