[English] 日本語
Yorodumi
- PDB-4jvw: IgM C4-domain from mouse -

+
Open data


ID or keywords:

Loading...

-
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 / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / B cell receptor complex / Cell surface interactions at the vascular wall / positive regulation of B cell activation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / pre-B cell allelic exclusion / early endosome to late endosome transport / B cell affinity maturation ...CD22 mediated BCR regulation / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / B cell receptor complex / Cell surface interactions at the vascular wall / positive regulation of B cell activation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / pre-B cell allelic exclusion / early endosome to late endosome transport / B cell affinity maturation / humoral immune response mediated by circulating immunoglobulin / regulation of cell morphogenesis / regulation of immunoglobulin production / immunoglobulin receptor binding / immunoglobulin complex, circulating / antigen processing and presentation / B cell activation / immunoglobulin mediated immune response / B cell proliferation / positive regulation of endocytosis / antigen binding / positive regulation of B cell proliferation / B cell receptor signaling pathway / positive regulation of immune response / transmembrane signaling receptor activity / MAPK cascade / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / external side of plasma membrane / perinuclear region of cytoplasm / cell surface / extracellular space / identical protein binding / membrane / plasma membrane / 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 / 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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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