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- PDB-2l0p: Solution structure of human apo-S100A1 protein by NMR spectroscopy -

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Basic information

Entry
Database: PDB / ID: 2l0p
TitleSolution structure of human apo-S100A1 protein by NMR spectroscopy
ComponentsS100 calcium binding protein A1
KeywordsCalcium binding protein / S100A1 / EF-hand / S100 family
Function / homology
Function and homology information


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 ...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 / ATPase binding / ER-Phagosome pathway / intracellular signal transduction / calcium ion binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / 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
Protein S100-A1 / Protein S100
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsNowakowski, M. / Jaremko, L. / Jaremko, M. / Bierzynski, A. / Zhukov, I. / Ejchart, A.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Solution NMR structure and dynamics of human apo-S100A1 protein.
Authors: Nowakowski, M. / Jaremko, L. / Jaremko, M. / Zhukov, I. / Belczyk, A. / Bierzynski, A. / Ejchart, A.
History
DepositionJul 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2017Group: Other
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S100 calcium binding protein A1
B: S100 calcium binding protein A1


Theoretical massNumber of molelcules
Total (without water)21,1142
Polymers21,1142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2702.3 Å2
ΔGint-31.6 kcal/mol
Surface area10825.5 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 130structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein S100 calcium binding protein A1 / S100 calcium binding protein A1 / isoform CRA_a


Mass: 10556.783 Da / Num. of mol.: 2 / Fragment: UNP residues 54-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A1, RP1-178F15.1-003, hCG_15470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T7Y6, UniProt: P23297*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D (HCA)CO(CA)NH
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D C(CO)NH
1913D HBHA(CO)NH
11013D (H)CCH-TOCSY
11122D 1H-15N HSQC (T1)
11222D 1H-15N HSQC (T2)
11322D 1H-15N HSQC based NOE
11412D 1H-13C HSQC aromatic
11512D 1H-13C HSQC aliphatic
11633D 1H-13C HSQC(aromatic)-NOESY
11733D 1H-13C HSQC(aliphatic)-NOESY
11813D 1H-15N HSQC-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] S100A1, 0.1 mM sodium azide, 50 mM TRIS-d11, 1 mM EDTA, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 15N] S100A1, 0.1 mM sodium azide, 50 mM TRIS(d11), 1 mM EDTA-13, 15 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-98% 13C; U-98% 15N] S100A1, 1 mM [U-98% 13C; U-98% 15N] S100A1, 0.1 mM sodium azide, 50 mM TRIS-d11, 1 mM EDTA, 50 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMS100A1(aa)_monomer-1[U-98% 13C; U-98% 15N]1
1 mMS100A1(aa)_monomer_without_MET-2[U-98% 13C; U-98% 15N]1
0.1 mMsodium azide-31
50 mMTRIS-d11-41
1 mMEDTA-51
50 mMsodium chloride-61
90 %H2O-71
10 %D2O-81
1 mMS100A1(aa)_monomer-9[U-98% 15N]2
1 mMS100A1(aa)_monomer_without_MET-10[U-98% 15N]2
0.1 mMsodium azide-112
50 mMTRIS(d11)-122
1 mMEDTA-132
15 mMsodium chloride-142
90 %H2O-152
10 %D2O-162
1 mMS100A1(aa)_monomer-17[U-98% 13C; U-98% 15N]3
1 mMS100A1(aa)_monomer_without_MET-18[U-98% 13C; U-98% 15N]3
0.1 mMsodium azide-193
50 mMTRIS-d11-203
1 mMEDTA-213
50 mMsodium chloride-223
Sample conditionspH: 6.8 / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA4001
Varian UnityPlusVarianUNITYPLUS5002
Varian Varian NMR SystemsVarianVarian NMR Systems7003
Varian Varian NMR SystemsVarianVarian NMR Systems8004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3.112Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing heteronuclear nmr spectra
SparkyGoddardanalysis of 3d heteronuclear spectra
X-PLOR NIH2.2.5Schwieters, Kuszewski, Tjandra and Clorestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: standrad sa.inp xplor protocol
NMR constraintsNOE constraints total: 3184 / NOE intraresidue total count: 566 / NOE long range total count: 544 / NOE medium range total count: 868 / NOE sequential total count: 942 / Hydrogen bond constraints total count: 186 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 130 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å / Torsion angle constraint violation method: xplor NIH
NMR ensemble rmsDistance rms dev: 0.0055 Å / Distance rms dev error: 0.0003 Å

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