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- PDB-6ocx: Structure of human CIB1 in complex with peptide inhibitor UNC10245109 -

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Basic information

Entry
Database: PDB / ID: 6ocx
TitleStructure of human CIB1 in complex with peptide inhibitor UNC10245109
Components
  • Calcium and integrin-binding protein 1
  • Peptide inhibitor UNC10245109
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 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
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

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Assembly

Deposited unit
A: Calcium and integrin-binding protein 1
B: Calcium and integrin-binding protein 1
C: Calcium and integrin-binding protein 1
D: Calcium and integrin-binding protein 1
F: Peptide inhibitor UNC10245109
H: Peptide inhibitor UNC10245109
J: Peptide inhibitor UNC10245109
L: Peptide inhibitor UNC10245109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,12616
Polymers93,8058
Non-polymers3218
Water6,792377
1
A: Calcium and integrin-binding protein 1
J: Peptide inhibitor UNC10245109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5314
Polymers23,4512
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-42 kcal/mol
Surface area9490 Å2
MethodPISA
2
B: Calcium and integrin-binding protein 1
L: Peptide inhibitor UNC10245109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5314
Polymers23,4512
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-42 kcal/mol
Surface area9670 Å2
MethodPISA
3
C: Calcium and integrin-binding protein 1
H: Peptide inhibitor UNC10245109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5314
Polymers23,4512
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-42 kcal/mol
Surface area9600 Å2
MethodPISA
4
D: Calcium and integrin-binding protein 1
F: Peptide inhibitor UNC10245109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5314
Polymers23,4512
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-43 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.866, 33.035, 162.402
Angle α, β, γ (deg.)90.00, 99.85, 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.: 4
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 UNC10245109


Mass: 1723.950 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000

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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: 1.9→27.64 Å / Num. obs: 63567 / % possible obs: 99.49 % / Redundancy: 6.1 % / Biso Wilson estimate: 30.73 Å2 / Rsym value: 0.066 / Net I/σ(I): 5.57
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 6305 / Rsym value: 0.637

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XO5

1xo5


Resolution: 1.9→27.64 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.141
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2989 4.7 %RANDOM
Rwork0.212 ---
obs0.214 63567 99.5 %-
Displacement parametersBiso mean: 37.78 Å2
Baniso -1Baniso -2Baniso -3
1-4.9246 Å20 Å2-0.0615 Å2
2---0.1891 Å20 Å2
3----4.7354 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 1.9→27.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 8 385 5747
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095517HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.927474HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1902SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes829HARMONIC5
X-RAY DIFFRACTIONt_it5517HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion15.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion749SEMIHARMONIC5
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_contact6405SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 266 5.64 %
Rwork0.225 4448 -
all0.226 4714 -
obs--99.66 %
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)
12.71081.4432-0.64211.3822-0.59760.96080.0504-0.0558-0.0494-0.0179-0.043-0.03-0.01180.0594-0.0074-0.0587-0.0050.0008-0.1049-0.0127-0.0081-12.2546-1.1456-60.3812
21.9485-0.95610.66181.359-0.73791.12540.03750.08230.01390.0021-0.03830.04580.04690.03130.0008-0.0619-0.0069-0.0374-0.003-0.0061-0.087825.5683-11.2684-19.8424
32.2141-1.0361-0.3521.32190.7671.422-0.012-0.0502-0.01420.0810.03430.012-0.01-0.029-0.0223-0.1006-0.012-0.0255-0.02510.046-0.0513-11.58392.0192-19.5475
41.79440.92130.44841.13060.75951.01690.0673-0.09690.02840.0177-0.0436-0.05680.0203-0.037-0.0237-0.01830.0014-0.0296-0.10070.0287-0.004526.3325-14.4804-60.251
50.7143-2.0847-2.13155.924-3.07633.3690.0394-0.040.34110.0401-0.00940.1585-0.11540.0401-0.030.0007-0.0095-0.0684-0.09480.01180.053826.8844-1.2398-56.5201
60.6362-0.82262.91453.7414-2.47391.4859-0.0361-0.0093-0.1354-0.09050.05620.11640.1422-0.024-0.0201-0.0473-0.0020.0044-0.02360.02340.0379-10.975-11.2408-23.2145
7-0.0220.28641.19323.77191.36953.03950.0095-0.1353-0.22110.0242-0.0244-0.04880.192-0.00180.01490.0012-0.01960.0145-0.10450.00360.0892-12.9379-14.3886-56.6727
80.5996-0.6403-1.75213.37082.37442.99240.02250.07310.2175-0.0334-0.0484-0.0358-0.1546-0.08990.0259-0.0314-0.0075-0.06790.01560.0012-0.014925.01331.9811-23.5068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ F|* }
6X-RAY DIFFRACTION6{ H|* }
7X-RAY DIFFRACTION7{ J|* }
8X-RAY DIFFRACTION8{ L|* }

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