[English] 日本語
Yorodumi
- PDB-3wld: Crystal structure of monomeric GCaMP6m -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wld
TitleCrystal structure of monomeric GCaMP6m
ComponentsMyosin light chain kinase, Green fluorescent protein, Calmodulin
KeywordsFLUORESCENT PROTEIN / CALCIUM SENSOR
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 / detection of calcium ion / calcium channel regulator activity / 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 / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / 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 kinase activity / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / 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 / 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 / Mainly Beta
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDing, J. / Luo, A.F. / Hu, L.Y. / Wang, D.C. / Shao, F.
CitationJournal: Sci China Life Sci / Year: 2014
Title: Structural basis of the ultrasensitive calcium indicator GCaMP6.
Authors: Ding, J. / Luo, A.F. / Hu, L. / Wang, D. / Shao, F.
History
DepositionNov 8, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _struct_ref.db_code ..._entity.details / _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.pdbx_seq_db_accession_code
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5585
Polymers50,3981
Non-polymers1604
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.880, 120.880, 97.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

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


Mass: 50398.176 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 37-55, 149-238, 2-144, 3-149
Mutation: M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, N61D, D79Y, M77G, K78S, T80R, S82T, R91G
Source method: isolated from a genetically manipulated source
Details: THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF UNP Q6LDG3, AN ENGINEERED LE LINKER, RESIDUES 149-239 OF UNP P42212, AN ENGINEERED ...Details: THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF UNP Q6LDG3, AN ENGINEERED LE LINKER, RESIDUES 149-239 OF UNP P42212, AN ENGINEERED GGTGGSMV LINKER, RESIDUES 2-144 OF UNP P42212, AN ENGINEERED LP LINKER, AND RESIDUES 3-149 OF UNP P0DP29. UNP P42212 RESIDUES S65, Y66, AND G67 ARE THE CHROMOPHORE CRO.
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat)
Plasmid: pSUMO / Gene: GFP, Calm, Cam / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Sequence details(1)THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 ...(1)THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF UNP Q6LDG3, AN ENGINEERED LE LINKER, RESIDUES 149-238 OF UNP P42212, AN ENGINEERED GGTGGSMV LINKER, RESIDUES 2-144 OF UNP P42212, AN ENGINEERED LP LINKER, AND RESIDUES 3-149 OF UNP P62161. (2)RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE CRO 66.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M HEPES, 18% w/v PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→60.44 Å / Num. all: 20398 / Num. obs: 20011 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 12.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2774 / Rsym value: 0.377 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SG4

3sg4


Resolution: 2.7→54.059 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 1020 5.11 %RANDOM
Rwork0.17 ---
all0.1722 20439 --
obs0.1722 19975 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.7→54.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 4 162 3299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063192
X-RAY DIFFRACTIONf_angle_d1.0844304
X-RAY DIFFRACTIONf_dihedral_angle_d14.8311200
X-RAY DIFFRACTIONf_chiral_restr0.066464
X-RAY DIFFRACTIONf_plane_restr0.004569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7001-2.84250.30811450.231256095
2.8425-3.02050.26671350.2137258395
3.0205-3.25370.23451530.1807262497
3.2537-3.58110.21631540.1622270899
3.5811-4.09920.18031400.15052773100
4.0992-5.16390.17461650.13742772100
5.1639-54.070.21831280.1872293599

+
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