[English] 日本語
Yorodumi
- PDB-9y0e: Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9y0e
TitleCrystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22
Components
  • (hIgE Fab 2H22 ...) x 2
  • Major pollen allergen Bet v 1-A
KeywordsALLERGEN/IMMUNE SYSTEM / allergen / IgE / IgE Fab / allergen-antibody complex / IMMUNE SYSTEM / ALLERGEN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Major pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBetula pendula (European white birch)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsO'Malley, A. / Borders, B.T. / Smith, S.A. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Allergy / Year: 2026
Title: Structural Determination of a Human IgE Epitope on Major Birch Allergen Bet v 1.
Authors: O'Malley, A. / Borders, B.T. / Wilson, J.M. / Smith, S.A. / Chruszcz, M.
History
DepositionAug 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Major pollen allergen Bet v 1-A
A: hIgE Fab 2H22 heavy chain
B: hIgE Fab 2H22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6106
Polymers64,1773
Non-polymers4333
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.971, 70.258, 78.247
Angle α, β, γ (deg.)90.000, 116.375, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Antibody , 2 types, 2 molecules AB

#2: Antibody hIgE Fab 2H22 heavy chain


Mass: 23953.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody hIgE Fab 2H22 light chain


Mass: 22630.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Protein / Sugars , 2 types, 2 molecules C

#1: Protein Major pollen allergen Bet v 1-A / Allergen Bet v I-A


Mass: 17592.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Gene: BETVIA, BETVI / Production host: Escherichia coli (E. coli) / References: UniProt: P15494
#5: 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: obtained synthetically / 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 , 2 types, 53 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.04 M potassium phosphate monobasic; 16% PEG 8000; 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 14960 / % possible obs: 91.8 % / Redundancy: 5.5 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.044 / Rrim(I) all: 0.11 / Net I/σ(I): 15.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 443 / CC1/2: 0.826 / CC star: 0.951 / Rpim(I) all: 0.186 / Rrim(I) all: 0.322 / % possible all: 53.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.873 / SU B: 40.159 / SU ML: 0.346 / Cross valid method: FREE R-VALUE / ESU R Free: 0.44
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.257 751 5.031 %
Rwork0.1962 14175 -
all0.199 --
obs-14926 90.603 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.908 Å2
Baniso -1Baniso -2Baniso -3
1-1.106 Å20 Å21.659 Å2
2--2.415 Å20 Å2
3----3.463 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 28 51 4477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124534
X-RAY DIFFRACTIONr_bond_other_d0.010.0164122
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.7926193
X-RAY DIFFRACTIONr_angle_other_deg0.5061.7219543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0755592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.464511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31510660
X-RAY DIFFRACTIONr_dihedral_angle_6_deg8.77810161
X-RAY DIFFRACTIONr_chiral_restr0.0550.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025306
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02970
X-RAY DIFFRACTIONr_nbd_refined0.2070.2691
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.23740
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22193
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22159
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.260.25
X-RAY DIFFRACTIONr_nbd_other0.210.260
X-RAY DIFFRACTIONr_mcbond_it2.1682.7712380
X-RAY DIFFRACTIONr_mcbond_other2.1662.7722380
X-RAY DIFFRACTIONr_mcangle_it3.7434.9732968
X-RAY DIFFRACTIONr_mcangle_other3.7434.9762969
X-RAY DIFFRACTIONr_scbond_it2.0362.8672154
X-RAY DIFFRACTIONr_scbond_other2.0362.872155
X-RAY DIFFRACTIONr_scangle_it3.475.173225
X-RAY DIFFRACTIONr_scangle_other3.475.1723226
X-RAY DIFFRACTIONr_lrange_it6.84932.32317926
X-RAY DIFFRACTIONr_lrange_other6.84932.3217920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.297190.272572X-RAY DIFFRACTION49.6222
2.975-3.0560.321360.269767X-RAY DIFFRACTION67.7066
3.056-3.1440.328550.259851X-RAY DIFFRACTION79.4737
3.144-3.240.247480.226933X-RAY DIFFRACTION88.8587
3.24-3.3460.296580.233975X-RAY DIFFRACTION96.4519
3.346-3.4620.364550.233975X-RAY DIFFRACTION99.5169
3.462-3.5920.265430.222964X-RAY DIFFRACTION99.4077
3.592-3.7370.298650.204889X-RAY DIFFRACTION98.0473
3.737-3.9020.256410.193873X-RAY DIFFRACTION97.1307
3.902-4.090.224410.186792X-RAY DIFFRACTION96.5238
4.09-4.3090.226420.164757X-RAY DIFFRACTION93.2322
4.309-4.5670.18360.147755X-RAY DIFFRACTION98.5056
4.567-4.8780.213390.144725X-RAY DIFFRACTION100
4.878-5.2620.199260.157682X-RAY DIFFRACTION100
5.262-5.7550.225250.186616X-RAY DIFFRACTION100
5.755-6.4170.309340.201578X-RAY DIFFRACTION100
6.417-7.3790.265260.215496X-RAY DIFFRACTION100
7.379-8.9610.258230.186434X-RAY DIFFRACTION100
8.961-12.3660.204250.176328X-RAY DIFFRACTION100
12.366-400.324140.269213X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0956-0.06681.29592.47351.45952.25270.13150.28920.2165-0.186-0.081-0.1012-0.11660.1043-0.05050.22780.0072-0.23670.05070.07020.45779.019-20.089-13.097
22.6423-1.3464-1.62473.8570.32971.986-0.0417-0.00170.0346-0.10470.0822-0.03250.13140.1102-0.04050.2816-0.0174-0.34410.04550.010.453436.465-31.549-3.684
33.2452-1.30360.45124.5181-1.00131.0070.2450.0451-0.3870.025-0.28920.16450.08010.01960.04420.2613-0.0073-0.31340.153-0.04740.43872.673-40.763-14.507
44.19391.48561.39464.36520.86431.6349-0.0836-0.068-0.00890.26740.08020.31680.00250.08690.00340.2360.0157-0.24390.0128-0.00110.368935.276-43.3387.197
53.9608-0.03740.85171.29990.924.0186-0.1154-0.3771-0.063-0.05220.09050.0948-0.274-0.42140.02490.2560.0478-0.28070.10940.02010.3668-15.191-26.241-38.926
610.24422.0732-4.96521.5067-0.70856.0836-0.27770.1027-0.390.10960.42180.01220.1812-0.0518-0.14410.31320.0129-0.21080.19020.13340.3528-12.975-32.839-40.131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION5ALLC2 - 118
2X-RAY DIFFRACTION6ALLC119 - 160

+
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