[English] 日本語
Yorodumi
- PDB-7nmc: Crystal structure of beta-2-microglobulin D76E mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nmc
TitleCrystal structure of beta-2-microglobulin D76E mutant
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / major histocompatibility complex class 1 / beta-2-microglobulin / mutant / D76E
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGuthertz, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustRGIMCB-109984 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: The effect of mutation on an aggregation-prone protein: An in vivo, in vitro, and in silico analysis.
Authors: Guthertz, N. / van der Kant, R. / Martinez, R.M. / Xu, Y. / Trinh, C. / Iorga, B.I. / Rousseau, F. / Schymkowitz, J. / Brockwell, D.J. / Radford, S.E.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2284
Polymers11,8931
Non-polymers3343
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint2 kcal/mol
Surface area6900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 28.871, 67.508
Angle α, β, γ (deg.)90.000, 102.023, 90.000
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Beta-2-microglobulin


Mass: 11893.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.81 % / Description: One molecule per asymmetric unit
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 nL mother liquor / 200 nL protein 15% Glycerol, 0.1 M NaAcetate pH 4.5-5.5, 28-32%PEG 4000, 0.2 M NH4Acetate
PH range: 4.5 - 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.2→46.6 Å / Num. obs: 31346 / % possible obs: 96.3 % / Redundancy: 5.6 % / CC1/2: 0.994 / Rpim(I) all: 0.046 / Net I/σ(I): 12.5
Reflection shellResolution: 1.2→1.22 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1236 / CC1/2: 0.828 / Rpim(I) all: 0.306

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata processing
Cootmodel building
PHASERphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YXF

2yxf


Resolution: 1.2→46.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.228 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1794 1499 4.782 %
Rwork0.1582 29846 -
all0.159 --
obs-31345 96.28 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.637 Å2
Baniso -1Baniso -2Baniso -3
1-0.415 Å20 Å20.341 Å2
2---0.054 Å20 Å2
3----0.465 Å2
Refinement stepCycle: LAST / Resolution: 1.2→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 22 167 1027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013900
X-RAY DIFFRACTIONr_bond_other_d0.0010.017804
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.6541214
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5841882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8995104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00122.88552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13915156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.962155
X-RAY DIFFRACTIONr_chiral_restr0.0930.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
X-RAY DIFFRACTIONr_nbd_refined0.2580.2144
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.2737
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2407
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.310.213
X-RAY DIFFRACTIONr_nbd_other0.2280.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.229
X-RAY DIFFRACTIONr_mcbond_it1.2731.052407
X-RAY DIFFRACTIONr_mcbond_other1.271.05406
X-RAY DIFFRACTIONr_mcangle_it1.7691.579508
X-RAY DIFFRACTIONr_mcangle_other1.7741.583509
X-RAY DIFFRACTIONr_scbond_it2.8821.649492
X-RAY DIFFRACTIONr_scbond_other2.8811.652493
X-RAY DIFFRACTIONr_scangle_it3.4622.251704
X-RAY DIFFRACTIONr_scangle_other3.4592.254705
X-RAY DIFFRACTIONr_lrange_it4.20816.9441018
X-RAY DIFFRACTIONr_lrange_other3.71515.236967
X-RAY DIFFRACTIONr_rigid_bond_restr2.07931703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.414920.4041775X-RAY DIFFRACTION78.2809
1.231-1.2650.313890.3082023X-RAY DIFFRACTION90.2564
1.265-1.3020.2441020.2262126X-RAY DIFFRACTION98.4099
1.302-1.3420.189940.1712080X-RAY DIFFRACTION98.8631
1.342-1.3850.183990.1462000X-RAY DIFFRACTION98.3599
1.385-1.4340.1791050.1321923X-RAY DIFFRACTION98.8786
1.434-1.4880.1881040.1331864X-RAY DIFFRACTION98.7952
1.488-1.5490.152720.1331815X-RAY DIFFRACTION98.3837
1.549-1.6180.167970.141721X-RAY DIFFRACTION98.4299
1.618-1.6970.153950.1411643X-RAY DIFFRACTION98.8061
1.697-1.7880.178720.1421599X-RAY DIFFRACTION99.228
1.788-1.8960.163770.1391501X-RAY DIFFRACTION98.8103
1.896-2.0270.129560.1281416X-RAY DIFFRACTION98.6595
2.027-2.1890.156680.1351300X-RAY DIFFRACTION97.9943
2.189-2.3980.165690.1341194X-RAY DIFFRACTION97.4537
2.398-2.680.181510.1491080X-RAY DIFFRACTION97.1649
2.68-3.0930.175540.162963X-RAY DIFFRACTION97.3206
3.093-3.7830.165430.146808X-RAY DIFFRACTION96.1582
3.783-5.3330.166340.154646X-RAY DIFFRACTION97.561
5.333-37.8860.254260.273369X-RAY DIFFRACTION96.1071

+
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