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- PDB-4ejx: Structure of ceruloplasmin-myeloperoxidase complex -

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Basic information

Entry
Database: PDB / ID: 4ejx
TitleStructure of ceruloplasmin-myeloperoxidase complex
Components
  • (Myeloperoxidase ...) x 2
  • Ceruloplasmin
KeywordsOXIDOREDUCTASE / cupredoxin domains / glycoproteins / protein-protein interaction
Function / homology
Function and homology information


glutathione-dependent peroxiredoxin / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / phospholipid-hydroperoxide glutathione peroxidase activity / Metal ion SLC transporters / myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor ...glutathione-dependent peroxiredoxin / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / phospholipid-hydroperoxide glutathione peroxidase activity / Metal ion SLC transporters / myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor / glutathione peroxidase / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / copper ion transport / respiratory burst involved in defense response / glutathione peroxidase activity / low-density lipoprotein particle remodeling / response to food / azurophil granule / ferroxidase / intracellular copper ion homeostasis / ferroxidase activity / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / Iron uptake and transport / Post-translational protein phosphorylation / defense response / peroxidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / azurophil granule lumen / signaling receptor activity / heparin binding / iron ion transport / protein-folding chaperone binding / intracellular iron ion homeostasis / response to oxidative stress / response to lipopolysaccharide / oxidoreductase activity / lysosome / blood microparticle / defense response to bacterium / copper ion binding / endoplasmic reticulum lumen / lysosomal membrane / intracellular membrane-bounded organelle / chromatin binding / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding / plasma membrane
Similarity search - Function
: / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Multicopper oxidase, C-terminal ...: / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Peroxidases proximal heme-ligand signature. / Multicopper oxidase, N-terminal / Multicopper oxidase / Haem peroxidase superfamily / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / Ceruloplasmin / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.69 Å
AuthorsSamygina, V.R. / Sokolov, A.V. / Bourenkov, G. / Vasilyev, V.B. / Bartunik, H.
CitationJournal: Plos One / Year: 2013
Title: Ceruloplasmin: macromolecular assemblies with iron-containing acute phase proteins.
Authors: Samygina, V.R. / Sokolov, A.V. / Bourenkov, G. / Petoukhov, M.V. / Pulina, M.O. / Zakharova, E.T. / Vasilyev, V.B. / Bartunik, H. / Svergun, D.I.
History
DepositionApr 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ceruloplasmin
B: Myeloperoxidase light chain
D: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,07316
Polymers188,5413
Non-polymers2,53313
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17540 Å2
ΔGint-119 kcal/mol
Surface area57850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.249, 106.249, 834.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ceruloplasmin / Ferroxidase


Mass: 122340.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00450, ferroxidase

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Myeloperoxidase ... , 2 types, 2 molecules BD

#2: Protein Myeloperoxidase light chain


Mass: 12894.465 Da / Num. of mol.: 1 / Fragment: UNP residues 165-278 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase
#3: Protein Myeloperoxidase heavy chain


Mass: 53305.266 Da / Num. of mol.: 1 / Fragment: UNP residues 279-745 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase

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Sugars , 2 types, 5 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 8 molecules

#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40% MPD, 0.2 M potassium fluoride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.98 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 16, 2006
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.69→138.68 Å / Num. all: 16100 / Num. obs: 15959 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.234
Reflection shellResolution: 4.69→4.8 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1KCW AND 1CXP

1kcw

1cxp


Resolution: 4.69→15 Å / Cor.coef. Fo:Fc: 0.737 / Cor.coef. Fo:Fc free: 0.685 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 1.67 / ESU R Free: 1.83 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.40063 752 5 %RANDOM
Rwork0.36566 ---
all0.36733 15953 --
obs0.36733 14416 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å21.64 Å20 Å2
2--3.29 Å20 Å2
3----4.93 Å2
Refinement stepCycle: LAST / Resolution: 4.69→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12948 0 145 0 13093
LS refinement shellResolution: 4.69→4.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 52 -
Rwork0.367 963 -
obs--98.45 %

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