[English] 日本語
Yorodumi
- PDB-2lp3: Solution structure of S100A1 Ca2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lp3
TitleSolution structure of S100A1 Ca2+
ComponentsProtein S100-A1
KeywordsMETAL BINDING PROTEIN / calcium binding protein / S100 protein family
Function / homology
Function and homology information


Regulation of TLR by endogenous ligand / RAGE receptor binding / MyD88 deficiency (TLR2/4) / S100 protein binding / regulation of heart contraction / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of sprouting angiogenesis / substantia nigra development / sarcoplasmic reticulum ...Regulation of TLR by endogenous ligand / RAGE receptor binding / MyD88 deficiency (TLR2/4) / S100 protein binding / regulation of heart contraction / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of sprouting angiogenesis / substantia nigra development / sarcoplasmic reticulum / positive regulation of nitric-oxide synthase activity / calcium-dependent protein binding / ER-Phagosome pathway / ATPase binding / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein S100-A1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...Protein S100-A1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBudzinska, M. / Ruszczynska-Bartnik, K. / Belczyk-Ciesielska, A. / Bierzynski, A. / Ejchart, A.
CitationJournal: Biochemistry / Year: 2013
Title: Impact of calcium binding and thionylation of S100A1 protein on its nuclear magnetic resonance-derived structure and backbone dynamics.
Authors: Nowakowski, M. / Ruszczynska-Bartnik, K. / Budzinska, M. / Jaremko, L. / Jaremko, M. / Zdanowski, K. / Bierzynski, A. / Ejchart, A.
History
DepositionJan 31, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein S100-A1
B: Protein S100-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0116
Polymers20,8512
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 210structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein S100-A1 / / S-100 protein alpha chain / S-100 protein subunit alpha / S100 calcium-binding protein A1


Mass: 10425.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A1, S100A / Production host: Escherichia coli (E. coli) / References: UniProt: P23297
#2: 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
1212D 1H-15N HSQC NH2 only
2322D 1H-13C HSQC aliphatic
2422D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D HN(CO)CA
21123D 1H-13C NOESY aliphatic
21223D (H)CCH-TOCSY
21323D 1H-13C NOESY aromatic
11413D 1H-15N NOESY
11532D 1H-15N heteronuclear NOE
11632D 1H-15N heteronuclear NOE
11732D 1H-15N heteronuclear NOE
11832D 1H-15N T1 relaxation
11932D 1H-15N T1 relaxation
12032D 1H-15N T1 relaxation
12132D 1H-15N T2 relaxation
12232D 1H-15N T2 relaxation
12332D 1H-15N T2 relaxation

-
Sample preparation

Details
Solution-IDContentsSolvent system
110 % D2O, 90 % H2O, 50 mM sodium chloride, 10 mM CALCIUM ION, 0.8 mM [U-99% 13C; U-99% 15N] S100A1, 50 mM TRIS-d11, 90% H2O/10% D2O90% H2O/10% D2O
2100 % D2O, 50 mM sodium chloride, 10 mM CALCIUM ION, 0.8 mM [U-99% 13C; U-99% 15N] S100A1, 50 mM TRIS-d11, 100% D2O100% D2O
310 % D2O, 90 % H2O, 50 mM sodium chloride, 10 mM CALCIUM ION, 0.8 mM [U-99% 15N] S100A1, 50 mM TRIS-d11, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 %D2O-11
90 %H2O-21
50 mMsodium chloride-31
10 mMCALCIUM ION-41
0.8 mMS100A1-5[U-99% 13C; U-99% 15N]1
50 mMTRIS-d11-61
100 %D2O-72
50 mMsodium chloride-82
10 mMCALCIUM ION-92
0.8 mMS100A1-10[U-99% 13C; U-99% 15N]2
50 mMTRIS-d11-112
10 %D2O-123
90 %H2O-133
50 mMsodium chloride-143
10 mMCALCIUM ION-153
0.8 mMS100A1-16[U-99% 15N]3
50 mMTRIS-d11-173
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 7.2 ambient 310 K
250 6.8 ambient 310 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA4001
Varian UnityPlusVarianUNITYPLUS5002
Varian Varian NMR SystemVarianVarian NMR System7003
Varian Varian NMR SystemVarianVarian NMR System8004

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichconstraints assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 210 / Conformers submitted total number: 20

+
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