[English] 日本語
Yorodumi
- PDB-2lgf: Solution structure of Ca2+/calmodulin complexed with a peptide re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lgf
TitleSolution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of L-selectin
Components
  • Calmodulin
  • L-selectin
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


glycosphingolipid binding / sialic acid binding / oligosaccharide binding / : / : / : / : / : / positive regulation of protein autophosphorylation / calcium-dependent cell-cell adhesion ...glycosphingolipid binding / sialic acid binding / oligosaccharide binding / : / : / : / : / : / positive regulation of protein autophosphorylation / calcium-dependent cell-cell adhesion / negative regulation of peptidyl-threonine phosphorylation / leukocyte tethering or rolling / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / Cam-PDE 1 activation / heterophilic cell-cell adhesion / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / 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 / response to corticosterone / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / leukocyte cell-cell adhesion / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / 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 / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / positive regulation of protein serine/threonine kinase activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / activation of adenylate cyclase activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / Protein methylation / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / enzyme regulator activity / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / response to cytokine / voltage-gated potassium channel complex / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / secretory granule membrane / response to amphetamine / calyx of Held / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity
Similarity search - Function
L-selectin / Selectin superfamily / Selectin, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. ...L-selectin / Selectin superfamily / Selectin, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / EGF-like domain / C-type lectin fold / : / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / 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
Similarity search - Domain/homology
Calmodulin-1 / L-selectin / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsGifford, J.L. / Ishida, H. / Vogel, H.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Insights into Calmodulin-regulated L-selectin Ectodomain Shedding.
Authors: Gifford, J.L. / Ishida, H. / Vogel, H.J.
History
DepositionJul 25, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Apr 27, 2016Group: Structure summary
Revision 1.4Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin
B: L-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6456
Polymers18,4852
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Calmodulin / CaM


Mass: 16650.273 Da / Num. of mol.: 1 / Fragment: sequence database residues 4-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide L-selectin / CD62 antigen-like family member L / Leukocyte adhesion molecule 1 / LAM-1 / Leukocyte surface ...CD62 antigen-like family member L / Leukocyte adhesion molecule 1 / LAM-1 / Leukocyte surface antigen Leu-8 / Leukocyte-endothelial cell adhesion molecule 1 / LECAM1 / Lymph node homing receptor / TQ1 / gp90-MEL


Mass: 1834.344 Da / Num. of mol.: 1 / Fragment: sequence database residues 349-363 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P14151
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1322D 1H-1H COSY
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D H(CCO)NH
11033D 1H-13C NOESY
11113D HN(CA)CO
11212D HMBC
11313D LRCH
1142F2-filtered 2D 1H-1H NOESY
21542D 1H-15N IPAP HSQC
21652D 1H-15N IPAP HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O90% H2O/10% D2O
20.5-0.8 mM [U-2H; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O90% H2O/10% D2O
30.5-0.8 mM [1H/13C-methyl Met; U-2H; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 100% D2O100% D2O
40.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 300 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O90% H2O/10% D2O
50.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 300 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 16 w/v Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-13C; U-15N]0.5-0.81
mMentity_2-20.5-0.81
4 mMCALCIUM ION-31
0.5 mMDSS-41
100 mMpotassium chloride-51
0.03 %sodium azide-61
20 mMBis-Tris-71
mMentity_1-8[U-2H; U-15N]0.5-0.82
mMentity_2-90.5-0.82
4 mMCALCIUM ION-102
0.5 mMDSS-112
100 mMpotassium chloride-122
0.03 %sodium azide-132
20 mMBis-Tris-142
mMentity_1-15[1H/13C-methyl Met; U-2H; U-15N]0.5-0.83
mMentity_2-160.5-0.83
4 mMCALCIUM ION-173
0.5 mMDSS-183
100 mMpotassium chloride-193
0.03 %sodium azide-203
20 mMBis-Tris-213
mMentity_1-22[U-13C; U-15N]0.5-0.84
mMentity_2-230.5-0.84
4 mMCALCIUM ION-244
0.5 mMDSS-254
300 mMpotassium chloride-264
0.03 %sodium azide-274
20 mMBis-Tris-284
mMentity_1-29[U-13C; U-15N]0.5-0.85
mMentity_2-300.5-0.85
4 mMCALCIUM ION-315
0.5 mMDSS-325
300 mMpotassium chloride-335
0.03 %sodium azide-345
20 mMBis-Tris-355
16 w/vPf1 phage-365
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.16.8ambient 303 K
20.36.8ambient 303 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
XwinNMRBruker Biospincollection
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 1

+
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