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- PDB-6od0: Structure of human CIB1 in complex with peptide inhibitor UNC10245092 -

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Basic information

Entry
Database: PDB / ID: 6od0
TitleStructure of human CIB1 in complex with peptide inhibitor UNC10245092
Components
  • Calcium and integrin-binding protein 1
  • Peptide inhibitor UNC10245092
KeywordsMETAL BINDING PROTEIN / CIB1 / cancer
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 megakaryocyte differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of substrate adhesion-dependent cell spreading / cytoplasmic microtubule organization / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / 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 / small GTPase binding / ruffle membrane / double-strand break repair / lamellipodium / negative regulation of neuron projection development / 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 / apical plasma membrane / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / axon / cell division / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPuhl, A.C. / Godoy, A.S. / Pearce, K.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Discovery and Characterization of Peptide Inhibitors for Calcium and Integrin Binding Protein 1.
Authors: Puhl, A.C. / Bogart, J.W. / Haberman, V.A. / Larson, J.E. / Godoy, A.S. / Norris-Drouin, J.L. / Cholensky, S.H. / Leisner, T.M. / Frye, S.V. / Parise, L.V. / Bowers, A.A. / Pearce, K.H.
History
DepositionMar 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_symmetry
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: Peptide inhibitor UNC10245092
E: Peptide inhibitor UNC10245092
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,48410
Polymers46,2444
Non-polymers2406
Water3,459192
1
A: Calcium and integrin-binding protein 1
D: Peptide inhibitor UNC10245092
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2425
Polymers23,1222
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-49 kcal/mol
Surface area9740 Å2
MethodPISA
2
B: Calcium and integrin-binding protein 1
E: Peptide inhibitor UNC10245092
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2425
Polymers23,1222
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-47 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.858, 85.966, 67.287
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number4
Space group name H-MP1211

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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: 21727.352 Da / Num. of mol.: 2
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: Protein/peptide Peptide inhibitor UNC10245092


Mass: 1394.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.8
Details: 137.5 mM calcium acetate, 16 % PEG 3350, 20 mM Bis-Tris propane (pH 6.8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→34.83 Å / Num. obs: 20253 / % possible obs: 94.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.74 Å2 / Net I/σ(I): 8.3
Reflection shellResolution: 2.15→2.25 Å / Num. unique obs: 1580

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xo5

1xo5


Resolution: 2.15→21.81 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.239 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.189
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1062 5.24 %RANDOM
Rwork0.187 ---
obs0.189 20253 93.7 %-
Displacement parametersBiso mean: 43.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.6344 Å20 Å2-1.2043 Å2
2---0.8921 Å20 Å2
3---1.5264 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.15→21.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 6 192 2881
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092734HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.893702HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d928SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes403HARMONIC5
X-RAY DIFFRACTIONt_it2734HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion16.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion370SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3228SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.241 148 6.03 %
Rwork0.215 2308 -
all0.216 2456 -
obs--78.37 %
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)
11.78180.35711.59170.4324-0.05282.4408-0.08510.0828-0.0858-0.05780.0639-0.0163-0.10080.09280.0211-0.0666-0.0070.0054-0.05860.0196-0.061413.69894.184271.8013
21.805-1.62750.37252.1896-0.40610.6154-0.0434-0.0618-0.08070.09980.04270.1268-0.05980.07010.0007-0.0364-0.02390.0029-0.0940.0011-0.030319.300821.659938.6192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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