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- PDB-4jvw: IgM C4-domain from mouse -

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Basic information

Entry
Database: PDB / ID: 4jvw
TitleIgM C4-domain from mouse
ComponentsIg mu chain C region secreted 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 / B cell affinity maturation ...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 / regulation of cell morphogenesis / regulation of immunoglobulin production / 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 / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _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 secreted form
B: Ig mu chain C region secreted form
C: Ig mu chain C region secreted form
D: Ig mu chain C region secreted form


Theoretical massNumber of molelcules
Total (without water)50,9744
Polymers50,9744
Non-polymers00
Water7,710428
1
A: Ig mu chain C region secreted form
D: Ig mu chain C region secreted form


Theoretical massNumber of molelcules
Total (without water)25,4872
Polymers25,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-15 kcal/mol
Surface area10920 Å2
MethodPISA
2
B: Ig mu chain C region secreted form
C: Ig mu chain C region secreted form


Theoretical massNumber of molelcules
Total (without water)25,4872
Polymers25,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-14 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.156, 41.207, 67.109
Angle α, β, γ (deg.)90.00, 92.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-692-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 900
2114B1 - 900
3114C1 - 900
4114D1 - 900

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.858621, 0.512386, 0.015177), (-0.511797, -0.85855, 0.030903), (0.028864, 0.018766, 0.999407)25.53759, 58.69688, -34.34932
3given(0.770901, -0.169418, -0.614011), (0.424042, -0.582805, 0.6932), (-0.47529, -0.794755, -0.377445)30.62411, 6.89823, 57.58217
4given(-0.77048, -0.144965, -0.620762), (-0.633571, 0.2816, 0.720617), (0.070343, 0.948518, -0.308813)42.45343, 29.83218, -12.84653

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Components

#1: Protein
Ig mu chain C region secreted form


Mass: 12743.415 Da / Num. of mol.: 4 / Fragment: uno residues 324-436
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: P01872
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M HEPES, 15% PEG 8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 15, 2009
RadiationMonochromator: Scanning emission monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 31721 / Num. obs: 31721 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 19
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.7.0029refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JVU

1jvu


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.441 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23415 1537 5.1 %RANDOM
Rwork0.19756 ---
all0.213 28566 --
obs0.19946 28566 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.083 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20.28 Å2
2--1.85 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 0 428 3785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193459
X-RAY DIFFRACTIONr_bond_other_d0.0020.023218
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9684746
X-RAY DIFFRACTIONr_angle_other_deg0.7433.0027454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6624.266143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68615527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0081515
X-RAY DIFFRACTIONr_chiral_restr0.0690.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02733
Refine LS restraints NCS

Ens-ID: 1 / Number: 1577 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL1.120.5
2BMEDIUM POSITIONAL0.840.5
3CMEDIUM POSITIONAL0.910.5
4DMEDIUM POSITIONAL1.330.5
1AMEDIUM THERMAL3.622
2BMEDIUM THERMAL3.242
3CMEDIUM THERMAL2.92
4DMEDIUM THERMAL3.812
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 86 -
Rwork0.254 1856 -
obs--84.69 %
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)
10.5248-0.1856-0.11010.38970.60711.16430.02690.04720.0367-0.0239-0.0554-0.029-0.0684-0.0910.02850.02360.0096-0.0130.01130.0020.03029.786128.657910.391
20.4266-0.12390.5091.1263-0.61383.41380.0307-0.00070.10150.0286-0.038-0.0649-0.0172-0.00760.00730.020.01890.01830.02770.02030.058330.168118.492543.6665
30.6425-0.2422-0.06011.93780.17480.06430.06490.05420.0208-0.0762-0.064-0.1495-0.0515-0.02-0.00090.04460.0168-0.00450.03060.01720.024815.567528.33945.5893
42.2085-0.83530.40532.08880.51530.9960.0648-0.1593-0.02360.197-0.0499-0.0339-0.04160.024-0.01490.0586-0.0365-0.00310.03410.01380.0327.726526.688812.3518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A449 - 556
2X-RAY DIFFRACTION1A601 - 734
3X-RAY DIFFRACTION2B448 - 556
4X-RAY DIFFRACTION2B601 - 702
5X-RAY DIFFRACTION3C449 - 556
6X-RAY DIFFRACTION3C601 - 711
7X-RAY DIFFRACTION4D450 - 556
8X-RAY DIFFRACTION4D601 - 681

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