[English] 日本語
Yorodumi
- PDB-4z78: Weak TCR binding to an unstable insulin epitope drives type 1 diabetes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z78
TitleWeak TCR binding to an unstable insulin epitope drives type 1 diabetes
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-D alpha chain
  • Insulin
KeywordsIMMUNE SYSTEM / Immunoglobulin / H-2Kd / Type 1 Diabetes
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of dendritic spine maintenance / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of respiratory burst involved in inflammatory response / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / COPI-mediated anterograde transport / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / positive regulation of glycolytic process / endosome lumen / acute-phase response / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / positive regulation of D-glucose import across plasma membrane / positive regulation of protein secretion / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / insulin receptor binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / positive regulation of cell differentiation / cellular response to iron(III) ion / Regulation of insulin secretion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / wound healing / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / hormone activity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of neuron projection development / MHC class I protein complex / negative regulation of protein catabolic process / peptide antigen assembly with MHC class II protein complex / regulation of synaptic plasticity / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / specific granule lumen / cognition / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / glucose metabolic process / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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
Insulin / H-2 class I histocompatibility antigen, K-D alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.304 Å
Model detailsG9GF in H-2Kd, Orthorhombic form
AuthorsRizkallah, P.J. / Cole, D.K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Distortion of the Major Histocompatibility Complex Class I Binding Groove to Accommodate an Insulin-derived 10-Mer Peptide.
Authors: Motozono, C. / Pearson, J.A. / De Leenheer, E. / Rizkallah, P.J. / Beck, K. / Trimby, A. / Sewell, A.K. / Wong, F.S. / Cole, D.K.
History
DepositionApr 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-D alpha chain
B: Beta-2-microglobulin
C: Insulin
D: H-2 class I histocompatibility antigen, K-D alpha chain
E: Beta-2-microglobulin
F: Insulin
G: H-2 class I histocompatibility antigen, K-D alpha chain
H: Beta-2-microglobulin
I: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,89729
Polymers136,1699
Non-polymers1,72720
Water6,557364
1
A: H-2 class I histocompatibility antigen, K-D alpha chain
B: Beta-2-microglobulin
C: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,14412
Polymers45,3903
Non-polymers7559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-86 kcal/mol
Surface area19180 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-D alpha chain
E: Beta-2-microglobulin
F: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,02010
Polymers45,3903
Non-polymers6317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-84 kcal/mol
Surface area19010 Å2
MethodPISA
3
G: H-2 class I histocompatibility antigen, K-D alpha chain
H: Beta-2-microglobulin
I: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7327
Polymers45,3903
Non-polymers3424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-27 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.170, 151.570, 182.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22G
13B
23E
14B
24H
15D
25G
16E
26H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA0 - 2761 - 277
21PROPRODD0 - 2761 - 277
12PROPROAA0 - 2761 - 277
22PROPROGG0 - 2761 - 277
13METMETBB0 - 991 - 100
23METMETEE0 - 991 - 100
14METMETBB0 - 991 - 100
24METMETHH0 - 991 - 100
15PROPRODD0 - 2761 - 277
25PROPROGG0 - 2761 - 277
16METMETEE0 - 991 - 100
26METMETHH0 - 991 - 100

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 2 types, 6 molecules ADGBEH

#1: Protein H-2 class I histocompatibility antigen, K-D alpha chain / Leukocyte antigen heavy chain / H-2K(D)


Mass: 32353.016 Da / Num. of mol.: 3 / Fragment: UNP residues 22-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P01902
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 3 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P61769

-
Protein/peptide , 1 types, 3 molecules CFI

#3: Protein/peptide Insulin


Mass: 1157.363 Da / Num. of mol.: 3 / Fragment: UNP residues 39-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: synthetic construct (others) / References: UniProt: P01308

