[English] 日本語
Yorodumi
- PDB-3d5o: Structural recognition and functional activation of FcrR by innat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d5o
TitleStructural recognition and functional activation of FcrR by innate pentraxins
Components
  • Low affinity immunoglobulin gamma Fc region receptor II-a
  • Serum amyloid P-component
KeywordsIMMUNE SYSTEM / complex structure / SAP / Fc RIIa / Fc receptor activation / pentraxins / Amyloid / Glycoprotein / Lectin / Metal-binding / Secreted / Cell membrane / IgG-binding protein / Immunoglobulin domain / Membrane / Phosphoprotein / Receptor / Transmembrane
Function / homology
Function and homology information


negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / IgG receptor activity / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / negative regulation of viral entry into host cell ...negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / IgG receptor activity / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / negative regulation of viral entry into host cell / virion binding / antibody-dependent cellular cytotoxicity / IgG binding / negative regulation of acute inflammatory response / FCGR activation / chaperone-mediated protein complex assembly / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / acute-phase response / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production / unfolded protein binding / protein folding / carbohydrate binding / collagen-containing extracellular matrix / cell surface receptor signaling pathway / blood microparticle / Amyloid fiber formation / external side of plasma membrane / innate immune response / calcium ion binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Immunoglobulin domain / Jelly Rolls - #200 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Immunoglobulin domain / Jelly Rolls - #200 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serum amyloid P-component / Low affinity immunoglobulin gamma Fc region receptor II-a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLu, J. / Marnell, L.L. / Marjon, K.D. / Mold, C. / Du Clos, T.W. / Sun, P.D.
CitationJournal: Nature / Year: 2008
Title: Structural recognition and functional activation of FcgammaR by innate pentraxins.
Authors: Lu, J. / Marnell, L.L. / Marjon, K.D. / Mold, C. / Du Clos, T.W. / Sun, P.D.
History
DepositionMay 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serum amyloid P-component
B: Serum amyloid P-component
C: Serum amyloid P-component
D: Serum amyloid P-component
E: Serum amyloid P-component
F: Low affinity immunoglobulin gamma Fc region receptor II-a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,22228
Polymers136,4876
Non-polymers2,73522
Water55831
1
F: Low affinity immunoglobulin gamma Fc region receptor II-a
hetero molecules

D: Serum amyloid P-component
hetero molecules

A: Serum amyloid P-component
B: Serum amyloid P-component
C: Serum amyloid P-component
E: Serum amyloid P-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,22228
Polymers136,4876
Non-polymers2,73522
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-243 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.197, 143.477, 161.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 6 molecules ABCDEF

#1: Protein
Serum amyloid P-component / SAP / 9.5S alpha-1-glycoprotein / Serum amyloid P-component(1-203)


Mass: 23282.455 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02743
#2: Protein Low affinity immunoglobulin gamma Fc region receptor II-a / IgG Fc receptor II-a / Fc-gamma RII-a / Fc-gamma-RIIa / FcRII-a / CDw32


Mass: 20074.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P12318

-
Sugars , 1 types, 5 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / 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

-
Non-polymers , 3 types, 48 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsAUTHORS STATE THAT CHAIN F IS THE ECTODOMAIN OF FC GAMMA RECEPTOR IIA, WHICH HAS A POLYMORPHISM AT ...AUTHORS STATE THAT CHAIN F IS THE ECTODOMAIN OF FC GAMMA RECEPTOR IIA, WHICH HAS A POLYMORPHISM AT THIS POSITION, E.G. R131 IN THIS STRUCTURE AND H167 IN SEQUENCE DATABASE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0 M NH4SO4, 5% iso-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 37599 / Num. obs: 36697 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 68.7 Å2 / Rsym value: 0.091
Reflection shellResolution: 2.8→2.87 Å / % possible all: 82.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 1401 Random
Rwork0.207 --
all0.248 37585 -
obs0.221 35208 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9468 0 156 31 9655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.3676 102 -
Rwork0.2999 --
obs-2646 0.748 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more