[English] 日本語
Yorodumi
- PDB-2akr: Structural basis of sulfatide presentation by mouse CD1d -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2akr
TitleStructural basis of sulfatide presentation by mouse CD1d
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • T-cell surface glycoprotein CD1d1
KeywordsIMMUNE SYSTEM / NKT cells / CD1d / MHC fold / sulfatide / self-antigen / TCR
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / positive regulation of NK T cell activation / NK T cell differentiation / 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 ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / positive regulation of NK T cell activation / NK T cell differentiation / 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 / positive thymic T cell selection / positive regulation of macrophage 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 / regulation of membrane depolarization / antigen processing and presentation / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / Neutrophil degranulation / cell adhesion molecule binding / T cell receptor binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / late endosome / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / histone binding / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / lysosome / learning or memory / early endosome / endosome membrane / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol / cytoplasm
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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CIS / : / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZajonc, D.M. / Halder, R. / Wu, D. / Maricic, I. / Roy, K. / Wong, C.-H. / Kumar, V. / Wilson, I.A.
CitationJournal: J.Exp.Med. / Year: 2005
Title: Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity
Authors: Zajonc, D.M. / Maricic, I. / Wu, D. / Halder, R. / Roy, K. / Wong, C.-H. / Kumar, V. / Wilson, I.A.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The Swiss-Prot entry P11609 conflicts with Bradbury et al., 1988 which suggests a ...SEQUENCE The Swiss-Prot entry P11609 conflicts with Bradbury et al., 1988 which suggests a histidine in place of aspartate. Author sequence agrees with the citation.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell surface glycoprotein CD1d1
B: Beta-2-microglobulin
C: T-cell surface glycoprotein CD1d1
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,89712
Polymers88,5864
Non-polymers3,3118
Water13,475748
1
A: T-cell surface glycoprotein CD1d1
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8476
Polymers44,2932
Non-polymers1,5544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-17 kcal/mol
Surface area18370 Å2
MethodPISA
2
C: T-cell surface glycoprotein CD1d1
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0506
Polymers44,2932
Non-polymers1,7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-13 kcal/mol
Surface area18590 Å2
MethodPISA
3
C: T-cell surface glycoprotein CD1d1
D: Beta-2-microglobulin
hetero molecules

A: T-cell surface glycoprotein CD1d1
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,89712
Polymers88,5864
Non-polymers3,3118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area12160 Å2
ΔGint-44 kcal/mol
Surface area35560 Å2
MethodPISA
4
C: T-cell surface glycoprotein CD1d1
D: Beta-2-microglobulin
hetero molecules

A: T-cell surface glycoprotein CD1d1
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,89712
Polymers88,5864
Non-polymers3,3118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area11260 Å2
ΔGint-29 kcal/mol
Surface area36460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.858, 74.843, 101.564
Angle α, β, γ (deg.)90.00, 102.10, 90.00
Int Tables number4
Space group name H-MP1211
Detailsheterodimer formed by CD1d and beta-2-microglobulin

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein T-cell surface glycoprotein CD1d1 / CD1.1 antigen


Mass: 32632.668 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 cells / References: UniProt: P11609
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11660.350 Da / Num. of mol.: 2 / Fragment: residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 cells / References: GenBank: 55153801, UniProt: P01887*PLUS

-
Sugars , 2 types, 6 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.: 1 / Source method: obtained synthetically
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
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / 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, 750 molecules

#5: Chemical ChemComp-CIS / (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE / (2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL / CIS-TETRACOSENOYL SULFATIDE


Mass: 890.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H91NO11S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 277 K / pH: 6.5
Details: ammonium sulfate, NaCl, sodium cacodylate, manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 6.50

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97976
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2005
RadiationMonochromator: CURVED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 67171 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.089 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.58 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z5L

1z5l


Resolution: 1.9→41.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.941 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1359 2 %RANDOM
Rwork0.186 ---
obs0.187 65745 98.6 %-
all-67104 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.481 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 220 748 6918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.958632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60424.178292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.911151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3161530
X-RAY DIFFRACTIONr_chiral_restr0.1410.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22744
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24222
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2637
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.294
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0121.53787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51725968
X-RAY DIFFRACTIONr_scbond_it2.52433013
X-RAY DIFFRACTIONr_scangle_it3.7714.52664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 99 -
Rwork0.262 4796 -
obs--98.37 %
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)
12.9898-0.33360.59951.8394-1.29941.97970.0620.0406-0.1172-0.1218-0.03430.07050.0312-0.0531-0.0278-0.1114-0.0323-0.0045-0.1290.0059-0.0894-5.827-2.505817.228
22.1851.6141.73693.79481.4832.3038-0.0341-0.09330.019-0.0064-0.0268-0.1323-0.0893-0.00830.0609-0.1181-0.01140.0069-0.15220.0168-0.144724.81629.554236.8879
33.8165-0.2870.90491.1256-0.15752.33110.08140.113-0.1086-0.0745-0.00250.0021-0.00560.0838-0.0788-0.1034-0.02940.0246-0.19930.0137-0.105322.6581-3.822819.3974
41.0906-0.21980.26621.5957-1.15832.18420.0213-0.0311-0.0018-0.0510.02620.1836-0.0565-0.1246-0.0475-0.1244-0.02260.0033-0.1519-0.0244-0.120621.153938.474421.4037
54.1672.09021.67183.21881.55332.826-0.0809-0.16580.1647-0.0762-0.0631-0.0829-0.2551-0.02640.1441-0.0929-0.0061-0.0141-0.11050.0096-0.113851.578447.841642.7105
65.5793-1.12541.62041.0567-0.63542.07420.03980.3522-0.1015-0.0885-0.0557-0.11740.04180.26970.016-0.103-0.01880.0335-0.1328-0.0167-0.091349.739836.909323.6334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1857 - 185
2X-RAY DIFFRACTION1AE - G500 - 511
3X-RAY DIFFRACTION1AK1001
4X-RAY DIFFRACTION2AA186 - 279186 - 279
5X-RAY DIFFRACTION3BB2 - 992 - 99
6X-RAY DIFFRACTION4CC7 - 1857 - 185
7X-RAY DIFFRACTION4CH - J500 - 503
8X-RAY DIFFRACTION4CL1002
9X-RAY DIFFRACTION5CC186 - 279186 - 279
10X-RAY DIFFRACTION6DD2 - 992 - 99

+
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