[English] 日本語
Yorodumi
- PDB-7dr4: Complex of anti-human IL-2 antibody and human IL-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dr4
TitleComplex of anti-human IL-2 antibody and human IL-2
Components
  • Interleukin-2
  • anti-human IL-2 antibody, mouse Ig G, heavy chain
  • anti-human IL-2 antibody, mouse Ig G, kappa chain
KeywordsIMMUNE SYSTEM / Complex / human IL-2 / antibody / Tcell / PROTEIN BINDING
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / natural killer cell activation / positive regulation of regulatory T cell differentiation / : / kinase activator activity / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / cell adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsKim, M.S. / Kim, J.E.
CitationJournal: Oncoimmunology / Year: 2021
Title: Crystal structure of human interleukin-2 in complex with TCB2, a new antibody-drug candidate with antitumor activity.
Authors: Kim, J. / Lee, J.Y. / Park, S.Y. / Lee, Y.J. / Kim, M.S.
History
DepositionDec 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: anti-human IL-2 antibody, mouse Ig G, heavy chain
L: anti-human IL-2 antibody, mouse Ig G, kappa chain
A: anti-human IL-2 antibody, mouse Ig G, heavy chain
B: anti-human IL-2 antibody, mouse Ig G, kappa chain
C: anti-human IL-2 antibody, mouse Ig G, heavy chain
D: anti-human IL-2 antibody, mouse Ig G, kappa chain
E: anti-human IL-2 antibody, mouse Ig G, heavy chain
F: anti-human IL-2 antibody, mouse Ig G, kappa chain
G: Interleukin-2
I: Interleukin-2
J: Interleukin-2
K: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)252,25212
Polymers252,25212
Non-polymers00
Water7,602422
1
H: anti-human IL-2 antibody, mouse Ig G, heavy chain
L: anti-human IL-2 antibody, mouse Ig G, kappa chain
K: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)63,0633
Polymers63,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: anti-human IL-2 antibody, mouse Ig G, heavy chain
B: anti-human IL-2 antibody, mouse Ig G, kappa chain
J: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)63,0633
Polymers63,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: anti-human IL-2 antibody, mouse Ig G, heavy chain
D: anti-human IL-2 antibody, mouse Ig G, kappa chain
G: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)63,0633
Polymers63,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: anti-human IL-2 antibody, mouse Ig G, heavy chain
F: anti-human IL-2 antibody, mouse Ig G, kappa chain
I: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)63,0633
Polymers63,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.334, 72.261, 210.930
Angle α, β, γ (deg.)90.000, 92.711, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Antibody
anti-human IL-2 antibody, mouse Ig G, heavy chain


Mass: 23880.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
anti-human IL-2 antibody, mouse Ig G, kappa chain


Mass: 23746.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein
Interleukin-2 / IL-2 / T-cell growth factor / TCGF


Mass: 15435.979 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60568
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M NH4NO3, pH4.8, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.49→48.25 Å / Num. obs: 80414 / % possible obs: 96.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 34.01 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.083 / Rrim(I) all: 0.179 / Net I/σ(I): 1.34
Reflection shellResolution: 2.5→2.5 Å / Num. unique obs: 5025 / CC1/2: 0.442

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LQB

5lqb


Resolution: 2.49→29.79 Å / SU ML: 0.3544 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 1994 2.48 %
Rwork0.1948 78382 -
obs0.1964 80376 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.41 Å2
Refinement stepCycle: LAST / Resolution: 2.49→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16907 0 0 422 17329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008217290
X-RAY DIFFRACTIONf_angle_d1.013923495
X-RAY DIFFRACTIONf_chiral_restr0.05512699
X-RAY DIFFRACTIONf_plane_restr0.0062969
X-RAY DIFFRACTIONf_dihedral_angle_d19.94876299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.35761310.26275025X-RAY DIFFRACTION87.38
2.55-2.620.27481310.24735414X-RAY DIFFRACTION93.38
2.62-2.70.32761380.245438X-RAY DIFFRACTION94.05
2.7-2.790.29411410.23215427X-RAY DIFFRACTION93.22
2.79-2.890.31891380.22195461X-RAY DIFFRACTION93.91
2.89-30.32091380.21995624X-RAY DIFFRACTION96.66
3-3.140.26681470.22185611X-RAY DIFFRACTION96.97
3.14-3.30.29041470.20335701X-RAY DIFFRACTION97.76
3.3-3.510.30951460.19695692X-RAY DIFFRACTION98.12
3.51-3.780.23161430.18735723X-RAY DIFFRACTION97.49
3.78-4.160.21241480.16185795X-RAY DIFFRACTION99.27
4.16-4.760.2051490.14325769X-RAY DIFFRACTION98.83
4.76-5.990.20341470.16815805X-RAY DIFFRACTION97.98
5.99-29.790.25081500.21275897X-RAY DIFFRACTION97.69

+
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