[English] 日本語
Yorodumi
- PDB-5ckg: Human beta-2 microglobulin mutant V85E -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ckg
TitleHuman beta-2 microglobulin mutant V85E
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / Aggregation propensity / Amyloid / beta-sandwitch / fold stability
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / 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 ...Beta-2-Microglobulin / 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
ACETATE ION / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSala, B.M. / De Rosa, M. / Bolognesi, M. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of University and ResearchFIRB RBFR109EOS Italy
CitationJournal: Sci Rep / Year: 2016
Title: Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.
Authors: Camilloni, C. / Sala, B.M. / Sormanni, P. / Porcari, R. / Corazza, A. / De Rosa, M. / Zanini, S. / Barbiroli, A. / Esposito, G. / Bolognesi, M. / Bellotti, V. / Vendruscolo, M. / Ricagno, S.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-2-microglobulin
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0295
Polymers23,8192
Non-polymers2103
Water2,162120
1
A: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9682
Polymers11,9091
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0603
Polymers11,9091
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.578, 28.860, 87.719
Angle α, β, γ (deg.)90.00, 110.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-269-

HOH

-
Components

#1: Protein Beta-2-microglobulin


Mass: 11909.339 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119 / Mutation: V85E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET29B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium acetate, 30% w/v PEG 4000, 15% glycerol, 0.2 M ammonium acetate

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.75→27.71 Å / Num. obs: 20777 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.9 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z9T

2z9t


Resolution: 1.75→27.71 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1995 9.63 %
Rwork0.183 --
obs0.188 20722 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→27.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 14 120 1785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181825
X-RAY DIFFRACTIONf_angle_d1.7892495
X-RAY DIFFRACTIONf_dihedral_angle_d14.321697
X-RAY DIFFRACTIONf_chiral_restr0.095264
X-RAY DIFFRACTIONf_plane_restr0.009328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79370.32261420.27921341X-RAY DIFFRACTION96
1.7937-1.84220.25541380.24681314X-RAY DIFFRACTION97
1.8422-1.89640.28191370.2151285X-RAY DIFFRACTION94
1.8964-1.95760.24141390.19561301X-RAY DIFFRACTION95
1.9576-2.02760.23511450.19441346X-RAY DIFFRACTION97
2.0276-2.10870.22441430.19621336X-RAY DIFFRACTION97
2.1087-2.20470.27871420.19111341X-RAY DIFFRACTION97
2.2047-2.32080.27971370.19781286X-RAY DIFFRACTION94
2.3208-2.46620.26671450.19891357X-RAY DIFFRACTION98
2.4662-2.65640.23041430.20571337X-RAY DIFFRACTION97
2.6564-2.92350.23551450.19851361X-RAY DIFFRACTION97
2.9235-3.34590.23541420.18091341X-RAY DIFFRACTION97
3.3459-4.21310.21981470.15381370X-RAY DIFFRACTION96
4.2131-27.71270.19791500.16431411X-RAY DIFFRACTION96
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)
16.08144.0012-5.09954.8299-3.66584.95780.1650.4150.1519-0.13530.16360.0046-0.3783-0.5392-0.39440.3370.03810.04280.25320.02950.217414.82617.27520.2253
27.307-1.1469-3.84921.761-2.25942.02230.523-0.72190.46310.51250.83091.94551.5183-1.83810.47520.2820.08660.27340.90040.43440.8162-6.8371-2.512513.5967
36.52012.4432-6.1044.6644-4.37038.3999-0.22110.7602-0.0289-0.13210.45240.10720.2244-1.0477-0.22050.2413-0.03010.00990.207-0.00690.140810.66510.0413.8551
48.23391.7999-5.37125.9545-1.4794.6333-0.2069-0.7004-0.9536-0.068-0.3003-0.17221.23840.68190.36520.40830.0048-0.00990.33590.05910.311411.9042-5.142815.3734
54.18282.9061-4.22536.8465-5.05685.4869-0.62481.1455-0.5086-0.7810.5674-0.00120.9857-1.50960.1250.3906-0.0572-0.02510.45530.01360.305610.3379-2.46630.0144
67.55931.4216-5.11743.7284-0.74867.2542-0.2138-1.1234-0.09740.42070.10720.3544-0.312-0.3395-0.05990.36220.11130.06530.46760.0520.27036.81961.248217.8662
78.6944.5217-2.29283.6699-2.99942.97860.2118-0.8019-0.10070.8078-0.46470.2163-0.35630.2507-0.090.4557-0.06870.07620.2209-0.02330.254522.37048.24748.4635
84.53474.2833-4.14985.9403-3.01014.40920.04610.57672.52450.57180.91251.4065-1.2551-1.4709-0.43160.50880.11770.10780.4128-0.02670.48984.15037.062314.4056
94.15984.4203-2.97613.2323-2.55326.14430.3745-0.15620.30160.1-0.15940.0683-0.2856-0.0491-0.12450.19870.0445-0.03760.1215-0.01180.217929.522319.3515-40.1714
104.1488-1.1527-2.10848.8091-2.01536.76610.0968-0.84810.24120.6161-0.06330.7257-0.0087-0.8123-0.05920.2213-0.01250.01210.6615-0.04810.31887.565911.1292-29.6757
119.68381.4858-2.81291.8911-0.40162.2436-0.0417-0.1936-0.24920.1035-0.0018-0.1560.0453-0.31980.07020.1756-0.0164-0.0490.2106-0.02190.169925.423312.3459-38.1375
125.972.8984-3.92223.0086-2.91523.110.1337-0.96790.00280.0575-0.078-0.01270.17890.0096-0.01070.2658-0.0076-0.09350.38030.03440.228728.16199.5737-28.6991
132.063-0.9624-0.30838.46014.69563.3012-0.2447-1.0754-2.3197-0.0051-0.31640.33551.6695-0.11020.51720.7528-0.01660.06290.5640.07070.550824.64154.0858-26.0297
148.88534.7383-4.42799.8595-3.40333.1392-0.40630.4568-0.1064-0.85070.03010.12230.2945-0.02080.37320.2634-0.0254-0.04980.2836-0.01770.187529.139911.125-48.0717
157.18873.0919-5.1093.7163-2.55094.1464-0.23670.3407-0.19390.0780.13430.22680.1769-0.72950.11960.1854-0.0464-0.02820.26020.00880.183821.85028.7582-37.2922
164.2088-1.4438-4.99825.4649-1.83288.5243-0.0094-1.46291.46570.6761-0.05210.0394-0.7692-0.4637-0.07270.53430.0614-0.01770.7802-0.01470.397713.637712.2889-19.3094
175.19881.9272-2.03141.0771-0.98945.8270.3172-0.7160.13860.2955-0.2803-0.2047-0.69570.56550.01780.2396-0.0507-0.08270.2557-0.0090.242532.682816.6382-30.8694
182.80444.5612-1.76867.5454-1.56658.35630.3727-0.75592.43370.5885-0.16861.027-1.1201-0.9227-0.00780.35750.0865-0.0090.3924-0.15420.390919.279118.9832-27.5458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 11 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 12 THROUGH 19 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 20 THROUGH 35 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 36 THROUGH 50 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 51 THROUGH 71 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 72 THROUGH 83 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 84 THROUGH 90 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 91 THROUGH 99 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 0 THROUGH 11 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 12 THROUGH 19 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 20 THROUGH 35 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 36 THROUGH 41 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 42 THROUGH 50 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 51 THROUGH 60 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 61 THROUGH 71 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 72 THROUGH 77 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 78 THROUGH 90 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 91 THROUGH 99 )

+
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://pdbjlvh1.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