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- PDB-4lzx: Complex of IQCG and Ca2+-free CaM -

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Basic information

Entry
Database: PDB / ID: 4lzx
TitleComplex of IQCG and Ca2+-free CaM
Components
  • Calmodulin
  • IQ domain-containing protein G
KeywordsMETAL BINDING PROTEIN / Protein complex / IQ domain / EF hand domains / Calcium signalling
Function / homology
Function and homology information


sperm axoneme assembly / cilium organization / : / manchette / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / motile cilium / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...sperm axoneme assembly / cilium organization / : / manchette / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / motile cilium / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / spermatid development / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / sperm flagellum / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / Hsp70 protein binding / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT
Similarity search - Function
Dynein regulatory complex protein 9 / IQ calmodulin-binding motif / IQ motif profile. / IQ motif, EF-hand binding site / 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
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Dynein regulatory complex protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLiang, W.X. / Chen, L.T. / Chen, Z. / Chen, S.J. / Chen, S.
CitationJournal: Nat Commun / Year: 2014
Title: Functional and molecular features of the calmodulin-interacting protein IQCG required for haematopoiesis in zebrafish
Authors: Chen, L.T. / Liang, W.X. / Chen, S. / Li, R.K. / Tan, J.L. / Xu, P.F. / Luo, L.F. / Wang, L. / Yu, S.H. / Meng, G. / Li, K.K. / Liu, T.X. / Chen, Z. / Chen, S.J.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Calmodulin
B: IQ domain-containing protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4093
Polymers21,3132
Non-polymers961
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-34 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.577, 60.922, 64.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calmodulin / / CaM


Mass: 16721.350 Da / Num. of mol.: 1 / Fragment: UNP residues 2-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide IQ domain-containing protein G


Mass: 4591.490 Da / Num. of mol.: 1 / Fragment: UNP residues 389-423, IQ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQCG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H095
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M ammonium sulfate, 1M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2012
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 28793 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 14.97 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 29.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.514 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.27 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 1456 5.07 %Random
Rwork0.1527 ---
obs0.1545 28738 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 5 333 1779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081572
X-RAY DIFFRACTIONf_angle_d1.1972119
X-RAY DIFFRACTIONf_dihedral_angle_d13.691623
X-RAY DIFFRACTIONf_chiral_restr0.069224
X-RAY DIFFRACTIONf_plane_restr0.005286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.55390.22741420.1526265899
1.5539-1.61610.2171440.13732681100
1.6161-1.68970.20821560.13392674100
1.6897-1.77870.21171480.14122706100
1.7787-1.89020.18221450.13692694100
1.8902-2.03610.18881300.14142736100
2.0361-2.2410.16561310.13682736100
2.241-2.56530.18711450.14422735100
2.5653-3.23180.19621680.16672757100
3.2318-44.28910.17311470.16652905100

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