[English] 日本語
Yorodumi
- PDB-7l1d: Crystal structure of human 21LT2-2 TCR bound to HLA-A*03:01 in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l1d
TitleCrystal structure of human 21LT2-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide
Components
  • (T cell receptor, ...T-cell receptor) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Mutant PIK3CA peptide
KeywordsIMMUNE SYSTEM / T cell receptor / peptide major histocompatibility complex
Function / homology
Function and homology information


response to muscle inactivity / negative regulation of actin filament depolymerization / response to L-leucine / regulation of actin filament organization / response to butyrate / autosome genomic imprinting / IRS-mediated signalling / cellular response to hydrostatic pressure / PI3K events in ERBB4 signaling / Activated NTRK2 signals through PI3K ...response to muscle inactivity / negative regulation of actin filament depolymerization / response to L-leucine / regulation of actin filament organization / response to butyrate / autosome genomic imprinting / IRS-mediated signalling / cellular response to hydrostatic pressure / PI3K events in ERBB4 signaling / Activated NTRK2 signals through PI3K / positive regulation of protein localization to membrane / Activated NTRK3 signals through PI3K / negative regulation of fibroblast apoptotic process / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IB / vasculature development / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / phosphatidylinositol 3-kinase complex / anoikis / Nephrin family interactions / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Costimulation by the CD28 family / vascular endothelial growth factor signaling pathway / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / PI3K/AKT activation / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase / relaxation of cardiac muscle / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / negative regulation of macroautophagy / Signaling by ALK / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / protein kinase activator activity / response to dexamethasone / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / PI3K events in ERBB2 signaling / Signaling by ALK fusions and activated point mutants / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / negative regulation of anoikis / RET signaling / regulation of multicellular organism growth / insulin receptor substrate binding / positive regulation of CD8-positive, alpha-beta T cell activation / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD8-positive, alpha-beta T cell activation / PI3K Cascade / intercalated disc / positive regulation of TOR signaling / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endothelial cell migration / RAC2 GTPase cycle / GAB1 signalosome / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / adipose tissue development / Interleukin receptor SHC signaling / endoplasmic reticulum exit site / beta-2-microglobulin binding / positive regulation of lamellipodium assembly / phagocytosis / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / energy homeostasis / Signaling by FGFR4 in disease / TAP binding / Signaling by FLT3 ITD and TKD mutants / protection from natural killer cell mediated cytotoxicity / cardiac muscle contraction / Signaling by FGFR3 in disease / GPVI-mediated activation cascade / Tie2 Signaling / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Signaling by FGFR2 in disease / RAC1 GTPase cycle / T cell costimulation / response to muscle stretch / Signaling by FLT3 fusion proteins / detection of bacterium / FLT3 Signaling / Signaling by FGFR1 in disease / T cell receptor binding / Downstream signal transduction / insulin-like growth factor receptor signaling pathway
Similarity search - Function
PI3Kalpha, catalytic domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Phosphoinositide 3-kinase C2 ...PI3Kalpha, catalytic domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Armadillo-type fold / Ubiquitin-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / HLA class I histocompatibility antigen, A alpha chain / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsMa, J. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129543 United States
CitationJournal: Nat Med / Year: 2022
Title: Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA.
Authors: Chandran, S.S. / Ma, J. / Klatt, M.G. / Dundar, F. / Bandlamudi, C. / Razavi, P. / Wen, H.Y. / Weigelt, B. / Zumbo, P. / Fu, S.N. / Banks, L.B. / Yi, F. / Vercher, E. / Etxeberria, I. / ...Authors: Chandran, S.S. / Ma, J. / Klatt, M.G. / Dundar, F. / Bandlamudi, C. / Razavi, P. / Wen, H.Y. / Weigelt, B. / Zumbo, P. / Fu, S.N. / Banks, L.B. / Yi, F. / Vercher, E. / Etxeberria, I. / Bestman, W.D. / Da Cruz Paula, A. / Aricescu, I.S. / Drilon, A. / Betel, D. / Scheinberg, D.A. / Baker, B.M. / Klebanoff, C.A.
History
DepositionDec 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 25, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Mutant PIK3CA peptide
D: T cell receptor, alpha chain
E: T cell receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0007
Polymers94,8495
Non-polymers1512
Water0
1
D: T cell receptor, alpha chain
E: T cell receptor, beta chain
hetero molecules

A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Mutant PIK3CA peptide


Theoretical massNumber of molelcules
Total (without water)95,0007
Polymers94,8495
Non-polymers1512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area10910 Å2
ΔGint-38 kcal/mol
Surface area38840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.282, 72.282, 475.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 31628.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P04439
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Mutant PIK3CA peptide / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase catalytic subunit alpha isoform / PtdIns-3-kinase ...Phosphatidylinositol 4 / 5-bisphosphate 3-kinase catalytic subunit alpha isoform / PtdIns-3-kinase subunit alpha / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha / p110alpha / Phosphoinositide-3-kinase catalytic alpha polypeptide / Serine/threonine protein kinase PIK3CA


Mass: 972.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42336

-
T cell receptor, ... , 2 types, 2 molecules DE

#4: Protein T cell receptor, alpha chain / T-cell receptor


Mass: 22681.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T cell receptor, beta chain / T-cell receptor


