[English] 日本語
Yorodumi
- PDB-1mim: IGG FAB FRAGMENT (CD25-BINDING) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mim
TitleIGG FAB FRAGMENT (CD25-BINDING)
Components(CHIMERIC SDZ CHI621) x 2
KeywordsIMMUNOGLOBULIN / C REGION
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin mediated immune response / Scavenging of heme from plasma / 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 / 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 / Immunoglobulins ...: / 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
: / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsMikol, V.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of the fab fragment of SDZ CHI621: a chimeric antibody against CD25.
Authors: Mikol, V.
#1: Journal: Transplantation / Year: 1995
Title: Prolonged Action of a Chimeric Interleukin-2 Receptor (Cd25) Monoclonal Antibody Used in Cadaveric Renal Transplantation
Authors: Amlot, P.L. / Rawlings, E. / Fernando, O.N. / Griffin, P.J. / Heinrich, G. / Schreier, M.H. / Castaigne, J.P. / Moore, R. / Sweny, P.
History
DepositionDec 4, 1995Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: CHIMERIC SDZ CHI621
H: CHIMERIC SDZ CHI621


Theoretical massNumber of molelcules
Total (without water)46,0272
Polymers46,0272
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-21 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.580, 59.760, 102.090
Angle α, β, γ (deg.)90.00, 99.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody CHIMERIC SDZ CHI621


Mass: 22882.338 Da / Num. of mol.: 1 / Fragment: IGG FAB
Source method: isolated from a genetically manipulated source
Details: MURINE ANTI-CD25 MONOCLONAL ANTIBODY, RFT5, CHIMERIZED WITH THE CONSTANT REGIONS OF HUMAN 1GG1 HEAVY AND KAPPA LIGHT CHAINS
Source: (gene. exp.) Homo sapiens (human)
Fragment: CONSTANT REGIONS OF 1GG1 HEAVY AND KAPPA LIGHT CHAINS
References: UniProt: P01834
#2: Antibody CHIMERIC SDZ CHI621


Mass: 23144.826 Da / Num. of mol.: 1 / Fragment: IGG FAB
Source method: isolated from a genetically manipulated source
Details: MURINE ANTI-CD25 MONOCLONAL ANTIBODY, RFT5, CHIMERIZED WITH THE CONSTANT REGIONS OF HUMAN 1GG1 HEAVY AND KAPPA LIGHT CHAINS
Source: (gene. exp.) Homo sapiens (human)
Fragment: CONSTANT REGIONS OF 1GG1 HEAVY AND KAPPA LIGHT CHAINS
References: GenBank: 9857755
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE WATER MOLECULE 2 WAS POSITIONED ON A STRONG ELECTRON DENSITY PEAK WHICH WAS OBSERVED BETWEEN ...THE WATER MOLECULE 2 WAS POSITIONED ON A STRONG ELECTRON DENSITY PEAK WHICH WAS OBSERVED BETWEEN TWO STRANDS OF THE BETA SHEET OF THE VARIABLE DOMAIN OF THE HEAVY CHAIN. IT MAKES SHORT CONTACTS WITH TWO CARBONYL OXYGENS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
27.5 %(w/v)PEG80001drop
30.02 %(w/v)1dropNaN3
40.33 mMprotein1drop
5100 mMTris-HCl1reservoir
615.0 %(w/v)PEG80001reservoir
70.04 %(w/v)1reservoirNaN3

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 14331 / % possible obs: 90.6 % / Observed criterion σ(I): 2
Reflection
*PLUS
Num. measured all: 32477 / Rmerge(I) obs: 0.057

-
Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.196 -
obs0.196 13210
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 0 69 3303
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.38
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2

+
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