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- PDB-2lls: solution structure of human apo-S100A1 C85M -

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Basic information

Entry
Database: PDB / ID: 2lls
Titlesolution structure of human apo-S100A1 C85M
ComponentsProtein S100-A1
KeywordsMETAL BINDING PROTEIN / S100 protein family / calcium binding protein
Function / homology
Function and homology information


RAGE receptor binding / Regulation of TLR by endogenous ligand / MyD88 deficiency (TLR2/4) / S100 protein binding / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of heart contraction / positive regulation of sprouting angiogenesis / substantia nigra development / positive regulation of nitric-oxide synthase activity ...RAGE receptor binding / Regulation of TLR by endogenous ligand / MyD88 deficiency (TLR2/4) / S100 protein binding / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of heart contraction / positive regulation of sprouting angiogenesis / substantia nigra development / positive regulation of nitric-oxide synthase activity / sarcoplasmic reticulum / 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 / cytoplasm / cytosol
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 detailsclosest to the average, model 19
AuthorsBudzinska, M. / Jaremko, L. / Jaremko, M. / Zdanowski, K. / Zhukov, I. / Bierzynski, A. / Ejchart, A.
CitationJournal: To be Published
Title: Chemical Shift Assignments and solution structure of human apo-S100A1 C85M mutant
Authors: Budzinska, M. / Jaremko, L. / Jaremko, M. / Zdanowski, K. / Zhukov, I. / Bierzynski, A. / Ejchart, A.
History
DepositionNov 17, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,9072
Polymers20,9072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 10453.641 Da / Num. of mol.: 2 / Mutation: C85M
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

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Experimental details

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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 HN(CO)CA
11013D HBHA(CO)NH
21123D (H)CCH-TOCSY
11213D 1H-15N NOESY
21323D 1H-13C NOESY aliphatic
21423D 1H-13C NOESY aromatic
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

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM TRIS-d11, 10 % D2O, 50 mM sodium chloride, 1 mM [U-99% 13C; U-99% 15N] S100A1C85M, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
250 mM TRIS-d11, 50 mM sodium chloride, 1 mM [U-99% 13C; U-99% 15N] S100A1C85M, 100 % D2O, 100% D2O100% D2O
350 mM TRIS-d11, 10 % D2O, 50 mM sodium chloride, 1 mM [U-99% 15N] S100A1C85M, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMTRIS-d11-11
10 %D2O-21
50 mMsodium chloride-31
1 mMS100A1C85M-4[U-99% 13C; U-99% 15N]1
90 %H2O-51
50 mMTRIS-d11-62
50 mMsodium chloride-72
1 mMS100A1C85M-8[U-99% 13C; U-99% 15N]2
100 %D2O-92
50 mMTRIS-d11-103
10 %D2O-113
50 mMsodium chloride-123
1 mMS100A1C85M-13[U-99% 15N]3
90 %H2O-143
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 6.8 ambient 310 K
250 7.2 ambient 310 K

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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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichconstraints assignments
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CARAKeller and Wuthrichchemical shift assignment
MARSJung, Zweckstetterautomated chemical shift assignments
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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