[English] 日本語
Yorodumi
- PDB-4r9h: Crystal structure of dimeric S33C beta-2 microglobulin mutant at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r9h
TitleCrystal structure of dimeric S33C beta-2 microglobulin mutant at 1.9 Angstrom resolution
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / amyloidosis / protein aggregation / covalent dimer / oligomerization / beta sandwich / inclusion bodies
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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / 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 / membrane / identical protein binding / 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
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHalabelian, L. / Bolognesi, M. / Ricagno, S.
CitationJournal: Sci Rep / Year: 2015
Title: A covalent homodimer probing early oligomers along amyloid aggregation.
Authors: Halabelian, L. / Relini, A. / Barbiroli, A. / Penco, A. / Bolognesi, M. / Ricagno, S.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Jun 27, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.4Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-2-microglobulin
B: Beta-2-microglobulin
C: Beta-2-microglobulin
D: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)47,5824
Polymers47,5824
Non-polymers00
Water3,027168
1
A: Beta-2-microglobulin
D: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)23,7912
Polymers23,7912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area12120 Å2
MethodPISA
2
B: Beta-2-microglobulin
C: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)23,7912
Polymers23,7912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-10 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.840, 68.840, 200.039
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-122-

HOH

-
Components

#1: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11895.422 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119 / Mutation: S33C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P, NM_004048 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG4000, 0.2 M imidazole-malate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2013 / Details: bent cylindrical mirror
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→68.84 Å / Num. all: 39024 / Num. obs: 38985 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5533 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OV6

3ov6


Resolution: 1.9→68.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.457 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24736 1965 5.1 %RANDOM
Rwork0.21179 ---
all0.21353 39024 --
obs0.21353 36945 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.779 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2--1.18 Å20 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→68.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 0 168 3465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193410
X-RAY DIFFRACTIONr_bond_other_d0.0010.023112
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9394624
X-RAY DIFFRACTIONr_angle_other_deg2.15737197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53524180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67215590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0371520
X-RAY DIFFRACTIONr_chiral_restr0.1110.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213822
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02826
X-RAY DIFFRACTIONr_mcbond_it3.142.8491582
X-RAY DIFFRACTIONr_mcbond_other3.142.8471581
X-RAY DIFFRACTIONr_mcangle_it4.5994.2421974
X-RAY DIFFRACTIONr_mcangle_other4.5994.2451975
X-RAY DIFFRACTIONr_scbond_it4.1983.4091828
X-RAY DIFFRACTIONr_scbond_other4.1973.4111829
X-RAY DIFFRACTIONr_scangle_other6.3574.8992651
X-RAY DIFFRACTIONr_long_range_B_refined8.47523.823643
X-RAY DIFFRACTIONr_long_range_B_other8.49523.6993603
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 140 -
Rwork0.329 2640 -
obs--98.9 %
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)
11.24820.8820.10580.98590.2440.52160.0926-0.0249-0.08960.0993-0.0888-0.12840.0975-0.0501-0.00390.04610.0018-0.01870.10410.02650.07036.9631.043515.8611
23.28460.088-2.10010.5589-0.07491.419-0.04040.2273-0.01350.07510.06640.00840.0428-0.1278-0.0260.03570.0546-0.00190.12620.00720.0673-23.863410.923512.9647
31.0881-0.10571.56220.88640.68433.3365-0.1548-0.0675-0.0354-0.27970.1536-0.1117-0.4693-0.01570.00120.20410.00280.04660.0695-0.05840.1056-36.24111.09841.294
41.213-0.43350.38670.70530.91992.4742-0.04780.0324-0.0461-0.1154-0.11790.1943-0.1955-0.2160.16570.12090.0204-0.05710.0331-0.02470.147214.81527.99327.59
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 99
2X-RAY DIFFRACTION2B1 - 98
3X-RAY DIFFRACTION3C1 - 98
4X-RAY DIFFRACTION4D0 - 97

+
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