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- PDB-6ds2: Crystal structure of Ni(II)-bound human calprotectin -

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Basic information

Entry
Database: PDB / ID: 6ds2
TitleCrystal structure of Ni(II)-bound human calprotectin
Components
  • Protein S100-A8
  • Protein S100-A9
KeywordsMETAL BINDING PROTEIN / S100 / nickel / sodium / EF-hand
Function / homology
Function and homology information


S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / regulation of respiratory burst involved in inflammatory response / modulation of process of another organism / autocrine signaling / Toll-like receptor 4 binding ...S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / regulation of respiratory burst involved in inflammatory response / modulation of process of another organism / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Metal sequestration by antimicrobial proteins / peptide secretion / leukocyte migration involved in inflammatory response / RAGE receptor binding / Regulation of TLR by endogenous ligand / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonic acid binding / intermediate filament cytoskeleton / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / response to zinc ion / regulation of toll-like receptor signaling pathway / regulation of cytoskeleton organization / peptidyl-cysteine S-nitrosylation / antioxidant activity / RHO GTPases Activate NADPH Oxidases / endothelial cell migration / defense response to fungus / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / autophagy / positive regulation of neuron projection development / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / activation of cysteine-type endopeptidase activity involved in apoptotic process / calcium-dependent protein binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of cell growth / microtubule binding / secretory granule lumen / response to ethanol / collagen-containing extracellular matrix / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...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 / 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
NICKEL (II) ION / Protein S100-A8 / Protein S100-A9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNolan, E.M. / Drennan, C.L. / Nakashige, T.G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1352132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM126376 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118695 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM069857 United States
CitationJournal: Biochemistry / Year: 2018
Title: Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the EF-Hand Domains and His3Asp Site.
Authors: Nakashige, T.G. / Bowman, S.E.J. / Zygiel, E.M. / Drennan, C.L. / Nolan, E.M.
History
DepositionJun 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A8
B: Protein S100-A9
C: Protein S100-A8
D: Protein S100-A9
E: Protein S100-A8
F: Protein S100-A9
G: Protein S100-A8
H: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,92424
Polymers96,3428
Non-polymers58216
Water10,773598
1
A: Protein S100-A8
B: Protein S100-A9
C: Protein S100-A8
D: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,46212
Polymers48,1714
Non-polymers2918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-171 kcal/mol
Surface area17700 Å2
MethodPISA
2
E: Protein S100-A8
F: Protein S100-A9
G: Protein S100-A8
H: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,46212
Polymers48,1714
Non-polymers2918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-173 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.145, 78.082, 223.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein S100-A8 / Calgranulin-A / Calprotectin L1L subunit / Cystic fibrosis antigen / CFAG / Leukocyte L1 complex ...Calgranulin-A / Calprotectin L1L subunit / Cystic fibrosis antigen / CFAG / Leukocyte L1 complex light chain / Migration inhibitory factor-related protein 8 / p8 / S100 calcium-binding protein A8 / Urinary stone protein band A


Mass: 10837.463 Da / Num. of mol.: 4 / Mutation: C42S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A8, CAGA, CFAG, MRP8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05109
#2: Protein
Protein S100-A9 / Calgranulin-B / Calprotectin L1H subunit / Leukocyte L1 complex heavy chain / Migration inhibitory ...Calgranulin-B / Calprotectin L1H subunit / Leukocyte L1 complex heavy chain / Migration inhibitory factor-related protein 14 / p14 / S100 calcium-binding protein A9


Mass: 13247.955 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A9, CAGB, CFAG, MRP14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06702
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 200 mM Li2SO4, 100 mM Tris, 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→45.48 Å / Num. obs: 59476 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rsym value: 0.069 / Net I/σ(I): 26.1
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 5815 / CC1/2: 0.918 / % possible all: 99.7

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XJK

4xjk


Resolution: 2.1→45.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.2219 1999 3.36 %
Rwork0.1855 --
obs0.1868 59476 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6454 0 16 598 7068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036762
X-RAY DIFFRACTIONf_angle_d0.5179108
X-RAY DIFFRACTIONf_dihedral_angle_d15.4124124
X-RAY DIFFRACTIONf_chiral_restr0.037969
X-RAY DIFFRACTIONf_plane_restr0.0031173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0986-2.15110.27531380.22363979X-RAY DIFFRACTION99
2.1511-2.20920.25541420.20564060X-RAY DIFFRACTION100
2.2092-2.27420.21431400.19394038X-RAY DIFFRACTION100
2.2742-2.34770.24881420.19074069X-RAY DIFFRACTION100
2.3477-2.43160.271410.19784055X-RAY DIFFRACTION100
2.4316-2.52890.25261420.19054063X-RAY DIFFRACTION100
2.5289-2.6440.24381410.17914062X-RAY DIFFRACTION100
2.644-2.78340.22721420.18694103X-RAY DIFFRACTION100
2.7834-2.95770.24771430.19184093X-RAY DIFFRACTION100
2.9577-3.1860.22691420.20184113X-RAY DIFFRACTION100
3.186-3.50660.23681430.19184110X-RAY DIFFRACTION100
3.5066-4.01370.18871450.17074168X-RAY DIFFRACTION100
4.0137-5.05590.19511450.15684191X-RAY DIFFRACTION100
5.0559-46.12550.20731530.19524373X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 139.2973 Å / Origin y: 26.1835 Å / Origin z: 28.532 Å
111213212223313233
T0.1743 Å20.0156 Å2-0.0159 Å2-0.2251 Å2-0.0058 Å2--0.1839 Å2
L0.9372 °20.1358 °20.2972 °2-0.4246 °20.2179 °2--1.2426 °2
S-0.0521 Å °0.0029 Å °-0.085 Å °-0.0737 Å °0.0253 Å °-0.0664 Å °-0.1039 Å °0.0272 Å °0.0244 Å °
Refinement TLS groupSelection details: all

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