[English] 日本語
Yorodumi
- PDB-6b8l: Crystal Structure of the Apo/CaM:Kv7.4 (KCNQ4) AB Domain Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b8l
TitleCrystal Structure of the Apo/CaM:Kv7.4 (KCNQ4) AB Domain Complex
Components
  • Calmodulin-1
  • Potassium voltage-gated channel subfamily KQT member 4
KeywordsMETAL TRANSPORT / ion channel / complex
Function / homology
Function and homology information


negative regulation of synaptic transmission, dopaminergic / Voltage gated Potassium channels / Sensory processing of sound by outer hair cells of the cochlea / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Sensory processing of sound by inner hair cells of the cochlea / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor ...negative regulation of synaptic transmission, dopaminergic / Voltage gated Potassium channels / Sensory processing of sound by outer hair cells of the cochlea / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Sensory processing of sound by inner hair cells of the cochlea / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / CASP4 inflammasome assembly / Glycogen breakdown (glycogenolysis) / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / regulation of cell communication by electrical coupling involved in cardiac conduction / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / potassium channel activity / Regulation of MECP2 expression and activity / Smooth Muscle Contraction / potassium ion transport / detection of calcium ion / regulation of cardiac muscle contraction / voltage-gated potassium channel activity / cellular response to interferon-beta / RHO GTPases activate IQGAPs / presynaptic cytosol / calcium channel inhibitor activity / catalytic complex / sensory perception of sound / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of heart rate / Protein methylation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / titin binding / calcium channel complex / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / potassium ion transmembrane transport / sperm midpiece / basal plasma membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of receptor signaling pathway via JAK-STAT / calyx of Held / Ras activation upon Ca2+ influx through NMDA receptor / adenylate cyclase activator activity / regulation of cytokinesis / VEGFR2 mediated cell proliferation / spindle microtubule / VEGFR2 mediated vascular permeability / calcium channel regulator activity / sarcomere / Translocation of SLC2A4 (GLUT4) to the plasma membrane / myelin sheath / Transcriptional activation of mitochondrial biogenesis / long-term synaptic potentiation / cellular response to type II interferon / Enterobacterial factors antagonize host defense / RAF activation / response to calcium ion / Stimuli-sensing channels / calcium-dependent protein binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / RAS processing / Signaling by BRAF and RAF1 fusions / Platelet degranulation
Similarity search - Function
Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / EF-hand / Recoverin; domain 1 / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / EF-hand / Recoverin; domain 1 / : / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsChang, A. / Abderemane-Ali, F. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC007664 United States
CitationJournal: Neuron / Year: 2018
Title: A Calmodulin C-Lobe Ca2+-Dependent Switch Governs Kv7 Channel Function
Authors: Chang, A. / Abderemane-Ali, F. / Hura, G.L. / Rossen, N.D. / Gate, R.E. / Minor, D.L.
History
DepositionOct 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily KQT member 4
B: Calmodulin-1
C: Potassium voltage-gated channel subfamily KQT member 4
D: Calmodulin-1
E: Potassium voltage-gated channel subfamily KQT member 4
F: Calmodulin-1
G: Potassium voltage-gated channel subfamily KQT member 4
H: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,54513
Polymers107,0658
Non-polymers4805
Water5,116284
1
A: Potassium voltage-gated channel subfamily KQT member 4
B: Calmodulin-1


Theoretical massNumber of molelcules
Total (without water)26,7662
Polymers26,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-31 kcal/mol
Surface area11890 Å2
MethodPISA
2
C: Potassium voltage-gated channel subfamily KQT member 4
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9584
Polymers26,7662
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-41 kcal/mol
Surface area12220 Å2
MethodPISA
3
E: Potassium voltage-gated channel subfamily KQT member 4
F: Calmodulin-1


Theoretical massNumber of molelcules
Total (without water)26,7662
Polymers26,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-42 kcal/mol
Surface area11700 Å2
MethodPISA
4
G: Potassium voltage-gated channel subfamily KQT member 4
H: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0545
Polymers26,7662
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-64 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.435, 142.453, 164.313
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein
Potassium voltage-gated channel subfamily KQT member 4 / KQT-like 4 / Potassium channel subunit alpha KvLQT4 / Voltage-gated potassium channel subunit Kv7.4


