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- PDB-3u0k: Crystal Structure of the genetically encoded calcium indicator RCaMP -

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Basic information

Entry
Database: PDB / ID: 3u0k
TitleCrystal Structure of the genetically encoded calcium indicator RCaMP
ComponentsRCaMP
KeywordsFLUORESCENT PROTEIN / calcium binding / EF-hand / genetically encoded calcium indicator
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / calcium ion binding
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAkerboom, J. / Looger, L.L. / Schreiter, E.R.
CitationJournal: Front Mol Neurosci / Year: 2013
Title: Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.
Authors: Akerboom, J. / Carreras Calderon, N. / Tian, L. / Wabnig, S. / Prigge, M. / Tolo, J. / Gordus, A. / Orger, M.B. / Severi, K.E. / Macklin, J.J. / Patel, R. / Pulver, S.R. / Wardill, T.J. / ...Authors: Akerboom, J. / Carreras Calderon, N. / Tian, L. / Wabnig, S. / Prigge, M. / Tolo, J. / Gordus, A. / Orger, M.B. / Severi, K.E. / Macklin, J.J. / Patel, R. / Pulver, S.R. / Wardill, T.J. / Fischer, E. / Schuler, C. / Chen, T.W. / Sarkisyan, K.S. / Marvin, J.S. / Bargmann, C.I. / Kim, D.S. / Kugler, S. / Lagnado, L. / Hegemann, P. / Gottschalk, A. / Schreiter, E.R. / Looger, L.L.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RCaMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5146
Polymers49,2941
Non-polymers2195
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.918, 75.918, 123.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RCaMP


Mass: 49294.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: K4DIE3*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE IS OF AN ENGINEERED CHIMERA OF PROTEIN DOMAINS THAT TOGETHER FUNCTION AS A ...THE STRUCTURE IS OF AN ENGINEERED CHIMERA OF PROTEIN DOMAINS THAT TOGETHER FUNCTION AS A FLUORESCENT CALCIUM SENSOR. THE LARGEST PORTION OF THE POLYPEPTIDE IS DERIVED FROM EQFP611, BUT THE EQFP611 DOMAIN HAS BEEN CIRCULARLY PERMUTED AND HIGHLY MUTATED TO IMPROVE THE CALCIUM SENSOR FUNCTION.

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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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 2, 2010
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→34.82 Å / Num. all: 24632 / Num. obs: 24607 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.21 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SPECdata collection
PHASERphasing
REFMAC5.6.0111refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UIS
Resolution: 2.1→21.58 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.635 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23852 1253 5.1 %RANDOM
Rwork0.18931 ---
all0.19181 23348 --
obs0.19181 23294 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 8 138 3270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223226
X-RAY DIFFRACTIONr_bond_other_d0.0020.022232
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9614341
X-RAY DIFFRACTIONr_angle_other_deg0.97335422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1145406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17224.359156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30315580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2041523
X-RAY DIFFRACTIONr_chiral_restr0.1130.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023645
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02669
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 88 -
Rwork0.222 1533 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.13825.5724-1.3743.8378-0.89482.6536-0.10050.27080.752-0.10860.25360.5624-0.29290.0961-0.15310.2742-0.1425-0.08430.34450.13490.1853-52.748-5.835-6.501
21.78270.0005-0.03352.2176-0.95873.41350.06480.1406-0.0995-0.03610.01530.00820.0957-0.252-0.08010.119-0.0477-0.02510.13980.01340.0114-36.60314.447-15.323
31.2730.15810.34292.0608-0.20133.02430.02070.209-0.0264-0.00090.0025-0.0842-0.16820.1127-0.02320.1391-0.0555-0.02160.16490.01490.0088-33.56418.233-16.061
49.75054.6905-1.555413.0063-5.52927.0024-0.231.5221.9892-0.12770.51811.8209-0.6564-0.4082-0.28810.392-0.1045-0.20220.58790.51010.9411-62.0765.34-15.959
53.81881.6119-0.91383.8181-1.33631.6423-0.10350.19190.42040.07590.13260.2789-0.2153-0.0175-0.0290.1914-0.0857-0.07480.21350.0930.13-61.026-11.207-4.846
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 61
2X-RAY DIFFRACTION2A62 - 127
3X-RAY DIFFRACTION3A128 - 313
4X-RAY DIFFRACTION4A314 - 355
5X-RAY DIFFRACTION5A356 - 440

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