[English] 日本語
Yorodumi
- PDB-7rew: Crystal Structure of IL-13 in complex with MMAb3 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rew
TitleCrystal Structure of IL-13 in complex with MMAb3 Fab
Components
  • IL13
  • anti-cyno interleukin 13 Fab heavy chain
  • anti-cyno interleukin 13 Fab light chain
KeywordsCYTOKINE / alpha-helical bundle / protein-Fab complex
Function / homology
Function and homology information


cytokine receptor binding / immune response / extracellular region
Similarity search - Function
Interleukin-13 / Interleukin-13 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Macaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Model detailsFc
AuthorsSudom, A. / Min, X.
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Development of a potent high-affinity human therapeutic antibody via novel application of recombination signal sequence-based affinity maturation.
Authors: Kielczewska, A. / D'Angelo, I. / Amador, M.S. / Wang, T. / Sudom, A. / Min, X. / Rathanaswami, P. / Pigott, C. / Foltz, I.N.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: anti-cyno interleukin 13 Fab heavy chain
L: anti-cyno interleukin 13 Fab light chain
A: anti-cyno interleukin 13 Fab heavy chain
B: anti-cyno interleukin 13 Fab light chain
G: IL13
I: IL13


Theoretical massNumber of molelcules
Total (without water)118,2966
Polymers118,2966
Non-polymers00
Water2,360131
1
H: anti-cyno interleukin 13 Fab heavy chain
L: anti-cyno interleukin 13 Fab light chain
I: IL13


Theoretical massNumber of molelcules
Total (without water)59,1483
Polymers59,1483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: anti-cyno interleukin 13 Fab heavy chain
B: anti-cyno interleukin 13 Fab light chain
G: IL13


Theoretical massNumber of molelcules
Total (without water)59,1483
Polymers59,1483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.790, 74.352, 76.530
Angle α, β, γ (deg.)96.848, 109.890, 112.494
Int Tables number1
Space group name H-MP1
Space group name HallP1

-
Components

#1: Antibody anti-cyno interleukin 13 Fab heavy chain


Mass: 24108.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human) / Tissue (production host): kidney
#2: Antibody anti-cyno interleukin 13 Fab light chain


Mass: 22737.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human) / Tissue (production host): kidney
#3: Protein IL13


Mass: 12302.288 Da / Num. of mol.: 2 / Fragment: UNP residues 22-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: IL13 / Cell line (production host): 293T / Production host: Homo sapiens (human) / Tissue (production host): kidney / References: UniProt: Q0PW92
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.31 Å3/Da / Density % sol: 46.83 % / Mosaicity: 0.3 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 0.2 M LiSO4, 0.1 M Tris HCl pH 8.5, 25% PEG 5,000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 4, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→68.94 Å / Num. obs: 54189 / % possible obs: 88 % / Redundancy: 2.1 % / Biso Wilson estimate: 39.04 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.044 / Rrim(I) all: 0.068 / Net I/σ(I): 7.2 / Num. measured all: 115864 / Scaling rejects: 418
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.170.381976045980.8320.3510.5192.890.4
8.93-68.940.04816617850.9760.0430.06511.896.3

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CQI

4cqi


Resolution: 2.1→35.96 Å / SU ML: 0.3344 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 36.4314 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2909 2617 4.83 %
Rwork0.245 51516 -
obs0.2473 54133 87.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7581 0 0 131 7712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317768
X-RAY DIFFRACTIONf_angle_d0.679310576
X-RAY DIFFRACTIONf_chiral_restr0.04381203
X-RAY DIFFRACTIONf_plane_restr0.00481334
X-RAY DIFFRACTIONf_dihedral_angle_d10.0444597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.40671490.3772829X-RAY DIFFRACTION90.74
2.14-2.180.39981600.36432787X-RAY DIFFRACTION90.37
2.18-2.230.39041350.33822730X-RAY DIFFRACTION89.81
2.23-2.280.4231440.34992737X-RAY DIFFRACTION88.95
2.28-2.330.37881490.3232750X-RAY DIFFRACTION88.49
2.33-2.390.38371510.3112667X-RAY DIFFRACTION86.92
2.39-2.450.41661390.29932580X-RAY DIFFRACTION84.49
2.45-2.520.34411320.29032461X-RAY DIFFRACTION80.33
2.52-2.610.37071140.292355X-RAY DIFFRACTION76.16
2.61-2.70.38561310.29352851X-RAY DIFFRACTION92.58
2.7-2.810.39571080.282913X-RAY DIFFRACTION92.7
2.81-2.930.34171360.29152820X-RAY DIFFRACTION91.6
2.93-3.090.37581460.28472780X-RAY DIFFRACTION90.59
3.09-3.280.34131060.26722790X-RAY DIFFRACTION89.22
3.28-3.540.32281350.25142630X-RAY DIFFRACTION85
3.54-3.890.23791630.23332375X-RAY DIFFRACTION78.33
3.89-4.450.24141140.19062961X-RAY DIFFRACTION94.85
4.45-5.610.20321460.17992848X-RAY DIFFRACTION92.61
5.61-35.960.22481590.20112652X-RAY DIFFRACTION86.87

+
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