[English] 日本語
Yorodumi
- PDB-6bmh: Crystal structure of MHC-I like protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bmh
TitleCrystal structure of MHC-I like protein
Components
  • Antigen-presenting glycoprotein CD1d2
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / Major Histocompatibility complex / MHC-I / CD1d / antigen
Function / homology
Function and homology information


positive regulation of NK T cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / cellular defense response / Neutrophil degranulation ...positive regulation of NK T cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / cellular defense response / Neutrophil degranulation / positive regulation of interleukin-2 production / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome membrane / external side of plasma membrane / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-F61 / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsKhandokar, Y.B. / Le Nours, J. / Rossjohn, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Differing roles of CD1d2 and CD1d1 proteins in type I natural killer T cell development and function.
Authors: Sundararaj, S. / Zhang, J. / Krovi, S.H. / Bedel, R. / Tuttle, K.D. / Veerapen, N. / Besra, G.S. / Khandokar, Y. / Praveena, T. / Le Nours, J. / Matsuda, J.L. / Rossjohn, J. / Gapin, L.
History
DepositionNov 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 7, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d2
B: Beta-2-microglobulin
C: Antigen-presenting glycoprotein CD1d2
D: Beta-2-microglobulin
E: Antigen-presenting glycoprotein CD1d2
F: Beta-2-microglobulin
G: Antigen-presenting glycoprotein CD1d2
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,97421
Polymers172,5798
Non-polymers5,39513
Water5,423301
1
A: Antigen-presenting glycoprotein CD1d2
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4385
Polymers43,1452
Non-polymers1,2943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-16 kcal/mol
Surface area18110 Å2
MethodPISA
2
C: Antigen-presenting glycoprotein CD1d2
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4385
Polymers43,1452
Non-polymers1,2943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-15 kcal/mol
Surface area17790 Å2
MethodPISA
3
E: Antigen-presenting glycoprotein CD1d2
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4385
Polymers43,1452
Non-polymers1,2943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-15 kcal/mol
Surface area18060 Å2
MethodPISA
4
G: Antigen-presenting glycoprotein CD1d2
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6606
Polymers43,1452
Non-polymers1,5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-14 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.955, 74.229, 117.594
Angle α, β, γ (deg.)90.00, 102.94, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Antigen-presenting glycoprotein CD1d2


Mass: 31484.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d2, Cd1.2 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P11610
#2: Protein
Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P01887

-
Sugars , 2 types, 9 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 305 molecules

#4: Chemical
ChemComp-F61 / N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide


Mass: 647.924 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C35H69NO9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 100 mM BisTris (pH 6-6.5), 200 mM CaCl2, 21-26% PEG 3350
PH range: 6-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→45.93 Å / Num. obs: 79496 / % possible obs: 99.8 % / Redundancy: 7 % / Rpim(I) all: 0.043 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.38 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CD1

1cd1


Resolution: 2.298→45.931 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 4000 5.04 %
Rwork0.2298 --
obs0.2323 79388 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.298→45.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11694 0 363 301 12358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112475
X-RAY DIFFRACTIONf_angle_d0.90717006
X-RAY DIFFRACTIONf_dihedral_angle_d21.1914467
X-RAY DIFFRACTIONf_chiral_restr0.0561855
X-RAY DIFFRACTIONf_plane_restr0.0062137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.298-2.3250.38781390.29662517X-RAY DIFFRACTION96
2.325-2.35340.30911300.28092592X-RAY DIFFRACTION100
2.3534-2.38310.37821460.28032528X-RAY DIFFRACTION100
2.3831-2.41450.35421520.28272586X-RAY DIFFRACTION100
2.4145-2.44760.34291350.2732597X-RAY DIFFRACTION100
2.4476-2.48250.35721310.28082602X-RAY DIFFRACTION100
2.4825-2.51960.34821520.27482565X-RAY DIFFRACTION100
2.5196-2.5590.35611460.27652599X-RAY DIFFRACTION100
2.559-2.60090.2891290.26152566X-RAY DIFFRACTION100
2.6009-2.64580.31531250.2542652X-RAY DIFFRACTION100
2.6458-2.69390.3681330.262545X-RAY DIFFRACTION100
2.6939-2.74570.29461380.27052639X-RAY DIFFRACTION100
2.7457-2.80170.38091250.26892591X-RAY DIFFRACTION100
2.8017-2.86260.351490.27432600X-RAY DIFFRACTION100
2.8626-2.92920.32211280.26652574X-RAY DIFFRACTION100
2.9292-3.00240.31211330.26152598X-RAY DIFFRACTION100
3.0024-3.08360.30851410.26482613X-RAY DIFFRACTION100
3.0836-3.17430.34631350.26512564X-RAY DIFFRACTION100
3.1743-3.27670.31451480.25972611X-RAY DIFFRACTION100
3.2767-3.39380.29851470.23932624X-RAY DIFFRACTION100
3.3938-3.52970.28151290.23152595X-RAY DIFFRACTION100
3.5297-3.69020.26381410.22572594X-RAY DIFFRACTION100
3.6902-3.88470.24821310.2132636X-RAY DIFFRACTION100
3.8847-4.12790.22391520.19572589X-RAY DIFFRACTION100
4.1279-4.44640.23521370.17322614X-RAY DIFFRACTION100
4.4464-4.89340.19311580.15722618X-RAY DIFFRACTION100
4.8934-5.60040.23451340.18742660X-RAY DIFFRACTION100
5.6004-7.05190.23111350.22372635X-RAY DIFFRACTION100
7.0519-45.94050.24221210.21642684X-RAY DIFFRACTION98

+
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