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- PDB-3kg5: Crystal structure of human Ig-beta homodimer -

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Basic information

Entry
Database: PDB / ID: 3kg5
TitleCrystal structure of human Ig-beta homodimer
ComponentsB-cell antigen receptor complex-associated protein beta chain
KeywordsPROTEIN BINDING / CD79b / Ig-beta / BCR / Immunoglobulin domain
Function / homology
Function and homology information


IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell receptor signaling pathway / transmembrane signaling receptor activity / adaptive immune response / Potential therapeutics for SARS / immune response ...IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell receptor signaling pathway / transmembrane signaling receptor activity / adaptive immune response / Potential therapeutics for SARS / immune response / external side of plasma membrane / signal transduction / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
B-cell antigen receptor complex-associated protein alpha/beta chain / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...B-cell antigen receptor complex-associated protein alpha/beta chain / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / 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
B-cell antigen receptor complex-associated protein beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,9992
Polymers30,9992
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: B-cell antigen receptor complex-associated protein beta chain


Theoretical massNumber of molelcules
Total (without water)15,5001
Polymers15,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: B-cell antigen receptor complex-associated protein beta chain


Theoretical massNumber of molelcules
Total (without water)15,5001
Polymers15,5001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.8, 129.8, 129.8
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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


Mass: 15499.551 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B29, CD79B, IGB / Production host: Escherichia coli (E. coli) / References: UniProt: P40259
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4
Details: 0.6M Na formate, 100mM Na Acetate, pH 4.0, VAPOR DIFFUSION, temperature 298K

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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: 3.2→50 Å / Num. obs: 6616 / Observed criterion σ(I): -3 / Redundancy: 27.6 % / Biso Wilson estimate: 75.8 Å2 / Rsym value: 0.07 / Net I/σ(I): 55.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 28.7 % / Rsym value: 0.339

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→46 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 358 random
Rwork0.181 --
obs-6407 -
Refinement stepCycle: LAST / Resolution: 3.2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 0 2 1678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.39
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree: 0.362 / Rfactor Rwork: 0.207

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