[English] 日本語
Yorodumi
- PDB-6k7u: Crystal structure of beta-2 microglobulin (beta2m) of Bat (Pterop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k7u
TitleCrystal structure of beta-2 microglobulin (beta2m) of Bat (Pteropus Alecto)
ComponentsBat beta-2-microglobulin
KeywordsIMMUNE SYSTEM / Immune molecular
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / extracellular region
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 ...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 / Nucleic acid-binding, OB-fold / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsLu, D. / Liu, K.F. / Zhang, D. / Yue, C. / Lu, Q. / Cheng, H. / Chai, Y. / Qi, J.X. / Gao, F.G. / Liu, W.J.
CitationJournal: Plos Biol. / Year: 2019
Title: Peptide presentation by bat MHC class I provides new insight into the antiviral immunity of bats.
Authors: Lu, D. / Liu, K. / Zhang, D. / Yue, C. / Lu, Q. / Cheng, H. / Wang, L. / Chai, Y. / Qi, J. / Wang, L.F. / Gao, G.F. / Liu, W.J.
History
DepositionJun 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 4, 2019Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Bat beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,5761
Polymers11,5761
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6370 Å2
Unit cell
Length a, b, c (Å)33.707, 114.641, 57.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-176-

HOH

-
Components

#1: Protein Bat beta-2-microglobulin


Mass: 11575.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: L5K3Y9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH 6.5, 8% w/v Polyethylene glycol monomethyl ether 5000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: SDMS / Detector: OSCILLATION CAMERA / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 15045 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 28.036
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 15045

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→40.527 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 21.16
RfactorNum. reflection% reflection
Rfree0.2022 713 4.79 %
Rwork0.1954 --
obs0.1958 14900 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→40.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 0 87 887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006849
X-RAY DIFFRACTIONf_angle_d1.0151159
X-RAY DIFFRACTIONf_dihedral_angle_d26.291319
X-RAY DIFFRACTIONf_chiral_restr0.086117
X-RAY DIFFRACTIONf_plane_restr0.007153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6006-1.72410.30121480.25282635X-RAY DIFFRACTION94
1.7241-1.89760.23691460.22092808X-RAY DIFFRACTION100
1.8976-2.17220.21321360.19162861X-RAY DIFFRACTION100
2.1722-2.73670.22151420.21222872X-RAY DIFFRACTION100
2.7367-40.53990.16191410.1723011X-RAY DIFFRACTION100

+
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