-
Non-polymers , 4 types, 384 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 4% PEG 4000, 0.1 M sodium acetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.304→182.23 Å / Num. all: 57725 / Num. obs: 57725 / % possible obs: 100 % / Redundancy: 7.2 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.148 / Rsym value: 0.127 / Net I/av σ(I): 5.2 / Net I/σ(I): 10.4 / Num. measured all: 418482
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.367.30.9290.83023841650.3990.9293100
2.36-2.437.50.7850.93084241220.3320.7853.5100
2.43-2.57.40.69912922139400.2980.6993.9100
2.5-2.587.20.6011.22808439060.2620.6014.399.9
2.58-2.667.10.4921.42658237340.2150.4925100
2.66-2.757.40.3971.82700836550.170.3976100
2.75-2.867.10.3162.22500035380.1380.3167100
2.86-2.987.30.2552.82459733760.1090.2558.299.9
2.98-3.117.40.1913.72413032740.0820.1919.8100
3.11-3.267.30.1474.82280331160.0640.14711.4100
3.26-3.447.10.1166.12106429740.0510.11613.2100
3.44-3.647.50.097.72102528220.0380.0915.7100
3.64-3.97.10.0788.71896126800.0340.07817100
3.9-4.217.60.0689.41894525000.0280.06819.2100
4.21-4.617.40.06110.31691322970.0250.06120.9100
4.61-5.157.10.0619.71504821050.0260.06120.899.9
5.15-5.957.10.0639.71312018600.0270.06319.6100
5.95-7.297.30.0679.51166116060.0280.06719100
7.29-10.316.70.04711.8854112740.020.04721.1100
10.31-182.2360.04113.146997810.0190.04121.399.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.43 Å37.1 Å
Translation5.43 Å37.1 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.304→78.09 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2301 / WRfactor Rwork: 0.1861 / FOM work R set: 0.832 / SU B: 14.573 / SU ML: 0.174 / SU R Cruickshank DPI: 0.3705 / SU Rfree: 0.2344 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 2925 5.1 %RANDOM
Rwork0.1882 ---
obs0.1904 54718 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.6 Å2 / Biso mean: 39.766 Å2 / Biso min: 15.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å2-0 Å2-0 Å2
2--0.67 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 2.304→78.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9615 0 101 364 10080
Biso mean--65.72 37.3 -
Num. residues----1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910007
X-RAY DIFFRACTIONr_bond_other_d0.0060.029029
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.93913576
X-RAY DIFFRACTIONr_angle_other_deg1.214320733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87951156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5623.048538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.029151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.361591
X-RAY DIFFRACTIONr_chiral_restr0.1080.21377
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111304
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022531
X-RAY DIFFRACTIONr_mcbond_it1.5461.8714645
X-RAY DIFFRACTIONr_mcbond_other1.5461.8714644
X-RAY DIFFRACTIONr_mcangle_it2.542.7955794
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A158460.08
12D158460.08
21A157360.09
22G157360.09
31B58100.09
32E58100.09
41B58000.08
42H58000.08
51D156280.09
52G156280.09
61E57650.09
62H57650.09
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 222 -
Rwork0.237 3937 -
all-4159 -
obs--99.98 %
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)
12.44880.3464-0.51761.3641-0.64563.30250.0171-0.0075-0.1836-0.0609-0.0070.06660.20410.013-0.01010.0665-0.0091-0.00790.0159-0.02060.05245.726746.94958.6295
21.8416-0.33240.48356.60610.91911.8723-0.0560.11290.3443-0.11640.08430.2561-0.28470.0164-0.02830.1459-0.01390.01030.1486-0.03150.124240.140279.18125.7609
32.24710.28390.37662.56062.17635.612-0.0287-0.23850.1590.20110.0506-0.3106-0.15720.2516-0.02190.08080.0021-0.04160.071-0.05480.143157.347564.10126.2458
43.03910.7735-1.00251.2736-0.6913.28170.0011-0.159-0.31960.0151-0.00910.03780.31560.05120.00790.11240.0015-0.00470.01690.0030.085222.776621.858836.2935
51.48191.13620.43397.2192-0.41161.55080.0004-0.0850.29960.2061-0.14780.6926-0.256-0.15040.14750.19320.0031-0.01960.1962-0.0760.177416.956152.795154.9085
64.01570.1903-0.04372.6881.58815.781-0.0721-0.63650.26080.43860.0793-0.2634-0.14830.3588-0.00730.16230.0047-0.04380.1764-0.05620.143334.200937.659655.0469
73.23920.3621.54172.55570.0064.0906-0.04070.20690.1174-0.0946-0.0553-0.2472-0.22860.2370.0960.1272-0.03310.00660.03210.04570.184946.511880.050471.7466
82.16830.8421-0.68217.19870.5521.1675-0.09350.21-0.3191-0.24750.0338-0.470.21520.10850.05960.2140.02970.00910.1690.07390.212151.682346.552285.885
92.17530.19990.16732.8779-2.03534.9186-0.0172-0.1467-0.11040.21520.09030.2430.1028-0.3771-0.07310.1328-0.00890.0180.04950.02560.192434.937461.77788.1897
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D0 - 180
6X-RAY DIFFRACTION4F1 - 10
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99
9X-RAY DIFFRACTION7G0 - 180
10X-RAY DIFFRACTION7I1 - 10
11X-RAY DIFFRACTION8G181 - 276
12X-RAY DIFFRACTION9H0 - 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