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- PDB-1xo5: Crystal structure of CIB1, an EF-hand, integrin and kinase-bindin... -

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Basic information

Entry
Database: PDB / ID: 1xo5
TitleCrystal structure of CIB1, an EF-hand, integrin and kinase-binding protein
ComponentsCalcium and integrin-binding protein 1
Keywordscalcium-binding protein / Calcium and Integrin binding / EF-hand / Kinase Interacting Protein / calmyrin
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 / positive regulation of catalytic activity / protein serine/threonine kinase inhibitor activity / positive regulation of cell adhesion mediated by integrin ...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 / positive regulation of catalytic activity / protein serine/threonine kinase inhibitor activity / positive regulation of cell adhesion mediated by integrin / platelet formation / positive regulation of cell-matrix adhesion / positive regulation of cell migration involved in sprouting angiogenesis / regulation of cell division / spermatid development / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein targeting to membrane / negative regulation of megakaryocyte differentiation / positive regulation of substrate adhesion-dependent cell spreading / cytoplasmic microtubule organization / protein-membrane adaptor activity / 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 / positive regulation of protein serine/threonine kinase activity / sarcolemma / 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 / positive regulation of cell growth / perikaryon / angiogenesis / vesicle / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / cell adhesion / positive regulation of cell migration / neuron projection / positive regulation of protein phosphorylation / apical plasma membrane / negative regulation of cell population proliferation / axon / cell division / neuronal cell body / centrosome / calcium ion binding / DNA damage response / positive regulation of cell population proliferation / negative regulation of apoptotic process / 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 ...: / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsGentry, H.R. / Singer, A.U. / Betts, L. / Yang, C. / Ferrara, J.D. / Parise, L.V. / Sondek, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural and Biochemical Characterization of CIB1 Delineates a New Family of EF-hand-containing Proteins
Authors: Gentry, H.R. / Singer, A.U. / Betts, L. / Yang, C. / Ferrara, J.D. / Sondek, J. / Parise, L.V.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
B: Calcium and integrin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,28210
Polymers41,9612
Non-polymers3218
Water7,152397
1
A: Calcium and integrin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1415
Polymers20,9801
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium and integrin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1415
Polymers20,9801
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.663, 51.009, 77.214
Angle α, β, γ (deg.)90.00, 103.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calcium and integrin-binding protein 1 / Calmyrin / DNA-PKcs interacting protein / Kinase interacting protein / KIP / CIB / SNK interacting ...Calmyrin / DNA-PKcs interacting protein / Kinase interacting protein / KIP / CIB / SNK interacting protein 2-28 / SIP2-28 / CIB1


Mass: 20980.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIB1, PRKDCIP, KIP, CIB / Plasmid: pProEX HTc (Invitrogen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99828
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20 mM Bis-Tris-propane (BTP), 300 mM calcium acetate, 18% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→40 Å / Num. obs: 29442 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.058 / Net I/σ(I): 32
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 2370 / Rsym value: 0.023 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→40.32 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.236 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25672 1430 5.1 %RANDOM
Rwork0.21209 ---
all0.21437 ---
obs0.214 26651 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.01 Å2
2--0.03 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.99→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 8 397 3186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222829
X-RAY DIFFRACTIONr_bond_other_d0.0010.022572
X-RAY DIFFRACTIONr_angle_refined_deg1.051.9763821
X-RAY DIFFRACTIONr_angle_other_deg0.78535989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2565340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12424.286147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46815509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4271523
X-RAY DIFFRACTIONr_chiral_restr0.060.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
X-RAY DIFFRACTIONr_nbd_refined0.2190.2869
X-RAY DIFFRACTIONr_nbd_other0.1750.22912
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21442
X-RAY DIFFRACTIONr_nbtor_other0.0820.21638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.2329
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1210.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.246
X-RAY DIFFRACTIONr_mcbond_it0.5121.51771
X-RAY DIFFRACTIONr_mcbond_other0.1041.5682
X-RAY DIFFRACTIONr_mcangle_it0.87522804
X-RAY DIFFRACTIONr_scbond_it1.27431145
X-RAY DIFFRACTIONr_scangle_it1.9744.51017
LS refinement shellResolution: 1.99→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 70 -
Rwork0.244 1534 -
obs-1400 74.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2474-1.64550.41921.40580.11770.5388-0.1481-0.2244-0.07030.16760.169-0.26240.03030.1183-0.0209-0.2296-0.0031-0.0075-0.2162-0.0259-0.132818.96290.02173.4921
21.0409-0.9776-1.79042.0312.95666.0907-0.0177-0.5650.00580.68750.1898-0.0273-0.0430.0844-0.17210.24260.06740.03630.0870.0057-0.1401-0.435932.462531.521
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 1914 - 183
2X-RAY DIFFRACTION1AC11
3X-RAY DIFFRACTION1AG51
4X-RAY DIFFRACTION1AE31
5X-RAY DIFFRACTION1AI71
6X-RAY DIFFRACTION2BB12 - 1914 - 183
7X-RAY DIFFRACTION2BD21
8X-RAY DIFFRACTION2BH61
9X-RAY DIFFRACTION2BF41
10X-RAY DIFFRACTION2BJ81

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