[English] 日本語
Yorodumi
- PDB-1xo5: Crystal structure of CIB1, an EF-hand, integrin and kinase-bindin... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / extrinsic apoptotic signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / protein-membrane adaptor activity / cytoplasmic microtubule organization / 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 / positive regulation of protein phosphorylation / apical plasma membrane / negative regulation of cell population proliferation / cell division / axon / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more