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- PDB-5xof: Crystal structure of human paired immunoglobulin-like type 2 rece... -

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Basic information

Entry
Database: PDB / ID: 5xof
TitleCrystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I
Components
  • Paired immunoglobulin-like type 2 receptor alpha
  • Peptide from Nitric oxide synthase, endothelial
KeywordsIMMUNE SYSTEM / membrane protein / immune receptor / viral entry inhibitor / glycopeptide
Function / homology
Function and homology information


regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / positive regulation of guanylate cyclase activity / Nitric oxide stimulates guanylate cyclase / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / aortic valve morphogenesis / arginine binding / endocardial cushion morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / cadmium ion binding / negative regulation of potassium ion transport / negative regulation of platelet activation / negative regulation of calcium ion transport / actin monomer binding / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / blood vessel remodeling / MHC class I protein binding / nitric-oxide synthase activity / eNOS activation / nitric oxide mediated signal transduction / arginine catabolic process / homeostasis of number of cells within a tissue / regulation of sodium ion transport / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / nitric oxide biosynthetic process / negative regulation of blood pressure / blood vessel diameter maintenance / removal of superoxide radicals / mitochondrion organization / response to hormone / cell redox homeostasis / VEGFR2 mediated vascular permeability / caveola / negative regulation of smooth muscle cell proliferation / establishment of localization in cell / lung development / potassium ion transport / regulation of blood pressure / vasodilation / endocytic vesicle membrane / positive regulation of angiogenesis / calcium ion transport / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to heat / scaffold protein binding / angiogenesis / in utero embryonic development / response to lipopolysaccharide / Extra-nuclear estrogen signaling / cytoskeleton / calmodulin binding / negative regulation of cell population proliferation / Golgi membrane / heme binding / positive regulation of gene expression / Golgi apparatus / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily ...Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nitric oxide synthase 3 / Paired immunoglobulin-like type 2 receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.963 Å
AuthorsFurukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. ...Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, H. / Anada, M. / Ose, T. / Hashimoto, S. / Maenaka, K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and thermodynamic analyses reveal critical features of glycopeptide recognition by the human PILR alpha immune cell receptor.
Authors: Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, S. / ...Authors: Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, S. / Anada, M. / Ose, T. / Hashimoto, S. / Maenaka, K.
History
DepositionMay 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Paired immunoglobulin-like type 2 receptor alpha
B: Paired immunoglobulin-like type 2 receptor alpha
C: Paired immunoglobulin-like type 2 receptor alpha
D: Paired immunoglobulin-like type 2 receptor alpha
O: Peptide from Nitric oxide synthase, endothelial
P: Peptide from Nitric oxide synthase, endothelial
Q: Peptide from Nitric oxide synthase, endothelial
R: Peptide from Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,35912
Polymers58,3098
Non-polymers2,0504
Water4,648258
1
A: Paired immunoglobulin-like type 2 receptor alpha
O: Peptide from Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0903
Polymers14,5772
Non-polymers5121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint1 kcal/mol
Surface area6950 Å2
MethodPISA
2
B: Paired immunoglobulin-like type 2 receptor alpha
P: Peptide from Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0903
Polymers14,5772
Non-polymers5121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint1 kcal/mol
Surface area7080 Å2
MethodPISA
3
C: Paired immunoglobulin-like type 2 receptor alpha
Q: Peptide from Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0903
Polymers14,5772
Non-polymers5121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint1 kcal/mol
Surface area7060 Å2
MethodPISA
4
D: Paired immunoglobulin-like type 2 receptor alpha
R: Peptide from Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0903
Polymers14,5772
Non-polymers5121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint1 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.660, 63.009, 78.599
Angle α, β, γ (deg.)90.00, 108.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Paired immunoglobulin-like type 2 receptor alpha / Cell surface receptor FDF03 / Inhibitory receptor PILR-alpha


Mass: 13967.697 Da / Num. of mol.: 4 / Fragment: UNP residues 32-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PILRA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKJ1
#2: Protein/peptide
Peptide from Nitric oxide synthase, endothelial /


Mass: 609.671 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P29474, nitric-oxide synthase (NADPH)
#3: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 512.463 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGlcpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GlcpNAc]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 36271 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 20.9
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1754 / % possible all: 96.35

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WV0

3wv0


Resolution: 1.963→40.05 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2692 1670 -
Rwork0.2145 --
obs-32742 99.4 %
Refinement stepCycle: LAST / Resolution: 1.963→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 136 258 4510
LS refinement shellResolution: 1.963→2.033 Å
RfactorNum. reflection
Rfree0.3341 -
Rwork0.2671 -
obs-1670

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