[English] 日本語
Yorodumi
- PDB-1etz: THE THREE-DIMENSIONAL STRUCTURE OF AN ANTI-SWEETENER FAB, NC10.14... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1etz
TitleTHE THREE-DIMENSIONAL STRUCTURE OF AN ANTI-SWEETENER FAB, NC10.14, SHOWS THE EXTENT OF STRUCTURAL DIVERSITY IN ANTIGEN RECOGNITION BY IMMUNOGLOBULINS
Components
  • FAB NC10.14 - HEAVY CHAIN
  • FAB NC10.14 - LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Anti-sweetener Fab / Antigen-antibody / Complex / Receptor Mimicry / Antigen Recognition
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-GAS / Anti-human Langerin 2G3 lambda chain / Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsGuddat, L.W. / Shan, L. / Broomell, C. / Ramsland, P.A. / Fan, Z. / Anchin, J.M. / Linthicum, D.S. / Edmundson, A.B.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The three-dimensional structure of a complex of a murine Fab (NC10. 14) with a potent sweetener (NC174): an illustration of structural diversity in antigen recognition by immunoglobulins.
Authors: Guddat, L.W. / Shan, L. / Broomell, C. / Ramsland, P.A. / Fan, Z. / Anchin, J.M. / Linthicum, D.S. / Edmundson, A.B.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Local and Transmitted Conformational Changes on Complexation of an Anti-sweetener Fab
Authors: Guddat, L.W. / Shan, L. / Anchin, J.M. / Linthicum, D.S. / Edmundson, A.B.
History
DepositionApr 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: FAB NC10.14 - LIGHT CHAIN
H: FAB NC10.14 - HEAVY CHAIN
A: FAB NC10.14 - LIGHT CHAIN
B: FAB NC10.14 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0376
Polymers95,2684
Non-polymers7692
Water1,38777
1
L: FAB NC10.14 - LIGHT CHAIN
H: FAB NC10.14 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0183
Polymers47,6342
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-33 kcal/mol
Surface area19520 Å2
MethodPISA
2
A: FAB NC10.14 - LIGHT CHAIN
B: FAB NC10.14 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0183
Polymers47,6342
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-27 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.9, 66.3, 75.2
Angle α, β, γ (deg.)106.7, 107.6, 97.3
Int Tables number1
Space group name H-MP1
DetailsA Fab is formed by Light Chain and Heavy Chain. There are two Fab with non-crystallographic symmetry in a unit cell.

-
Components

#1: Antibody FAB NC10.14 - LIGHT CHAIN


Mass: 23165.719 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: ASCITES / References: UniProt: G0YP42*PLUS
#2: Antibody FAB NC10.14 - HEAVY CHAIN


Mass: 24468.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: ASCITES / References: UniProt: P01867*PLUS
#3: Chemical ChemComp-GAS / N-(P-CYANOPHENYL)-N'-DIPHENYLMETHYL-GUANIDINE-ACETIC ACID


Mass: 384.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: NC10.14 Fab with excess molarity NC174, 10%(w/v) PEG 8000, 0.05M NaCl, 0.05%(w/v) Sodium Azide, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal
*PLUS
Density % sol: 50.2 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 mg/mlprotein11
20.05 M11NaCl
30.05 %sodium azide11
433 %(w/w)PEG800011

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 9, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→10 Å / Num. all: 26144 / Num. obs: 26144 / % possible obs: 90.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.2
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.125 / Num. unique all: 2420 / % possible all: 66.8
Reflection
*PLUS
Num. measured all: 101821
Reflection shell
*PLUS
% possible obs: 66.8 %

-
Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
MERLOTphasing
X-PLOR3.851refinement
RefinementResolution: 2.6→10 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2638 -Random
Rwork0.198 ---
all0.211 26144 --
obs0.211 26144 10 %-
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 58 77 6833
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg28
X-RAY DIFFRACTIONx_torsion_impr_deg1.3
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

+
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://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