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- PDB-7vmb: Crystal structure of IQSEC1-IQ motif, Sec7PH tandem in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7vmb
TitleCrystal structure of IQSEC1-IQ motif, Sec7PH tandem in complex with calmodulin
Components
  • (IQ motif and SEC7 domain-containing protein 1) x 2
  • Calmodulin-1
KeywordsMETAL BINDING PROTEIN / Complex / GEF activity
Function / homology
Function and homology information


regulation of ARF protein signal transduction / dendritic spine development / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...regulation of ARF protein signal transduction / dendritic spine development / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / 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 / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / eNOS activation / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / guanyl-nucleotide exchange factor activity / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion / RAS processing / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / synaptic vesicle / Platelet degranulation / myelin sheath
Similarity search - Function
IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / IQ motif profile. / : ...IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / IQ motif profile. / : / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / PH-like domain superfamily
Similarity search - Domain/homology
Calmodulin-1 / IQ motif and SEC7 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99777371992 Å
AuthorsYang, W. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: J.Cell Biol. / Year: 2023
Title: Ca2+-induced release of IQSEC2/BRAG1 autoinhibition under physiological and pathological conditions.
Authors: Bai, G. / Li, H. / Qin, P. / Guo, Y. / Yang, W. / Lian, Y. / Ye, F. / Chen, J. / Wu, M. / Huang, R. / Li, J. / Lu, Y. / Zhang, M.
History
DepositionOct 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IQ motif and SEC7 domain-containing protein 1
B: IQ motif and SEC7 domain-containing protein 1
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4006
Polymers69,1243
Non-polymers2763
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-31 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.010, 81.436, 124.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein IQ motif and SEC7 domain-containing protein 1 / ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine ...ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine nucleotide-exchange protein 2 / Brefeldin-resistant Arf-GEF 2 protein / BRAG2


Mass: 43256.031 Da / Num. of mol.: 1 / Fragment: SEC7 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQSEC1, ARFGEP100, BRAG2, KIAA0763 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DN90
#2: Protein IQ motif and SEC7 domain-containing protein 1 / ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine ...ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine nucleotide-exchange protein 2 / Brefeldin-resistant Arf-GEF 2 protein / BRAG2


Mass: 8716.847 Da / Num. of mol.: 1 / Fragment: IQ motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQSEC1, ARFGEP100, BRAG2, KIAA0763 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DN90
#3: Protein Calmodulin-1


Mass: 17150.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 4% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 46959 / % possible obs: 99.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 28.450133922 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.36
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.3 % / Num. unique obs: 2345 / CC1/2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C0A

4c0a


Resolution: 1.99777371992→49.5215947181 Å / SU ML: 0.188309187815 / Cross valid method: FREE R-VALUE / σ(F): 1.33788165874 / Phase error: 24.1960452601
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252312224672 2357 5.0664201883 %
Rwork0.19780022887 44165 -
obs0.200412394071 46522 98.8735866701 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.3984455212 Å2
Refinement stepCycle: LAST / Resolution: 1.99777371992→49.5215947181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 18 268 4430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007223088678864246
X-RAY DIFFRACTIONf_angle_d0.7775997808295714
X-RAY DIFFRACTIONf_chiral_restr0.054826271941628
X-RAY DIFFRACTIONf_plane_restr0.00548665929168757
X-RAY DIFFRACTIONf_dihedral_angle_d11.28051489093423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9978-2.03860.2653291321591500.2205233917522534X-RAY DIFFRACTION97.4228675136
2.0386-2.08290.2457939231661360.211542769342573X-RAY DIFFRACTION99.963099631
2.0829-2.13130.2827918710651240.2125462484882585X-RAY DIFFRACTION99.7422680412
2.1313-2.18460.2284769293141480.2133437666542570X-RAY DIFFRACTION99.2332968237
2.1846-2.24370.3380045599771310.2627364941032566X-RAY DIFFRACTION98.2155863074
2.2437-2.30970.3450492128861240.2798836783732269X-RAY DIFFRACTION87.719941349
2.3097-2.38430.2519690476671300.2099826942672598X-RAY DIFFRACTION100
2.3843-2.46950.2701099222241490.2113485075452591X-RAY DIFFRACTION100
2.4695-2.56840.2406678114991480.2055905300952610X-RAY DIFFRACTION99.9275362319
2.5684-2.68520.2603763487781480.2026967347832588X-RAY DIFFRACTION100
2.6852-2.82680.2468903639251520.2033794811512595X-RAY DIFFRACTION99.6734397678
2.8268-3.00390.2585003879861250.2032830401432630X-RAY DIFFRACTION100
3.0039-3.23580.271360636481470.2053327160832621X-RAY DIFFRACTION99.9277978339
3.2358-3.56130.219163847151550.1928394550822649X-RAY DIFFRACTION100
3.5613-4.07640.2534972642621340.174278096512660X-RAY DIFFRACTION99.7857142857
4.0764-5.1350.2383786365061360.1647199812462697X-RAY DIFFRACTION99.9294532628
5.135-100.237929759991200.1987519373692829X-RAY DIFFRACTION99.3598382749

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