[English] 日本語
Yorodumi
- PDB-6xuk: AbLIFT design 15 of Ab 1116NS19.9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xuk
TitleAbLIFT design 15 of Ab 1116NS19.9
Components
  • Heavy chain
  • Light chain
KeywordsANTITUMOR PROTEIN / pancreatic cancer / diagnosis / in-silico optimized antibody / CA19-9 binder / immunotherapeutic reagent
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsDiskin, R. / Borenstein-Katz, A.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies.
Authors: Borenstein-Katz, A. / Warszawski, S. / Amon, R. / Eilon, M. / Cohen-Dvashi, H. / Leviatan Ben-Arye, S. / Tasnima, N. / Yu, H. / Chen, X. / Padler-Karavani, V. / Fleishman, S.J. / Diskin, R.
History
DepositionJan 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_PDB_obs_spr
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Mar 8, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 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
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5705
Polymers47,5652
Non-polymers1,0053
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-10 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.936, 64.936, 244.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11H-674-

HOH

-
Components

#1: Antibody Heavy chain


Mass: 23751.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Light chain


Mass: 23813.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 820.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-2-3-4/a3-b1_a4-d1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Ammonium citrate, Immidazole pH7, PEG 2K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97371 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97371 Å / Relative weight: 1
ReflectionResolution: 1.42→62.754 Å / Num. obs: 99787 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.42-1.461.0663887472410.5580.491.1791.199.7
6.35-62.750.05727913520.9950.0240.05619.5100

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7W

3u7w


Resolution: 1.42→62.754 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.37
RfactorNum. reflection% reflection
Rfree0.1846 5022 5.04 %
Rwork0.1487 --
obs0.1505 99620 99.89 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 118.18 Å2 / Biso mean: 23.7146 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 1.42→62.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 134 661 4089
Biso mean--27.03 34.2 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.42-1.43610.30871620.2649308299
1.4361-1.4530.3161550.24183077100
1.453-1.47070.29121360.2153150100
1.4707-1.48940.27831840.21163062100
1.4894-1.5090.26161770.19173123100
1.509-1.52960.24631540.17933096100
1.5296-1.55150.22361490.16543130100
1.5515-1.57460.22191620.16283086100
1.5746-1.59930.19971590.1553115100
1.5993-1.62550.19611730.15643119100
1.6255-1.65350.22151620.15043093100
1.6535-1.68360.20611660.1453132100
1.6836-1.7160.20131630.13913136100
1.716-1.7510.18651640.14023133100
1.751-1.78910.20051440.13743126100
1.7891-1.83070.19011990.14233092100
1.8307-1.87650.19611560.14093133100
1.8765-1.92720.1611610.13193143100
1.9272-1.98390.16121680.12963151100
1.9839-2.0480.12841660.12593142100
2.048-2.12120.17631830.12983128100
2.1212-2.20610.17041660.13183159100
2.2061-2.30650.18541850.13043173100
2.3065-2.42810.16971760.13463149100
2.4281-2.58020.17561650.13693191100
2.5802-2.77950.16251790.14193198100
2.7795-3.05920.20031740.15133223100
3.0592-3.50180.18051720.14413239100
3.5018-4.41170.16081800.13933297100
4.4117-62.7540.19741820.18293520100

+
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