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- PDB-5w1f: Crystal structure of Ni(II)- and Ca(II)-bound human calprotectin -

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Basic information

Entry
Database: PDB / ID: 5w1f
TitleCrystal structure of Ni(II)- and Ca(II)-bound human calprotectin
Components(Protein S100- ...) x 2
KeywordsMETAL BINDING PROTEIN / calprotectin / innate immunity / metal sequestration / nickel / calcium / S100 protein
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 / leukocyte migration involved in inflammatory response / peptide secretion / Regulation of TLR by endogenous ligand / RAGE receptor binding / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / calcium-dependent protein binding / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of cell growth / microtubule binding / secretory granule lumen / collagen-containing extracellular matrix / response to ethanol / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
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: 2.6 Å
AuthorsNakashige, T.G. / Drennan, C.L. / Nolan, E.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)P30- ES002109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)HHSN272200700055C United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Nickel Sequestration by the Host-Defense Protein Human Calprotectin.
Authors: Nakashige, T.G. / Zygiel, E.M. / Drennan, C.L. / Nolan, E.M.
History
DepositionJun 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Data collection / Database references / Category: citation / diffrn_radiation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
G: Protein S100-A8
H: Protein S100-A9
E: Protein S100-A8
F: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,23330
Polymers96,3428
Non-polymers89122
Water2,666148
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)48,61615
Polymers48,1714
Non-polymers44511
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-211 kcal/mol
Surface area16890 Å2
MethodPISA
2
G: Protein S100-A8
H: Protein S100-A9
E: Protein S100-A8
F: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,61615
Polymers48,1714
Non-polymers44511
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-208 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.020, 77.611, 222.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein S100- ... , 2 types, 8 molecules ACGEBDHF

#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 / Mutation: C3S
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

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Non-polymers , 4 types, 170 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NiCl2, HEPES, NaCl, Li2SO4, Tris, PEG 3350, CaCl2

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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: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→45.24 Å / Num. obs: 29660 / % possible obs: 94.5 % / Redundancy: 5.5 % / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.2 % / Num. unique obs: 2247 / % possible all: 72.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XJK

4xjk


Resolution: 2.6→45.24 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2617 989 3.35 %
Rwork0.2237 --
obs0.225 29506 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6382 0 22 148 6552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0016577
X-RAY DIFFRACTIONf_angle_d0.3478834
X-RAY DIFFRACTIONf_dihedral_angle_d12.5543984
X-RAY DIFFRACTIONf_chiral_restr0.033945
X-RAY DIFFRACTIONf_plane_restr0.0021139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5947-2.73150.31111110.26553195X-RAY DIFFRACTION75
2.7315-2.90260.31481350.27573807X-RAY DIFFRACTION89
2.9026-3.12670.35111400.27854172X-RAY DIFFRACTION97
3.1267-3.44120.30621480.26434286X-RAY DIFFRACTION100
3.4412-3.93890.21811510.20654321X-RAY DIFFRACTION100
3.9389-4.96170.24541490.18394353X-RAY DIFFRACTION99
4.9617-45.95870.22121550.20144383X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -3.5566 Å / Origin y: 12.8261 Å / Origin z: -28.4005 Å
111213212223313233
T0.4103 Å2-0.0302 Å20.0363 Å2-0.1572 Å2-0.0003 Å2--0.1832 Å2
L0.4237 °2-0.1902 °20.0193 °2-0.7978 °2-0.0662 °2--0.6477 °2
S-0.0428 Å °-0.0496 Å °0.0279 Å °0.2639 Å °0.0203 Å °0.0126 Å °-0.0064 Å °0.0116 Å °0.0108 Å °
Refinement TLS groupSelection details: all

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