[English] 日本語
Yorodumi
- PDB-3khq: Crystal structure of murine Ig-beta (CD79b) in the monomeric form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3khq
TitleCrystal structure of murine Ig-beta (CD79b) in the monomeric form
ComponentsB-cell antigen receptor complex-associated protein beta chain
KeywordsPROTEIN BINDING / CD79b / CD79a / Ig-beta / BCR / Ig domain / V-set / Immunoglobulin domain
Function / homology
Function and homology information


CD22 mediated BCR regulation / IgM B cell receptor complex / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell differentiation / B cell receptor signaling pathway / response to bacterium / transmembrane signaling receptor activity / adaptive immune response / external side of plasma membrane ...CD22 mediated BCR regulation / IgM B cell receptor complex / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell differentiation / B cell receptor signaling pathway / response to bacterium / transmembrane signaling receptor activity / adaptive immune response / external side of plasma membrane / identical protein binding / plasma membrane
Similarity search - Function
B-cell antigen receptor complex-associated protein alpha/beta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin I-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...B-cell antigen receptor complex-associated protein alpha/beta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin I-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / GLUTATHIONE / B-cell antigen receptor complex-associated protein beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRadaev, S. / Sun, P.D.
CitationJournal: Structure / Year: 2010
Title: Structural and Functional Studies of Igalphabeta and Its Assembly with the B Cell Antigen Receptor.
Authors: Radaev, S. / Zou, Z. / Tolar, P. / Nguyen, K. / Nguyen, A. / Krueger, P.D. / Stutzman, N. / Pierce, S. / Sun, P.D.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Non-polymer description
Revision 1.3Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: B-cell antigen receptor complex-associated protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6014
Polymers15,0801
Non-polymers5213
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.63, 79.72, 34.32
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein B-cell antigen receptor complex-associated protein beta chain / Ig-beta / B-cell-specific glycoprotein B29 / Immunoglobulin-associated B29 protein


Mass: 15079.915 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd79b, Igb / Production host: Escherichia coli (E. coli) / References: UniProt: P15530
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.62 Å3/Da / Density % sol: 23.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 20% Peg 750 MME, 0.2M MgCl2, 100mM Na Citrate, pH 5.0, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 10471 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.065 / Net I/σ(I): 21.5
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.317

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.87 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.114 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 515 4.9 %RANDOM
Rwork0.187 ---
obs0.18758 10071 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--1.54 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 34 58 844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021799
X-RAY DIFFRACTIONr_bond_other_d0.0010.02550
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9471069
X-RAY DIFFRACTIONr_angle_other_deg2.533.0061329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.724591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96324.10339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7415142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.123155
X-RAY DIFFRACTIONr_chiral_restr0.2460.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02161
X-RAY DIFFRACTIONr_nbd_refined0.2610.2125
X-RAY DIFFRACTIONr_nbd_other0.2770.2536
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2366
X-RAY DIFFRACTIONr_nbtor_other0.0910.2438
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.3834606
X-RAY DIFFRACTIONr_mcbond_other2.4284191
X-RAY DIFFRACTIONr_mcangle_it106748
X-RAY DIFFRACTIONr_scbond_it13.4774396
X-RAY DIFFRACTIONr_scangle_it16.3976321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 22 -
Rwork0.27 382 -
obs--51.27 %

+
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