[English] 日本語
Yorodumi
- PDB-1i7z: ANTIBODY GNC92H2 BOUND TO LIGAND -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i7z
TitleANTIBODY GNC92H2 BOUND TO LIGAND
Components
  • CHIMERA OF IG GAMMA-1 CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
  • CHIMERA OF IG KAPPA CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
KeywordsIMMUNE SYSTEM / IgG fold / antibody / chimera
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin mediated immune response / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / 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 ...: / : / 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
COCAINE / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLarsen, N.A. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of a cocaine-binding antibody.
Authors: Larsen, N.A. / Zhou, B. / Heine, A. / Wirsching, P. / Janda, K.D. / Wilson, I.A.
History
DepositionMar 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHIMERA OF IG KAPPA CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
B: CHIMERA OF IG GAMMA-1 CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
C: CHIMERA OF IG KAPPA CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
D: CHIMERA OF IG GAMMA-1 CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6536
Polymers95,0464
Non-polymers6072
Water4,197233
1
A: CHIMERA OF IG KAPPA CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
B: CHIMERA OF IG GAMMA-1 CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8263
Polymers47,5232
Non-polymers3031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-29 kcal/mol
Surface area19590 Å2
MethodPISA
2
C: CHIMERA OF IG KAPPA CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
D: CHIMERA OF IG GAMMA-1 CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8263
Polymers47,5232
Non-polymers3031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-29 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.020, 64.070, 129.370
Angle α, β, γ (deg.)90.00, 123.06, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody CHIMERA OF IG KAPPA CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION


Mass: 23951.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE CHIMERA CONSISTS OF RESIDUES 1-108 OF MOUSE PORTION AND 109-214 OF HUMAN PORTION OF IG KAPPA CHAIN.
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01834
#2: Antibody CHIMERA OF IG GAMMA-1 CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION


Mass: 23571.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE CHIMERA CONSISTS OF RESIDUES 1-113 OF MOUSE PORTION AND 114-228 OF HUMAN PORTION OF IG GAMMA-1 CHAIN.
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01857
#3: Chemical ChemComp-COC / COCAINE


Mass: 303.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO4 / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal grow
*PLUS
pH: 4.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125-30 %(w/v)PEG800011
20.2 M11Li2SO4
30.1 Macetate11pH4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.039 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 164865 / Num. obs: 43057 / % possible obs: 98.9 % / Observed criterion σ(F): 10.6 / Observed criterion σ(I): 113.1 / Redundancy: 3.8 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.4 / % possible all: 85.7
Reflection
*PLUS
Num. measured all: 164865
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 85.7 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NSN

1nsn


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 2153 Random
Rwork0.22 --
all0.22 43536 -
obs0.22 43057 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 44 233 6967
Refinement
*PLUS
Rfactor obs: 0.219 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg27.2
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.88

+
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