[English] 日本語
Yorodumi
- PDB-6hcs: Crystal structure of CaM-peptide complex containing AzF at positi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hcs
TitleCrystal structure of CaM-peptide complex containing AzF at position 108
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit beta
  • Calmodulin-1
KeywordsPROTEIN BINDING / calmodulin / unnatural amino acid / AzF
Function / homology
Function and homology information


regulation of synaptic transmission, cholinergic / activation of meiosis involved in egg activation / cell projection morphogenesis / HSF1-dependent transactivation / RAF activation / Ion transport by P-type ATPases / hippocampal neuron apoptotic process / calcium- and calmodulin-dependent protein kinase complex / cellular response to homocysteine / Interferon gamma signaling ...regulation of synaptic transmission, cholinergic / activation of meiosis involved in egg activation / cell projection morphogenesis / HSF1-dependent transactivation / RAF activation / Ion transport by P-type ATPases / hippocampal neuron apoptotic process / calcium- and calmodulin-dependent protein kinase complex / cellular response to homocysteine / Interferon gamma signaling / positive regulation of synapse maturation / Ca2+/calmodulin-dependent protein kinase / regulation of neuron migration / structural constituent of postsynaptic actin cytoskeleton / calcium-dependent protein serine/threonine kinase activity / positive regulation of dendritic spine morphogenesis / Trafficking of AMPA receptors / regulation of synapse maturation / CaM pathway / Cam-PDE 1 activation / RAF/MAP kinase cascade / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / calcium/calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / response to psychosocial stress / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / Ion homeostasis / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / phospholipase binding / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / neuromuscular process controlling balance / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / Unblocking of NMDA receptors, glutamate binding and activation / regulation of protein localization to plasma membrane / spindle midzone / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / eNOS activation / response to cadmium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / sarcoplasmic reticulum membrane / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of apoptotic signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / : / NTF2-like domain superfamily / 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 ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / : / NTF2-like domain superfamily / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Calcium/calmodulin-dependent protein kinase type II subunit beta / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCreon, A. / Josts, I. / Tidow, H.
CitationJournal: Struct Dyn / Year: 2018
Title: Conformation-specific detection of calmodulin binding using the unnatural amino acid p-azido-phenylalanine (AzF) as an IR-sensor.
Authors: Creon, A. / Josts, I. / Niebling, S. / Huse, N. / Tidow, H.
History
DepositionAug 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 17, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin-1
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
C: Calmodulin-1
D: Calcium/calmodulin-dependent protein kinase type II subunit beta
E: Calmodulin-1
F: Calcium/calmodulin-dependent protein kinase type II subunit beta
G: Calmodulin-1
H: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,24724
Polymers87,6068
Non-polymers64116
Water4,378243
1
A: Calmodulin-1
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0626
Polymers21,9012
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-75 kcal/mol
Surface area8300 Å2
MethodPISA
2
C: Calmodulin-1
D: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0626
Polymers21,9012
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-81 kcal/mol
Surface area8540 Å2
MethodPISA
3
E: Calmodulin-1
F: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0626
Polymers21,9012
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-54 kcal/mol
Surface area8600 Å2
MethodPISA
4
G: Calmodulin-1
H: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0626
Polymers21,9012
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-66 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.263, 37.214, 121.193
Angle α, β, γ (deg.)90.00, 100.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Calmodulin-1


Mass: 19014.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein/peptide
Calcium/calmodulin-dependent protein kinase type II subunit beta / CaMK-II subunit beta


Mass: 2886.528 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
References: UniProt: P08413, Ca2+/calmodulin-dependent protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 36.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 6000, lithium chloride, sodium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.917143 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917143 Å / Relative weight: 1
ReflectionResolution: 2→43.12 Å / Num. obs: 45156 / % possible obs: 97.59 % / Redundancy: 3.3 % / Net I/σ(I): 13.62
Reflection shellResolution: 2→2.07 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CDM

1cdm


Resolution: 2→43.119 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.59
RfactorNum. reflection% reflection
Rfree0.2944 2256 5.01 %
Rwork0.2602 --
obs0.2619 45027 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 16 243 5239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075031
X-RAY DIFFRACTIONf_angle_d0.8596711
X-RAY DIFFRACTIONf_dihedral_angle_d35.1481892
X-RAY DIFFRACTIONf_chiral_restr0.046744
X-RAY DIFFRACTIONf_plane_restr0.004893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.34881530.31732680X-RAY DIFFRACTION99
2.0435-2.0910.34281400.30472707X-RAY DIFFRACTION99
2.091-2.14330.30661380.29662654X-RAY DIFFRACTION99
2.1433-2.20130.28951210.27932725X-RAY DIFFRACTION99
2.2013-2.2660.31051480.27512638X-RAY DIFFRACTION98
2.266-2.33920.31591430.2692670X-RAY DIFFRACTION98
2.3392-2.42280.33521340.27022667X-RAY DIFFRACTION98
2.4228-2.51980.3041480.26652647X-RAY DIFFRACTION97
2.5198-2.63440.2851470.26072645X-RAY DIFFRACTION97
2.6344-2.77330.30431340.26152667X-RAY DIFFRACTION99
2.7733-2.9470.31261410.27922716X-RAY DIFFRACTION99
2.947-3.17450.32731470.27082673X-RAY DIFFRACTION98
3.1745-3.49380.30921480.2542599X-RAY DIFFRACTION95
3.4938-3.99910.25031250.24472640X-RAY DIFFRACTION95
3.9991-5.03720.26391600.23542672X-RAY DIFFRACTION96
5.0372-43.12890.28491290.24972771X-RAY DIFFRACTION95

+
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://pdbjlc1.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