Mass: 9913.735 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ4 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P56696
#2: Protein
Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pEGST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P0DP23
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.49 % / Mosaicity: 0.514 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2M ammonium sulfate, 0.1M BisTris pH 6.5

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
2801
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.9797
SYNCHROTRONAPS 23-ID-B21.072
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 27, 2015
DECTRIS PILATUS 6M2PIXELAug 20, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double flat crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111) double crystal KhozuSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
21.0721
ReflectionResolution: 2.3→50 Å / Num. obs: 57501 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.47 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.047 / Rrim(I) all: 0.128 / Χ2: 1.254 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.347.40.92828330.9320.3660.9981.43100
2.34-2.387.40.62328450.9610.2460.671.408100
2.38-2.437.40.59328320.9590.2340.6381.406100
2.43-2.487.40.52828380.970.2080.5671.422100
2.48-2.537.40.4428620.9740.1730.4731.409100
2.53-2.597.40.39228360.9730.1540.4211.41100
2.59-2.667.40.32528900.9820.1280.3491.438100
2.66-2.737.40.29928240.9840.1180.3221.476100
2.73-2.817.40.24528660.9880.0970.2641.456100
2.81-2.97.40.19328440.9910.0760.2071.486100
2.9-37.40.16128710.9920.0630.1731.36100
3-3.127.40.13728640.9930.0540.1481.276100
3.12-3.267.40.12228390.9930.0480.1311.141100
3.26-3.447.40.11228890.9940.0440.1211.147100
3.44-3.657.20.11228900.990.0450.121.027100
3.65-3.936.90.12728930.9870.0520.1371.179100
3.93-4.337.10.08728710.9940.0350.0941.00999.9
4.33-4.957.10.06829260.9960.0270.0730.859100
4.95-6.247.20.05829320.9970.0230.0630.868100
6.24-507.10.04630560.9990.0190.0490.84999.6

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.3→48.888 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.5
RfactorNum. reflection% reflection
Rfree0.2456 5475 9.96 %
Rwork0.1984 --
obs0.2031 54987 94.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.19 Å2 / Biso mean: 46.0271 Å2 / Biso min: 17.51 Å2
Refinement stepCycle: final / Resolution: 2.3→48.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6921 0 25 284 7230
Biso mean--74.68 38.05 -
Num. residues----858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077074
X-RAY DIFFRACTIONf_angle_d0.849505
X-RAY DIFFRACTIONf_chiral_restr0.0471042
X-RAY DIFFRACTIONf_plane_restr0.0051239
X-RAY DIFFRACTIONf_dihedral_angle_d21.6462713
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2825-2.30840.28421130.21081014112759
2.3084-2.33560.30581580.22861528168688
2.3356-2.36410.29391680.21091529169790
2.3641-2.3940.28431680.21311539170790
2.394-2.42550.28731720.23111585175791
2.4255-2.45870.32021670.22681554172190
2.4587-2.49380.28871750.2281585176092
2.4938-2.5310.31431780.21181635181394
2.531-2.57060.26891720.21941573174593
2.5706-2.61270.31781810.20151610179194
2.6127-2.65780.25791770.21431631180895
2.6578-2.70610.25651830.22311665184895
2.7061-2.75820.28641900.2331642183295
2.7582-2.81450.26121810.22231646182796
2.8145-2.87560.31541860.21511678186497
2.8756-2.94250.28991860.22271679186597
2.9425-3.01610.26341910.22591723191498
3.0161-3.09760.28181910.221715190699
3.0976-3.18880.26011900.2281720191099
3.1888-3.29170.26531930.21941722191599
3.2917-3.40930.26071900.21491708189899
3.4093-3.54580.26321930.19921728192199
3.5458-3.70710.26031890.21961709189898
3.7071-3.90250.22621960.181731192799
3.9025-4.14680.21871910.17011711190299
4.1468-4.46680.20391970.153117621959100
4.4668-4.91590.19061960.161817621958100
4.9159-5.62640.22851950.18417681963100
5.6264-7.08520.24112010.210918012002100
7.0852-48.89960.18462070.17081859206699

+
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