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- PDB-2h3n: Crystal structure of a surrogate light chain (LAMBDA5 and VpreB) ... -

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Basic information

Entry
Database: PDB / ID: 2h3n
TitleCrystal structure of a surrogate light chain (LAMBDA5 and VpreB) homodimer
Components
  • Ig lambda-5
  • VpreB protein
KeywordsIMMUNE SYSTEM / beta sheets / v- and c-type immunoglobulin fold
Function / homology
Function and homology information


IgG immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / Cell surface interactions at the vascular wall / immune response / endoplasmic reticulum / extracellular space / extracellular region / membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin iota chain / Immunoglobulin lambda-like polypeptide 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBankovich, A.J. / Garcia, K.C.
CitationJournal: Science / Year: 2007
Title: Structural insight into pre-B cell receptor function
Authors: Bankovich, A.J. / Raunser, S. / Juo, Z.S. / Walz, T. / Davis, M.M. / Garcia, K.C.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VpreB protein
B: Ig lambda-5
C: VpreB protein
D: Ig lambda-5


Theoretical massNumber of molelcules
Total (without water)48,1384
Polymers48,1384
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-54 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.169, 72.814, 115.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach VpreB molecule assembles with one lambda5 molecule to produce a surrogate light chain heterodimer. The structures displays a dimer of two of these heterodimers

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Components

#1: Protein VpreB protein / Immunoglobulin iota chain / V(pre)B protein / CD179a antigen


Mass: 11346.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPREB1, VPREB / Organ (production host): eggs / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P12018
#2: Protein Ig lambda-5 / Immunoglobulin lambda-like polypeptide 1 / Immunoglobulin-related protein 14.1 / Immunoglobulin ...Immunoglobulin lambda-like polypeptide 1 / Immunoglobulin-related protein 14.1 / Immunoglobulin omega polypeptide / CD179b antigen


Mass: 12722.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLL1, IGL1 / Organ (production host): eggs / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15814
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG 5000 MME and 100mM BisTris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 21790 / Num. obs: 20984 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.41 Å / % possible all: 84.9

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Processing

Software
NameClassification
ADSCdata collection
HKL-2000data reduction
PHASERphasing
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 1049 CNS
Rwork0.228 --
all0.2281 21790 -
obs0.2281 20984 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--19.686 Å20 Å20 Å2
2--11.941 Å20 Å2
3---7.744 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 0 68 3390
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it3.4481.5
X-RAY DIFFRACTIONc_mcangle_it4.6632
X-RAY DIFFRACTIONc_scbond_it5.5732
X-RAY DIFFRACTIONc_scangle_it6.8772.5

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