[English] 日本語
Yorodumi
- PDB-5jt8: Structural basis for the limited antibody cross reactivity betwee... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jt8
TitleStructural basis for the limited antibody cross reactivity between the mite allergens Blo t 1 and Der p 1
ComponentsBlo t 1 allergen
KeywordsALLERGEN / allergen mite
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
NITRATE ION / Cysteine protease
Similarity search - Component
Biological speciesBlomia tropicalis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMeno, K. / Kastrup, J.S. / Gajhede, M.
CitationJournal: Allergy / Year: 2017
Title: The structure of the mite allergen Blo t 1 explains the limited antibody cross-reactivity to Der p 1.
Authors: Meno, K.H. / Kastrup, J.S. / Kuo, I.C. / Chua, K.Y. / Gajhede, M.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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: Blo t 1 allergen
B: Blo t 1 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,60414
Polymers76,4452
Non-polymers1,15912
Water5,513306
1
A: Blo t 1 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7638
Polymers38,2221
Non-polymers5407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Blo t 1 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8426
Polymers38,2221
Non-polymers6195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.412, 117.412, 132.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Blo t 1 allergen


Mass: 38222.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blomia tropicalis (arthropod) / Production host: Komagataella pastoris (fungus) / References: UniProt: A1KXI0

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 316 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: single crystals were obtained with drops containing 4 ul sample solution containing 1 mg/ml rproBlo t 1, 0.5 mM YCl3, and 10 mM Tris-HCl pH 8.0, and 2 ul reservoir solution containing 4% w/v ...Details: single crystals were obtained with drops containing 4 ul sample solution containing 1 mg/ml rproBlo t 1, 0.5 mM YCl3, and 10 mM Tris-HCl pH 8.0, and 2 ul reservoir solution containing 4% w/v PEG-6000, 0.1 M Na-HEPES pH 6.6 and 0.8 M LiNO3

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→55.486 Å / Num. obs: 79280 / % possible obs: 100 % / Redundancy: 17.2 % / Net I/σ(I): 28.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XKG

1xkg


Resolution: 2.1→55.468 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 22.59
RfactorNum. reflection% reflection
Rfree0.2168 3981 5.02 %
Rwork0.1704 --
obs0.1728 79280 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→55.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 70 306 5444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085292
X-RAY DIFFRACTIONf_angle_d1.0297163
X-RAY DIFFRACTIONf_dihedral_angle_d16.3091889
X-RAY DIFFRACTIONf_chiral_restr0.045704
X-RAY DIFFRACTIONf_plane_restr0.004949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12560.30371480.25752740X-RAY DIFFRACTION100
2.1256-2.15250.271430.23572624X-RAY DIFFRACTION100
2.1525-2.18090.32771420.23392751X-RAY DIFFRACTION100
2.1809-2.21070.2741420.22472602X-RAY DIFFRACTION100
2.2107-2.24230.23091540.21352687X-RAY DIFFRACTION100
2.2423-2.27580.24161600.20692659X-RAY DIFFRACTION100
2.2758-2.31140.29821240.2122795X-RAY DIFFRACTION100
2.3114-2.34920.28561430.22172609X-RAY DIFFRACTION100
2.3492-2.38980.26161740.20062723X-RAY DIFFRACTION100
2.3898-2.43320.29391320.20292652X-RAY DIFFRACTION100
2.4332-2.480.22011280.18882676X-RAY DIFFRACTION100
2.48-2.53060.30961370.19432781X-RAY DIFFRACTION100
2.5306-2.58570.22041270.17872640X-RAY DIFFRACTION100
2.5857-2.64580.22541420.172676X-RAY DIFFRACTION100
2.6458-2.7120.24911480.18152719X-RAY DIFFRACTION100
2.712-2.78530.22481350.17742736X-RAY DIFFRACTION100
2.7853-2.86720.26641360.18912661X-RAY DIFFRACTION100
2.8672-2.95980.22841300.18572702X-RAY DIFFRACTION100
2.9598-3.06560.23351400.1892652X-RAY DIFFRACTION100
3.0656-3.18830.25431200.18232743X-RAY DIFFRACTION100
3.1883-3.33340.26781340.17482706X-RAY DIFFRACTION100
3.3334-3.50910.21091260.16742726X-RAY DIFFRACTION100
3.5091-3.72890.20171540.15422615X-RAY DIFFRACTION100
3.7289-4.01670.17551680.14082704X-RAY DIFFRACTION100
4.0167-4.42080.16191600.13012669X-RAY DIFFRACTION100
4.4208-5.06010.15611220.13012740X-RAY DIFFRACTION100
5.0601-6.37380.18631740.15622645X-RAY DIFFRACTION100
6.3738-55.4870.18661380.15552666X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 27.1992 Å / Origin y: 16.7066 Å / Origin z: -26.5859 Å
111213212223313233
T0.1547 Å2-0.0894 Å20.0314 Å2-0.2705 Å2-0.039 Å2--0.2195 Å2
L1.1392 °2-1.0417 °20.3695 °2-2.1009 °2-0.3167 °2--1.3726 °2
S-0.0677 Å °0.1133 Å °0.0559 Å °0.0154 Å °0.0067 Å °-0.3022 Å °-0.0574 Å °0.0741 Å °0.0479 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlc1.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