[English] 日本語
Yorodumi
- PDB-9fy8: L2A5 Fab in complex with STn-Thr -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fy8
TitleL2A5 Fab in complex with STn-Thr
Components
  • Human anti kappa variable heavy chain
  • L2A5 Fab Heavy chain
  • L2A5 Fab Light Chain
KeywordsSUGAR BINDING PROTEIN / Antibody / Fab / Immune system
Function / homology: / THREONINE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsLaugieri, M.E. / Ereno Orbea, J. / Jimenez Barbero, J. / Oyenarte, I.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI) Spain
European Commission101079417European Union
CitationJournal: Jacs Au / Year: 2025
Title: Decoding the Molecular Basis of the Specificity of an Anti-sTn Antibody.
Authors: Soares, C.O. / Laugieri, M.E. / Grosso, A.S. / Natale, M. / Coelho, H. / Behren, S. / Yu, J. / Cai, H. / Franconetti, A. / Oyenarte, I. / Magnasco, M. / Gimeno, A. / Ramos, N. / Chai, W. / ...Authors: Soares, C.O. / Laugieri, M.E. / Grosso, A.S. / Natale, M. / Coelho, H. / Behren, S. / Yu, J. / Cai, H. / Franconetti, A. / Oyenarte, I. / Magnasco, M. / Gimeno, A. / Ramos, N. / Chai, W. / Corzana, F. / Westerlind, U. / Jimenez-Barbero, J. / Palma, A.S. / Videira, P.A. / Ereno-Orbea, J. / Marcelo, F.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: L2A5 Fab Heavy chain
C: L2A5 Fab Light Chain
D: Human anti kappa variable heavy chain
I: L2A5 Fab Heavy chain
L: L2A5 Fab Light Chain
V: Human anti kappa variable heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,49510
Polymers117,2326
Non-polymers1,2634
Water2,504139
1
B: L2A5 Fab Heavy chain
C: L2A5 Fab Light Chain
D: Human anti kappa variable heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2475
Polymers58,6163
Non-polymers6322
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: L2A5 Fab Heavy chain
L: L2A5 Fab Light Chain
V: Human anti kappa variable heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2475
Polymers58,6163
Non-polymers6322
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.331, 128.144, 98.896
Angle α, β, γ (deg.)90.00, 98.17, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 2 types, 4 molecules BICL

#1: Antibody L2A5 Fab Heavy chain


Mass: 23231.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody L2A5 Fab Light Chain


Mass: 23313.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 4 molecules DV

#3: Protein Human anti kappa variable heavy chain


Mass: 12070.028 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 512.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sialyl-Tn (sTn) antigen is a truncated O-glycan containing a sialic acid alpha-2,6 linked to N-acetylgalactosamine (GalNAc) alpha-O-threonine or to N-acetylgalactosamine (GalNAc) alpha-O-serine.
References: BIRD: PRD_002574
DescriptorTypeProgram
DNeup5Aca2-6DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 141 molecules

#5: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking, Oligosaccharide / Class: Antigen / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
Details: Sialyl-Tn (sTn) antigen is a truncated O-glycan containing a sialic acid alpha-2,6 linked to N-acetylgalactosamine (GalNAc) alpha-O-threonine or to N-acetylgalactosamine (GalNAc) alpha-O-serine.
References: BIRD: PRD_002574
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsActivation of an aberrant glycosylation pathway in cancer cells can lead to expression of the onco- ...Activation of an aberrant glycosylation pathway in cancer cells can lead to expression of the onco-foetal sialyl-Tn (sTn) antigen.
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1M BisTris:Hcl, pH6.5, 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.62→97.892 Å / Num. obs: 34129 / % possible obs: 97.6 % / Redundancy: 5.13 % / CC1/2: 0.961 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.302 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Num. unique obsCC1/2Rrim(I) allDiffraction-ID
2.67-3.0841360.850.461
3.08-3.7792550.940.3011
3.77-5.3272040.9860.1271

-
Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5109: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→53.61 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3063 1696 4.98 %
Rwork0.2477 --
obs0.2505 34080 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→53.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7839 0 84 139 8062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.525
X-RAY DIFFRACTIONf_dihedral_angle_d12.712734
X-RAY DIFFRACTIONf_chiral_restr0.0391283
X-RAY DIFFRACTIONf_plane_restr0.0051410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.70.3691410.30532724X-RAY DIFFRACTION99
2.7-2.790.3711250.27982797X-RAY DIFFRACTION100
2.79-2.890.32221550.26792710X-RAY DIFFRACTION100
2.89-30.33081490.26032755X-RAY DIFFRACTION100
3-3.140.35151640.25632767X-RAY DIFFRACTION100
3.14-3.30.32671360.26382751X-RAY DIFFRACTION100
3.3-3.510.31211510.25432471X-RAY DIFFRACTION90
3.51-3.780.30911320.24622575X-RAY DIFFRACTION93
3.78-4.160.29561120.23242439X-RAY DIFFRACTION87
4.16-4.760.26811420.2132801X-RAY DIFFRACTION100
4.76-60.28861410.23662783X-RAY DIFFRACTION100
6-53.610.27171480.25012811X-RAY DIFFRACTION100

+
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