Mass: 27686.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 10% w/v Polyethylene glycol 8,000, 200mM Magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→50 Å / Num. obs: 24158 / % possible obs: 99.7 % / Redundancy: 20.2 % / Biso Wilson estimate: 84.91 Å2 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.032 / Rrim(I) all: 0.148 / Net I/σ(I): 25
Reflection shellResolution: 3.11→3.15 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.365 / Num. unique obs: 914 / CC1/2: 0.797 / Rpim(I) all: 0.335 / Rrim(I) all: 1.41 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XPG, 3QH3, 4PRH

2xpg

3qh3

4prh


Resolution: 3.11→49.51 Å / SU ML: 0.3871 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.9911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2497 1903 8.31 %
Rwork0.1979 21008 -
obs0.2021 22911 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.42 Å2
Refinement stepCycle: LAST / Resolution: 3.11→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 10 0 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026670
X-RAY DIFFRACTIONf_angle_d0.49399054
X-RAY DIFFRACTIONf_chiral_restr0.0392955
X-RAY DIFFRACTIONf_plane_restr0.00331196
X-RAY DIFFRACTIONf_dihedral_angle_d18.00652427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.190.34011020.33271227X-RAY DIFFRACTION80.06
3.19-3.270.34231270.28831323X-RAY DIFFRACTION86.26
3.27-3.370.36241290.25811372X-RAY DIFFRACTION90.8
3.37-3.480.29071250.2371430X-RAY DIFFRACTION91.79
3.48-3.60.25371330.23161464X-RAY DIFFRACTION94.89
3.6-3.740.31681360.23181472X-RAY DIFFRACTION95.89
3.74-3.910.32771380.22091498X-RAY DIFFRACTION97.32
3.92-4.120.25111400.18831539X-RAY DIFFRACTION98.36
4.12-4.380.25721410.16911550X-RAY DIFFRACTION99.35
4.38-4.720.19771420.15251580X-RAY DIFFRACTION99.6
4.72-5.190.20211440.15881601X-RAY DIFFRACTION99.6
5.19-5.940.22831460.18091595X-RAY DIFFRACTION99.71
5.94-7.480.2641440.21451624X-RAY DIFFRACTION99.21
7.48-49.510.2181560.19111733X-RAY DIFFRACTION96.67
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)
15.07000702862-1.32370911920.4494958653894.76027389389-0.1522112134654.45889580620.005038689020770.01328082136780.0443320901128-0.1043870906950.00329785384870.0397922925943-0.2822842504090.0831848039554-0.002290476901780.376406410522-0.0661751672196-0.1530081880230.5297087786240.02599947225190.46594516218535.4931543998-31.4342845703-39.1685273025
27.28188114208-1.215937927810.06311370749535.306927948471.888330955624.57862968192-0.1894864467050.120425538844-0.533114096937-0.04065849054620.2560020841930.702732208750.378726314698-0.636706331966-0.09993831242290.830271433404-0.10234676969-0.3250919023080.701765769410.2785718548861.079690000736.01243984088-22.7865378002-56.9340851007
33.91851706643-1.847744264651.11164226497.40038966045-2.695309699827.417812583980.3398249647841.147516909130.550864603852-1.06907574601-0.34458548993-0.181584410104-0.002050170787150.375832272308-0.01750355123490.7766415572460.0379088462451-0.2357058575190.8572619843220.1441063808270.71748926219427.1888621267-24.627871555-63.9954277261
49.900738374711.661545214590.5047561774054.06029936830.9302522062244.413272528810.568136786875-0.571031765246-0.1312972386670.972653104593-0.6212760553260.5198195217260.6262912198660.109349962012-0.07093728930730.454800662753-0.105115979143-0.07969846371670.897423313855-0.1229284461530.6027625780440.3462078006-35.582280596-34.3151367387
56.93511019829-1.25271112523-2.046947100992.94259319321-1.211104622276.70692901794-0.455956002576-0.4239281354740.1056305343640.363210362810.1350122680980.0040173594319-0.407501522297-0.3409038888120.3102253834590.5987099557840.184638286954-0.1453906049330.685908267416-0.1281961968670.632049752013-24.5730401978-32.7050715283-10.4825008897
65.4844722282-0.1318763209922.797736017483.344839109110.3243844780884.096074306340.01850707235840.32702233431-0.0252673535987-0.0382170235759-0.0440367270307-0.321134290981-0.04881102456270.808894833434-0.08190325722740.3393734116110.00998154989702-0.1185300065050.9350169970380.05080680353570.681183162714-9.51160977312-34.122146584-27.9400895751
78.69282134871-1.49063031202-3.304008710346.64432212317-1.519301044933.82728572632-0.240246727089-1.32715937205-0.04672227664681.332178221770.561826723574-0.147029525442-0.4283614733470.571734033508-0.2891862305110.9658360529110.180771199616-0.1460475440981.5521272476-0.1154239136020.6049878328490.338118783985-36.940465247412.6522762995
83.316873656560.343353577731-0.7842529640744.11208681659-0.5807142673585.62863737322-0.390468260721-0.136741699639-0.1201572913730.3505764419250.310564390970.003235703183970.4605411100260.6136360197930.1303612325820.5951266984230.205678884391-0.1339539284741.460461943880.1650231586330.9473185170897.34075229808-43.1402510884-2.45350945373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 274 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 99 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 9 )
5X-RAY DIFFRACTION5chain 'D' and (resid 8 through 112 )
6X-RAY DIFFRACTION6chain 'E' and (resid 3 through 119 )
7X-RAY DIFFRACTION7chain 'D' and (resid 113 through 198)
8X-RAY DIFFRACTION8chain 'E' and (resid 120 through 249)

+
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