[English] 日本語
Yorodumi
- PDB-3evu: Crystal structure of Calcium bound dimeric GCAMP2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3evu
TitleCrystal structure of Calcium bound dimeric GCAMP2
ComponentsMyosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimera
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 / muscle structure development / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / organelle localization by membrane tethering / regulation of synaptic vesicle exocytosis ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / organelle localization by membrane tethering / regulation of synaptic vesicle exocytosis / 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 / adenylate cyclase binding / catalytic complex / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / stress fiber / positive regulation of protein dephosphorylation / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / bioluminescence / regulation of cytokinesis / generation of precursor metabolites and energy / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / cellular response to type II interferon / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / 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 / cytoplasm / cytosol
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 / Recoverin; domain 1 / Green fluorescent protein-related ...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 / Recoverin; domain 1 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Gallus gallus (chicken)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 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_name_com / 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_ec / _entity.pdbx_fragment / _struct.title / _struct_ref.db_code / _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_db_accession / _struct_ref_seq.seq_align_beg
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 / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)50,8655
Polymers50,7051
Non-polymers1604
Water9,296516
1
A: Myosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimera
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)101,73010
Polymers101,4092
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7280 Å2
ΔGint-155 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.936, 47.310, 69.642
Angle α, β, γ (deg.)90.00, 100.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

21A-475-

HOH

31A-499-

HOH

-
Components

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


Mass: 50704.586 Da / Num. of mol.: 1
Fragment: UNP P11799 residues 1731-1749, UNP P42212 residues 2-144/147-238, UNP P0DP29 residues 3-238
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.) Gallus gallus (chicken), (gene. exp.) Rattus norvegicus (Norway rat)
Plasmid: pET21 / Gene: Mylk, GFP, Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11799, UniProt: P42212, UniProt: P0DP29, myosin-light-chain kinase
#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


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.77 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 41444 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.04 / Χ2: 0.939 / Net I/σ(I): 35.489
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.814.30.23940890.76599.9
1.81-1.894.60.16941330.806100
1.89-1.974.60.11541040.824100
1.97-2.074.60.08341140.905100
2.07-2.24.60.06441461.023100
2.2-2.384.60.05141060.982100
2.38-2.614.60.04441531.06100
2.61-2.994.60.03641501.008100
2.99-3.774.60.02941751.032100
3.77-504.50.02942740.9699.7

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.75→42.525 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.887 / SU ML: 0.22 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 4075 10.05 %
Rwork0.161 --
obs0.164 40536 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.697 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 120.45 Å2 / Biso mean: 26.039 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.847 Å20 Å2-0.37 Å2
2--4.134 Å20 Å2
3----2.288 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 4 516 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083222
X-RAY DIFFRACTIONf_angle_d1.1444350
X-RAY DIFFRACTIONf_chiral_restr0.078479
X-RAY DIFFRACTIONf_plane_restr0.004570
X-RAY DIFFRACTIONf_dihedral_angle_d16.281207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.2091190.178983110279
1.77-1.7910.2461350.1681224135993
1.791-1.8140.2141270.1631169129693
1.814-1.8380.1711250.1531245137094
1.838-1.8630.2421500.1531171132194
1.863-1.8890.2091390.1491275141496
1.889-1.9180.1741460.1481199134597
1.918-1.9480.1971290.1391275140496
1.948-1.980.2081440.1341193133797
1.98-2.0140.2071460.1411267141398
2.014-2.050.171480.1421270141898
2.05-2.090.211330.141254138798
2.09-2.1320.2011470.1571279142699
2.132-2.1790.191440.1461249139398
2.179-2.2290.1941500.1491258140899
2.229-2.2850.1851490.1571261141099
2.285-2.3470.2161510.1561277142899
2.347-2.4160.2381560.1621246140299
2.416-2.4940.211410.1711297143899
2.494-2.5830.2081360.1621289142599
2.583-2.6870.2181210.16913111432100
2.687-2.8090.2161270.1621303143099
2.809-2.9570.2041440.1691295143999
2.957-3.1420.1921420.16612811423100
3.142-3.3850.1971470.1613061453100
3.385-3.7250.2081290.14813091438100
3.725-4.2640.1431490.13113121461100
4.264-5.370.1541490.14213141463100
5.37-42.5370.2061520.2051349150199
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)
10.0525-0.04710.02580.0617-0.0544-0.0241-0.0524-0.01980.1284-0.0510.0682-0.1445-0.07050.0583-0.00090.12080.0211-0.02950.19120.0040.1849-23.7122-7.555245.3149
21.0635-0.2034-0.32540.5584-0.05560.850.035-0-0.02330.0005-0.03360.001-0.05250.0274-0.00030.0798-0.0105-0.00250.05120.00130.0671-18.8223-17.604111.0298
30.44790.514-0.01950.70950.23150.3060.0335-0.07580.08720.0229-0.05610.1269-0.0214-0.042400.1206-0.0139-0.01360.168-0.00710.137112.387-10.010924.5873
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)

+
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://pdbjlvh1.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