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- PDB-3evr: Crystal structure of Calcium bound monomeric GCAMP2 -

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Basic information

Entry
Database: PDB / ID: 3evr
TitleCrystal structure of Calcium bound monomeric GCAMP2
ComponentsMyosin light chain kinase, Green fluorescent protein, Calmodulin-1 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 / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / protein phosphatase activator activity / cleavage furrow / calcium channel regulator activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / stress fiber / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / sperm midpiece / response to amphetamine / calcium channel complex / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / bioluminescence / sarcomere / regulation of cytokinesis / generation of precursor metabolites and energy / calcium-mediated signaling / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / spindle pole / cellular response to type II interferon / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / lamellipodium / myelin sheath / growth cone / transmembrane transporter binding / calmodulin binding / protein domain specific binding / phosphorylation / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm
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)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 1.2Jul 26, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: diffrn_radiation_wavelength / diffrn_source ...diffrn_radiation_wavelength / diffrn_source / entity / entity_src_gen / pdbx_distant_solvent_atoms / software / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list ..._diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity.pdbx_description / _entity.pdbx_fragment / _struct.pdbx_descriptor / _struct_ref.db_code / _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_db_accession / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Dec 27, 2023Group: 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_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_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.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.ptnr1_label_seq_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_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-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5685
Polymers46,4081
Non-polymers1604
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.995, 121.995, 97.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

21A-830-

HOH

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Components

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


Mass: 46407.824 Da / Num. of mol.: 1
Fragment: UNP P42212 residues 2-238, UNP P0DP29 residues 148-305
Source method: isolated from a genetically manipulated source
Details: protein contains circular permuted EGFP from Aequorea victoria (Jellyfish), the M13 fragment of myosin light chain kinase, calmodulin from Rattus norvegicus (Rat)
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat)
Plasmid: pET21 / Gene: GFP, Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P42212, UniProt: P0DP29, 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.: 450 / 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: 3.92 Å3/Da / Density % sol: 68.65 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 50531 / % possible obs: 100 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 23.625
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2-2.0715.20.71100
2.07-2.1517.20.561100
2.15-2.2517.70.449100
2.25-2.3717.80.359100
2.37-2.52180.276100
2.52-2.71180.201100
2.71-2.9918.10.142100
2.99-3.42180.085100
3.42-4.3117.80.059100
4.31-5016.70.054100

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2→47.649 Å / SU ML: 0.23 / σ(F): 0.27 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 4821 10.04 %
Rwork0.1628 --
obs0.1655 48004 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.642 Å2 / ksol: 0.341 e/Å3
Refinement stepCycle: LAST / Resolution: 2→47.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 4 450 3650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093259
X-RAY DIFFRACTIONf_angle_d1.1374398
X-RAY DIFFRACTIONf_dihedral_angle_d16.2641223
X-RAY DIFFRACTIONf_chiral_restr0.078479
X-RAY DIFFRACTIONf_plane_restr0.004582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02070.24651430.18981307X-RAY DIFFRACTION88
2.0207-2.04450.20661430.1771353X-RAY DIFFRACTION91
2.0445-2.06940.19671770.16411355X-RAY DIFFRACTION93
2.0694-2.09560.21811500.16671384X-RAY DIFFRACTION92
2.0956-2.12320.22151580.15981363X-RAY DIFFRACTION93
2.1232-2.15230.17971490.15871417X-RAY DIFFRACTION93
2.1523-2.1830.19211470.15191408X-RAY DIFFRACTION94
2.183-2.21560.19111700.14691376X-RAY DIFFRACTION92
2.2156-2.25020.20691510.15551389X-RAY DIFFRACTION93
2.2502-2.28710.20411740.16611367X-RAY DIFFRACTION92
2.2871-2.32650.2021720.16621394X-RAY DIFFRACTION94
2.3265-2.36880.21281610.16041413X-RAY DIFFRACTION95
2.3688-2.41440.19511720.16071371X-RAY DIFFRACTION92
2.4144-2.46370.16271450.1641393X-RAY DIFFRACTION93
2.4637-2.51720.22191640.15761423X-RAY DIFFRACTION94
2.5172-2.57580.18761590.15341438X-RAY DIFFRACTION96
2.5758-2.64020.19371410.14981453X-RAY DIFFRACTION95
2.6402-2.71160.19541560.15851447X-RAY DIFFRACTION95
2.7116-2.79140.1651420.15461450X-RAY DIFFRACTION96
2.7914-2.88150.20511640.15891438X-RAY DIFFRACTION95
2.8815-2.98440.20241550.16911449X-RAY DIFFRACTION96
2.9844-3.10390.18361420.161491X-RAY DIFFRACTION97
3.1039-3.24510.17151660.15571498X-RAY DIFFRACTION98
3.2451-3.41620.1881530.15611512X-RAY DIFFRACTION98
3.4162-3.63010.18171740.15541512X-RAY DIFFRACTION99
3.6301-3.91030.17361880.15031529X-RAY DIFFRACTION100
3.9103-4.30360.14681560.12931508X-RAY DIFFRACTION98
4.3036-4.92580.15071770.12611537X-RAY DIFFRACTION99
4.9258-6.20380.18441730.16381569X-RAY DIFFRACTION99
6.2038-47.66270.17451990.18491639X-RAY DIFFRACTION99
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)
10.2781-0.1424-0.1503-0.8197-0.32370.5218-0.03090.01960.1447-0.04740.0134-0.0647-0.3920.0796-0.04880.2286-0.02190.0320.07950.01950.1406-40.401621.0325-5.1324
20.7612-0.02340.00490.32560.1050.549-0.0343-0.02540.02760.03620.02620.00410.1060.0020.0070.06570.0097-0.00160.03890.00250.0431-39.6949-10.67591.9952
30.508-0.197-0.25590.43360.59120.3727-0.0077-0.02870.093-0.20180.0485-0.0475-0.14270.054-0.0250.1156-0.00320.00890.02810.01410.0346-42.500720.0253-6.9176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 39:59)
2X-RAY DIFFRACTION2(chain A and resid 60:301)
3X-RAY DIFFRACTION3(chain A and resid 302:450)

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