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- PDB-4m1l: Complex of IQCG and Ca2+-bound CaM -

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Basic information

Entry
Database: PDB / ID: 4m1l
TitleComplex of IQCG and Ca2+-bound CaM
Components
  • Calmodulin
  • IQ domain-containing protein G
KeywordsMETAL BINDING PROTEIN / 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: 2.1 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 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_seq_id / _struct_conn.ptnr2_label_asym_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: Calmodulin
B: IQ domain-containing protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,80811
Polymers24,1672
Non-polymers6419
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-131 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.491, 40.491, 179.689
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-207-

SO4

21B-501-

SO4

31A-341-

HOH

41A-350-

HOH

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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 IQ domain-containing protein G


Mass: 7445.845 Da / Num. of mol.: 1 / Fragment: UNP residues 376-435, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.76 Å3/Da / Density % sol: 30.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M ammonium sulfate, 1xM 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: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2011
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 10570 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.18 Å / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EWT

3ewt


Resolution: 2.1→27.642 Å / SU ML: 0.06 / σ(F): 1.34 / Phase error: 21.06 / Stereochemistry target values: ML
Details: CHAIN A OF 3EWT WAS USED AS THE SEARCH MODEL FOR CAM (CHAIN A OF THIS STRUCTURE).
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 505 4.8 %Random
Rwork0.1869 ---
obs0.189 10518 97.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→27.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 29 108 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041396
X-RAY DIFFRACTIONf_angle_d0.6541879
X-RAY DIFFRACTIONf_dihedral_angle_d14.701529
X-RAY DIFFRACTIONf_chiral_restr0.049202
X-RAY DIFFRACTIONf_plane_restr0.003248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.30640.25251110.1959233594
2.3064-2.63990.26631360.1951244197
2.6399-3.32510.24161330.1958253899
3.3251-27.64420.1981250.1769269999
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)
14.9273-3.9384-2.7479.11656.84548.4768-0.26590.0253-0.2030.2327-0.20880.7067-0.0328-0.3790.52950.14740.06210.02110.21560.01740.202919.4674-1.737522.0509
22.6638-0.7889-0.99363.4241-0.08843.6829-0.1145-0.42570.33230.03830.088-0.4858-0.08740.62830.00810.1120.06160.02060.2471-0.04430.210632.2722-5.794613.5379
34.32663.9271.33747.13210.14715.1961-0.10280.18950.4573-0.1106-0.01930.0713-0.46210.43360.13680.12520.029-0.02290.233-0.00050.172727.48093.411523.5993
43.2957-0.4067-0.15182.95190.64314.21420.0880.3043-0.0781-0.2184-0.2097-0.69020.21360.7847-0.14240.06120.11290.02240.2030.05370.309124.716911.81093.9185
55.9399-4.33681.14735.443-2.2217.03160.00360.5415-0.3525-0.04410.18230.60530.5376-0.17170.0773-0.01940.02910.06840.2199-0.07320.33213.84752.84163.8773
65.706-3.1599-0.68582.52021.42811.5129-0.0877-1.064-1.31881.02510.22810.53960.6196-0.2423-0.03040.32720.08790.09750.31990.12150.476611.2879-2.144610.4249
73.36933.21770.9734.57780.02862.90.0937-0.10210.17870.6980.11121.50040.2923-1.31620.00350.2841-0.02620.06970.33070.00660.34018.28819.72511.7219
85.3961-2.14190.97062.8108-0.56772.1979-0.2799-0.02770.62610.2136-0.0253-0.1364-0.4129-0.05350.10280.06250.05030.0310.1342-0.04390.129318.655918.0498.6683
95.109-4.7242-3.60457.42084.80118.6953-0.0830.1279-0.0416-0.29390.0957-0.1845-0.192-0.1155-0.07510.2196-0.032-0.04740.13390.04320.206229.22314.120111.2975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 112 )
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 118 )
7X-RAY DIFFRACTION7chain 'A' and (resid 119 through 129 )
8X-RAY DIFFRACTION8chain 'A' and (resid 130 through 148 )
9X-RAY DIFFRACTION9chain 'B' and (resid 389 through 411 )

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