[English] 日本語
Yorodumi
- PDB-1m26: Crystal structure of jacalin-T-antigen complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m26
TitleCrystal structure of jacalin-T-antigen complex
Components
  • Jacalin, alpha chain
  • Jacalin, beta chain
KeywordsSUGAR BINDING PROTEIN / PLANT PROTEIN / All beta sheet protein / beta prism I fold
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Thomsen-Friedenreich antigen / : / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsJeyaprakash, A.A. / Rani, P.G. / Reddy, G.B. / Banumathi, S. / Betzel, C. / Surolia, A. / Vijayan, M.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexs
Authors: Jeyaprakash, A.A. / Rani, P.G. / Reddy, G.B. / Banumathi, S. / Betzel, C. / Surolia, A. / Vijayan, M.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold
Authors: Sankaranarayanan, R. / Sekar, K. / Banerjee, R. / Sharma, V. / Surolia, A. / Vijayan, M.
History
DepositionJun 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Jacalin, alpha chain
B: Jacalin, beta chain
C: Jacalin, alpha chain
D: Jacalin, beta chain
E: Jacalin, alpha chain
F: Jacalin, beta chain
G: Jacalin, alpha chain
H: Jacalin, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,86312
Polymers65,3298
Non-polymers1,5334
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14630 Å2
ΔGint-48 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.92, 78.00, 67.91
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsBiological molecule is a tetramer. There is one tetramer in the assymmetric unit

-
Components

#1: Protein
Jacalin, alpha chain / AGGLUTININ ALPHA CHAIN


Mass: 14673.479 Da / Num. of mol.: 4 / Fragment: residues 85-217 of GB sequence entry AA32678 / Source method: isolated from a natural source
Details: synonymous scientific name: Artocarpus heterophyllus
Source: (natural) Artocarpus integer (campedak) / Organ: seeds / References: GenBank: 289162, UniProt: P18670*PLUS
#2: Protein/peptide
Jacalin, beta chain / AGGLUTININ BETA CHAIN


Mass: 1658.874 Da / Num. of mol.: 4 / Fragment: residues 64-78 of GB sequence entry AA32678 / Source method: isolated from a natural source
Details: synonymous scientific name: Artocarpus heterophyllus
Source: (natural) Artocarpus integer (campedak) / Organ: seeds / References: GenBank: 289162, UniProt: P18673*PLUS
#3: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 4000, 0.02M phosphate buffer at pH 7.3, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.02 Mphosphate1droppH7.3
30.1 M1dropNaCl
40.025 %(w/v)sodium azide1drop
58-10 %(w/v)PEG40001drop
640 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.62→19.58 Å / Num. all: 76669 / Num. obs: 74262 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.073
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 1.8 % / Num. unique all: 3714 / % possible all: 95.8
Reflection
*PLUS
% possible obs: 96.7 % / Num. measured all: 188335
Reflection shell
*PLUS
% possible obs: 95.8 % / Num. unique obs: 3714 / Rmerge(I) obs: 0.289

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JAC

1jac


Resolution: 1.62→19.58 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3787 5.1 %RANDOM
Rwork0.189 ---
obs0.189 74262 96.7 %-
all-76669 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5119 Å2 / ksol: 0.345509 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å20 Å2-0.61 Å2
2--6.74 Å20 Å2
3----3.74 Å2
Refine analyzeLuzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.62→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 104 497 5185
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d2.69
X-RAY DIFFRACTIONc_mcbond_it0.891.5
X-RAY DIFFRACTIONc_mcangle_it1.422
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.372.5
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 675 5.5 %
Rwork0.291 11692 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMTAN.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.69

+
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://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