[English] 日本語
Yorodumi
- PDB-1gzq: CD1b in complex with Phophatidylinositol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gzq
TitleCD1b in complex with Phophatidylinositol
Components
  • B2-MICROGLOBULIN
  • T-CELL SURFACE GLYCOPROTEIN CD1B
KeywordsGLYCOPROTEIN / PHOPHATIDYLINOSITOL / MHC / ANTIGEN PRESENTATION
Function / homology
Function and homology information


: / : / : / : / : / negative regulation of receptor binding / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib ...: / : / : / : / : / negative regulation of receptor binding / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / retina homeostasis / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / positive regulation of protein binding / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of membrane depolarization / T cell differentiation in thymus / regulation of natural killer cell mediated immunity / early endosome lumen / positive regulation of T cell mediated cytotoxicity / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of neuron projection development / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / protein refolding / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / cellular response to lipopolysaccharide / ER-Phagosome pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / early endosome membrane / antibacterial humoral response / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / adaptive immune response / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / lysosomal membrane / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / 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
DODECANE / NITRATE ION / Chem-PII / DOCOSANE / Beta-2-microglobulin / T-cell surface glycoprotein CD1b / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsGadola, S.D. / Zaccai, N.R. / Harlos, K. / Shepherd, D. / Ritter, G. / Schmidt, R.R. / Jones, E.Y. / Cerundolo, V.
CitationJournal: Nat.Immunol. / Year: 2002
Title: Structure of Human Cd1B with Bound Ligands at 2.3 A, a Maze for Alkyl Chains
Authors: Gadola, S.D. / Zaccai, N.R. / Harlos, K. / Shepherd, D. / Castro-Palomino, J.C. / Ritter, G. / Schmidt, R.R. / Jones, E.Y. / Cerundolo, V.
History
DepositionMay 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen
Item: _diffrn_detector.detector / _diffrn_detector.type ..._diffrn_detector.detector / _diffrn_detector.type / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-CELL SURFACE GLYCOPROTEIN CD1B
B: B2-MICROGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4608
Polymers44,9682
Non-polymers1,4926
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.881, 176.998, 75.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein T-CELL SURFACE GLYCOPROTEIN CD1B / CD1B ANTIGEN


Mass: 33088.215 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P29016
#2: Protein B2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01884, UniProt: P61769*PLUS

-
Non-polymers , 5 types, 202 molecules

#3: Chemical ChemComp-PII / 2-[(HYDROXY{[(2R,3R,5S,6R)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL]OXY}PHOSPHORYL)OXY]-1-[(PALMITOYLOXY)METHYL]ETHYL HEPTADECANOATE


Mass: 825.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H81O13P
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#6: Chemical ChemComp-TWT / DOCOSANE


Mass: 310.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H46
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsRESIDUES GLYCINE A278 AND PROLINE A279 ARE THE STARTING RESIDUES OF A BIRA TAG ...RESIDUES GLYCINE A278 AND PROLINE A279 ARE THE STARTING RESIDUES OF A BIRA TAG (GPGSGGGLNDIFEAQKIEWH) WHICH WAS LOCATED AT THE C-TERMINUS OF THE RECOMBINANT CD1B HEAVY CHAIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / pH: 7.1
Details: 20 DEGREES C, 2UL OF PROTEIN + 1UL OF MOTHER LIQUOR, 0.2M LITHIUM NITRATE, 20% W/V POLYETHYLENE GLYCOL 3350, PH 7.1
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
10.2 Mlithium nitrate1reservoir
220 %(w/v)EG33501reservoirpH7.1
35 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 334867 / % possible obs: 92.3 % / Observed criterion σ(I): -0.5 / Redundancy: 12.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 39.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 15.8 / % possible all: 89.8
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 27623 / Num. measured all: 337867
Reflection shell
*PLUS
% possible obs: 89.8 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED STRUCTURE OF CD1B-GM2 COMPLEX

Resolution: 2.26→24.3 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1307389.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 751 3 %RANDOM
Rwork0.203 ---
obs0.203 25407 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4941 Å2 / ksol: 0.318222 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1-14.73 Å20 Å20 Å2
2---10.81 Å20 Å2
3----3.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.26→24.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 102 196 3295
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.561.5
X-RAY DIFFRACTIONc_mcangle_it3.912
X-RAY DIFFRACTIONc_scbond_it4.572
X-RAY DIFFRACTIONc_scangle_it6.062.5
LS refinement shellResolution: 2.26→2.4 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 100 3 %
Rwork0.314 3220 -
obs--72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3LIPID2_11.PARAMGM2_11.TOP
Refinement
*PLUS
Rfactor Rfree: 0.238 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

+
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