[English] 日本語
Yorodumi
- PDB-3sg7: Crystal Structure of GCaMP3-KF(linker 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sg7
TitleCrystal Structure of GCaMP3-KF(linker 1)
ComponentsMyosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimeraMyosin light-chain kinase
KeywordsFLUORESCENT PROTEIN / calcium sensor
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 / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / stress fiber / response to amphetamine / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / sperm midpiece / calcium channel complex / adenylate cyclase activator activity / protein serine/threonine kinase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / sarcomere / bioluminescence / regulation of cytokinesis / generation of precursor metabolites and energy / calcium-mediated signaling / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / cellular response to type II interferon / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / lamellipodium / myelin sheath / kinase activity / 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 / Green fluorescent protein, GFP / EF-hand / 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 / Green fluorescent protein, GFP / EF-hand / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Recoverin; domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / EF-hand domain pair / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / 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 / Myosin light chain kinase
Similarity search - Component
Biological speciesGallus gallus (chicken)
Aequorea victoria (jellyfish)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchreiter, E.R. / Akerboom, J. / Looger, L.L.
CitationJournal: J.Neurosci. / Year: 2012
Title: Optimization of a GCaMP calcium indicator for neural activity imaging.
Authors: Akerboom, J. / Chen, T.W. / Wardill, T.J. / Tian, L. / Marvin, J.S. / Mutlu, S. / Calderon, N.C. / Esposti, F. / Borghuis, B.G. / Sun, X.R. / Gordus, A. / Orger, M.B. / Portugues, R. / ...Authors: Akerboom, J. / Chen, T.W. / Wardill, T.J. / Tian, L. / Marvin, J.S. / Mutlu, S. / Calderon, N.C. / Esposti, F. / Borghuis, B.G. / Sun, X.R. / Gordus, A. / Orger, M.B. / Portugues, R. / Engert, F. / Macklin, J.J. / Filosa, A. / Aggarwal, A. / Kerr, R.A. / Takagi, R. / Kracun, S. / Shigetomi, E. / Khakh, B.S. / Baier, H. / Lagnado, L. / Wang, S.S. / Bargmann, C.I. / Kimmel, B.E. / Jayaraman, V. / Svoboda, K. / Kim, D.S. / Schreiter, E.R. / Looger, L.L.
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref.db_code ..._entity.pdbx_description / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.seq_num
Revision 1.3Sep 13, 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_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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7395
Polymers50,5781
Non-polymers1604
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.449, 61.531, 123.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 50578.473 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: KF(linker 1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: GFP, Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli (E. coli)
References: UniProt: Q6LDG3, 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.: 186 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF ...THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF UNP Q6LDG3, AN ENGINEERED KF LINKER, RESIDUES 149-239 OF UNP P42212, AN ENGINEERED GGTGGSMV LINKER, RESIDUES 2-144 OF UNP P42212, AN ENGINEERED TR LINKER, AND RESIDUES 3-149 OF UNP P62161. UNP P42212 RESIDUES S65, Y66, AND G67 ARE THE CHROMOPHORE CRO.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 33566 / Num. obs: 32056 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.068 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.825 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0111refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EK8
Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.142 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23035 1679 5 %RANDOM
Rwork0.18504 ---
all0.18732 33566 --
obs0.18732 32056 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.483 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3181 0 4 186 3371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223269
X-RAY DIFFRACTIONr_bond_other_d0.0010.022235
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9664411
X-RAY DIFFRACTIONr_angle_other_deg0.9935464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45825.412170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76115595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.031517
X-RAY DIFFRACTIONr_chiral_restr0.1180.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023682
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02647
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: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 122 -
Rwork0.316 2140 -
obs--94.88 %
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)
111.88173.41588.72291.84722.07356.639-0.23230.44690.08710.07590.0463-0.2572-0.21720.39360.1860.2510.01730.0030.1258-0.0210.155518.4960.56839.025
225.793914.7272-2.834410.7101-1.8974.6615-0.1894-0.22260.8351-0.13890.07910.2277-0.27960.25370.11020.22950.0270.00340.0457-0.01530.06256.4055.46124.817
30.74940.39890.06171.3964-0.66762.253-0.03190.0504-0.1156-0.1226-0.0377-0.0520.08210.15080.06970.1631-0.00120.04160.0461-0.02870.04826.089-3.47119.793
42.5032-1.67718.54523.6943-6.04229.3190.0808-0.1327-0.2351-0.02120.64950.33940.1713-0.4628-0.73030.3230.0140.08340.4536-0.00930.3436-0.844-20.19622.999
51.43040.4058-0.34282.5105-0.311.9308-0.03870.12860.0172-0.23250.0364-0.053-0.08150.08320.00230.1775-0.02390.02270.0485-0.01390.01054.0570.7813.751
64.35390.54640.92613.82090.70322.1254-0.0511-0.0897-0.2003-0.06210.0835-0.4337-0.06440.225-0.03250.2042-0.0172-0.02630.1180.01550.147518.741-6.60341.284
73.77030.92580.82526.42271.08567.5690.27810.1315-0.2246-0.1869-0.25610.09190.07270.0221-0.02210.1952-0.02930.02120.15680.01680.073525.6037.69554.131
87.4124-1.16520.58997.1615-0.43215.31590.0766-0.0375-0.2717-0.19220.0181-0.56840.01450.5332-0.09460.219-0.06990.070.18810.02830.198535.2210.44851.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 68
2X-RAY DIFFRACTION2A69 - 88
3X-RAY DIFFRACTION3A89 - 145
4X-RAY DIFFRACTION4A146 - 163
5X-RAY DIFFRACTION5A164 - 301
6X-RAY DIFFRACTION6A302 - 375
7X-RAY DIFFRACTION7A383 - 418
8X-RAY DIFFRACTION8A419 - 448

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more