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- PDB-4jvu: IgM C2-domain from mouse -

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Basic information

Entry
Database: PDB / ID: 4jvu
TitleIgM C2-domain from mouse
ComponentsIg mu chain C region membrane-bound form
KeywordsPROTEIN BINDING / Immunoglobulin M / antibody / oligomerization / Immunoglobulin fold / Receptor
Function / homology
Function and homology information


CD22 mediated BCR regulation / : / hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / pre-B cell allelic exclusion / Cell surface interactions at the vascular wall / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation ...CD22 mediated BCR regulation / : / hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / pre-B cell allelic exclusion / Cell surface interactions at the vascular wall / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / B cell affinity maturation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / regulation of immunoglobulin production / regulation of cell morphogenesis / phagocytosis, engulfment / positive regulation of endocytosis / B cell activation / immunoglobulin complex, circulating / B cell proliferation / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / complement activation, classical pathway / positive regulation of B cell proliferation / antigen binding / B cell receptor signaling pathway / positive regulation of immune response / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / antibacterial humoral response / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / adaptive immune response / membrane => GO:0016020 / defense response to bacterium / external side of plasma membrane / innate immune response / perinuclear region of cytoplasm / cell surface / extracellular space / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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/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 heavy constant mu / Immunoglobulin heavy constant mu
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMueller, R. / Graewert, A.M. / Kern, T. / Madl, T. / Peschek, J. / Sattler, M. / Groll, M. / Buchner, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: High-resolution structures of the IgM Fc domains reveal principles of its hexamer formation.
Authors: Muller, R. / Grawert, M.A. / Kern, T. / Madl, T. / Peschek, J. / Sattler, M. / Groll, M. / Buchner, J.
History
DepositionMar 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig mu chain C region membrane-bound form
B: Ig mu chain C region membrane-bound form


Theoretical massNumber of molelcules
Total (without water)25,5392
Polymers25,5392
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-7 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.440, 44.780, 54.570
Angle α, β, γ (deg.)90.00, 118.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-456-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.084094, -0.335465, -0.938292), (-0.292768, -0.908386, 0.298534), (-0.952478, 0.249597, -0.174603)19.93882, -6.364, 25.07184

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Components

#1: Protein Ig mu chain C region membrane-bound form


Mass: 12769.625 Da / Num. of mol.: 2 / Fragment: unp residues 103-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igh-6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01873, UniProt: P01872*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1.95 Å3/Da / Density % sol: 36.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.0 M LiCl, 0.1 M MES, 23% PEG 6000, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2008
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. all: 48547 / Num. obs: 48207 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.1
Reflection shellResolution: 1.3→1.4 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 5.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O0V

1o0v


Resolution: 1.3→10 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.448 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16814 2411 5 %RANDOM
Rwork0.13779 ---
all0.141 45796 --
obs0.1393 45796 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.239 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0 Å2-0.51 Å2
2--1.99 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 0 291 1906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021653
X-RAY DIFFRACTIONr_bond_other_d0.0030.021593
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9652256
X-RAY DIFFRACTIONr_angle_other_deg0.9073.0033676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8495202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95624.60363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2715276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.544157
X-RAY DIFFRACTIONr_chiral_restr0.1340.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_rigid_bond_restr5.07533246
X-RAY DIFFRACTIONr_sphericity_free35.714590
X-RAY DIFFRACTIONr_sphericity_bonded11.35253409
LS refinement shellResolution: 1.3→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 176 -
Rwork0.158 3347 -
obs--99.77 %
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)
10.0084-0.0029-0.00680.00860.00140.0056-0.0007-0.0004-0.00060.00020.00030.00080.00110.00030.00040.00850.00050.00090.0001-0.00050.00717.4001-11.313313.6122
20.01680.00190.00240.00920.00340.03040.00010.0007-0.00110.00080.0002-0.0009-0.00120.0026-0.00030.0076-0.00090.00120.00040.00030.006711.49113.01983.4642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A224 - 337
2X-RAY DIFFRACTION1A401 - 560
3X-RAY DIFFRACTION2B230 - 338
4X-RAY DIFFRACTION2B401 - 531

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