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- PDB-3evv: Crystal Structure of Calcium bound dimeric GCAMP2 (#2) -

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Entry
Database: PDB / ID: 3evv
TitleCrystal Structure of Calcium bound dimeric GCAMP2 (#2)
ComponentsMyosin light chain kinase, Green fluorescent protein, Calmodulin chimeraMyosin light-chain kinase
KeywordsSIGNALING PROTEIN / GCAMP2 / calcium sensor / GFP / Calmodulin / M13
Function / homology
Function and homology information


tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / 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 ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / 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 / 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) / 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 / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / 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 / protein phosphatase activator activity / RHO GTPases activate PAKs / cleavage furrow / 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 / 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 / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / stress fiber / 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 / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / bioluminescence / 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 / generation of precursor metabolites and energy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / 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 / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation
Similarity search - Function
Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Green Fluorescent Protein / Green fluorescent protein / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein ...Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Green Fluorescent Protein / Green fluorescent protein / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Recoverin; domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand domain pair / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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 / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Myosin light chain kinase, smooth muscle / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsWang, Q. / Shui, B. / Kotlikoff, M.I. / Sondermann, H.
CitationJournal: Structure / Year: 2008
Title: Structural Basis for Calcium Sensing by GCaMP2.
Authors: Wang, Q. / Shui, B. / Kotlikoff, M.I. / Sondermann, H.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 21, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_radiation_wavelength / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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.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_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: Myosin light chain kinase, Green fluorescent protein, Calmodulin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4675
Polymers51,3071
Non-polymers1604
Water97354
1
A: Myosin light chain kinase, Green fluorescent protein, Calmodulin chimera
hetero molecules

A: Myosin light chain kinase, Green fluorescent protein, Calmodulin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,93510
Polymers102,6142
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7440 Å2
ΔGint-150 kcal/mol
Surface area35390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.476, 46.955, 67.849
Angle α, β, γ (deg.)90.00, 100.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Myosin light chain kinase, Green fluorescent protein, Calmodulin chimera / Myosin light-chain kinase


Mass: 51307.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: protein contains the M13 fragment of myosin light chain kinase, circular permuted EGFP from Aequorea victoria (Jellyfish), calmodulin from Rattus norvegicus (Rat)
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, CALM1, CALM, CAM, CAM1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P42212, UniProt: P0DP23, UniProt: P11799*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE SER65 HAS BEEN MUTATED TO GLY. RESIDUES GLY65, TYR66, AND GLY67 CONSTITUTE THE CHROMOPHORE ...RESIDUE SER65 HAS BEEN MUTATED TO GLY. RESIDUES GLY65, TYR66, AND GLY67 CONSTITUTE THE CHROMOPHORE CRO. AUTHOR WOULD LIKE TO KEEP THE CONFLICTS SINCE THEY REPRESENT WHAT GCAMP2 IS. IT IS A MUTAGENESIS STUDY TO OPTIMIZE THE PERFORMACE AGAINST ITS VERY EARLY VERSION IN DATABASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.61 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12458 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 7.986
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.6-2.692.60.44185.5
2.69-2.830.40997.3
2.8-2.933.20.36999.5
2.93-3.083.40.304100
3.08-3.283.50.21299.9
3.28-3.533.50.17699.5
3.53-3.883.40.14199.4
3.88-4.453.40.09199.6
4.45-5.63.50.06999.9
5.6-503.30.05799.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.6→33.399 Å / SU ML: 0.39 / σ(F): 0.11 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1165 10.09 %
Rwork0.2151 --
obs0.2207 11550 91.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.613 Å2 / ksol: 0.384 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→33.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 4 54 3132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043129
X-RAY DIFFRACTIONf_angle_d0.734207
X-RAY DIFFRACTIONf_dihedral_angle_d13.8511162
X-RAY DIFFRACTIONf_chiral_restr0.036455
X-RAY DIFFRACTIONf_plane_restr0.002553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70110.35291180.30941039X-RAY DIFFRACTION75
2.7011-2.84340.34341390.25191234X-RAY DIFFRACTION86
2.8434-3.02140.30191440.22571264X-RAY DIFFRACTION91
3.0214-3.25460.2581540.20521365X-RAY DIFFRACTION95
3.2546-3.58170.25031510.20541329X-RAY DIFFRACTION94
3.5817-4.09920.25561450.19741312X-RAY DIFFRACTION93
4.0992-5.16150.21351560.16521420X-RAY DIFFRACTION98
5.1615-33.40220.25391580.20471422X-RAY DIFFRACTION97
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)
11.237-0.03550.25721.85080.12840.70970.0443-0.252-0.1454-0.41350.11940.0786-0.2187-0.1418-0.16170.13080.0021-0.01760.04860.1406-0.0738-16.475318.036411.1716
2-0.01310.00630.0650.59540.27560.56910.0753-0.0329-0.1073-0.0978-0.00440.04490.02850.013-0.0285-0.02390.00510.03-0.0036-0.0030.0098-12.92756.9296-23.1279
30.48260.71920.12010.63290.12220.47930.0044-0.07720.06220.0349-0.02090.01470.0355-0.1491-0.02630.04370.00540.00990.0728-0.0060.042117.995915.1297-9.6212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 39:59)
2X-RAY DIFFRACTION2chain A and resid 60:301)
3X-RAY DIFFRACTION3chain A and resid 302:450)

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