[English] 日本語
Yorodumi
- PDB-1xed: Crystal Structure of a Ligand-Binding Domain of the Human Polymer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xed
TitleCrystal Structure of a Ligand-Binding Domain of the Human Polymeric Ig Receptor, pIgR
ComponentsPolymeric-immunoglobulin receptor
KeywordsIMMUNE SYSTEM / Ig-like fold
Function / homology
Function and homology information


polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / azurophil granule membrane / receptor clustering / epidermal growth factor receptor signaling pathway / receptor complex ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / azurophil granule membrane / receptor clustering / epidermal growth factor receptor signaling pathway / receptor complex / Neutrophil degranulation / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / 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 V-Type / 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
Polymeric immunoglobulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsHamburger, A.E. / West Jr., A.P. / Bjorkman, P.J.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of a Polymeric Immunoglobulin Binding Fragment of the Human Polymeric Immunoglobulin Receptor
Authors: Hamburger, A.E. / West Jr., A.P. / Bjorkman, P.J.
History
DepositionSep 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymeric-immunoglobulin receptor
B: Polymeric-immunoglobulin receptor
C: Polymeric-immunoglobulin receptor
D: Polymeric-immunoglobulin receptor
E: Polymeric-immunoglobulin receptor
F: Polymeric-immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7998
Polymers77,7506
Non-polymers492
Water2,846158
1
A: Polymeric-immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9832
Polymers12,9581
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymeric-immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9832
Polymers12,9581
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Polymeric-immunoglobulin receptor


Theoretical massNumber of molelcules
Total (without water)12,9581
Polymers12,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Polymeric-immunoglobulin receptor


Theoretical massNumber of molelcules
Total (without water)12,9581
Polymers12,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Polymeric-immunoglobulin receptor


Theoretical massNumber of molelcules
Total (without water)12,9581
Polymers12,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Polymeric-immunoglobulin receptor


Theoretical massNumber of molelcules
Total (without water)12,9581
Polymers12,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
A: Polymeric-immunoglobulin receptor
B: Polymeric-immunoglobulin receptor
C: Polymeric-immunoglobulin receptor
D: Polymeric-immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8826
Polymers51,8334
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-20 kcal/mol
Surface area19130 Å2
MethodPISA
8
B: Polymeric-immunoglobulin receptor
D: Polymeric-immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9413
Polymers25,9172
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-7 kcal/mol
Surface area10750 Å2
MethodPISA
9
A: Polymeric-immunoglobulin receptor
C: Polymeric-immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9413
Polymers25,9172
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-6 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.996, 157.195, 53.860
Angle α, β, γ (deg.)90.00, 112.94, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a monomer

-
Components

#1: Protein
Polymeric-immunoglobulin receptor / Poly-Ig receptor / PIGR / Ig-like V-type 1 Domain


Mass: 12958.354 Da / Num. of mol.: 6 / Fragment: N-Terminal Domain I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIGR / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(de3) / References: UniProt: P01833
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / pH: 6.5
Details: PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.078
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 49755 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.462 / % possible all: 99.1

-
Phasing

PhasingMethod: MIR

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
SCALEPACKdata scaling
PDB_EXTRACT1.401data extraction
DENZOdata reduction
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: REFINED USING CNS HEMIHEDRAL TWINNING INPUT FILES TWIN FRACTION = 37.3% TWIN OPERATOR = H, K,L -> H, -K, -H-L
RfactorNum. reflectionSelection details
Rfree0.244 2476 THIN SHELL
Rwork0.183 --
obs0.183 49593 -
all-49755 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 2 158 5148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
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