[English] 日本語
Yorodumi
- PDB-5acm: Mcg immunoglobulin variable domain with methylene blue -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5acm
TitleMcg immunoglobulin variable domain with methylene blue
ComponentsMCG
KeywordsIMMUNE SYSTEM / MCG / IMMUNOGLOBULIN VARIABLE DOMAIN / METHYLENE BLUE
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / Immunoglobulin lambda variable 2-8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBrumshtein, B. / Esswein, S.R. / Salwinski, L. / Phillips, M.L. / Ly, A.T. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.S.
CitationJournal: Elife / Year: 2015
Title: Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain.
Authors: Brumshtein, B. / Esswein, S.R. / Salwinski, L. / Phillips, M.L. / Ly, A.T. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.S.
History
DepositionAug 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MCG
B: MCG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,08410
Polymers23,1312
Non-polymers9538
Water3,747208
1
A: MCG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2346
Polymers11,5661
Non-polymers6695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MCG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8504
Polymers11,5661
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.220, 31.080, 73.630
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody MCG


Mass: 11565.510 Da / Num. of mol.: 2 / Fragment: IG LAMBDA CHAIN V-II REGION MGC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01709
#2: Chemical ChemComp-MBT / 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / METHYLENE BLUE


Mass: 284.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N3S / Comment: medication*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M NH4CL, 2.2 M (NH4)2SO4, 0.5 M METHYLENE BLUE, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.907
11-h,-k,l20.093
ReflectionResolution: 1.05→40 Å / Num. obs: 73808 / % possible obs: 89 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 1.05→1.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 82

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UNU

4unu


Resolution: 1.05→39.22 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.23 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.004 / ESU R Free: 0.004 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.12234 4102 5 %RANDOM
Rwork0.11033 ---
obs0.11092 78400 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.864 Å2
Baniso -1Baniso -2Baniso -3
1--5.54 Å20 Å2-1.58 Å2
2--5.44 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.05→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 56 208 1860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0460.021698
X-RAY DIFFRACTIONr_bond_other_d0.0070.021482
X-RAY DIFFRACTIONr_angle_refined_deg3.2721.9842321
X-RAY DIFFRACTIONr_angle_other_deg2.1823.0033432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7152564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97115239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.251154
X-RAY DIFFRACTIONr_chiral_restr0.2440.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0211952
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0281.44875
X-RAY DIFFRACTIONr_mcbond_other2.031.44874
X-RAY DIFFRACTIONr_mcangle_it2.0522.1671090
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6421.734823
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.42733180
X-RAY DIFFRACTIONr_sphericity_free26.787574
X-RAY DIFFRACTIONr_sphericity_bonded8.15753281
LS refinement shellResolution: 1.049→1.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.079 315 -
Rwork0.071 5577 -
obs--96.09 %

+
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