[English] 日本語
Yorodumi
- PDB-8ge0: Crystal structure of JADE1 PZP domain in complex with Histone H3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ge0
TitleCrystal structure of JADE1 PZP domain in complex with Histone H3
ComponentsHistone H3.1,Protein Jade-1
KeywordsTRANSCRIPTION / histone acetylation / transcription activation / Nucleosome / pVHL
Function / homology
Function and homology information


regulation of DNA biosynthetic process / negative regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / histone acetyltransferase complex / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication ...regulation of DNA biosynthetic process / negative regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / histone acetyltransferase complex / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / ciliary basal body / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / regulation of cell growth / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of canonical Wnt signaling pathway / HDMs demethylate histones / negative regulation of cell growth / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / nuclear speck / cadherin binding / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / apoptotic process / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Jade-1, PHD finger / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. ...Jade-1, PHD finger / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3.1 / Protein Jade-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKlein, B.J. / Liu, J. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Guiding the HBO1 complex function through the JADE subunit.
Authors: Gaurav, N. / Kanai, A. / Lachance, C. / Cox, K.L. / Liu, J. / Grzybowski, A.T. / Saksouk, N. / Klein, B.J. / Komata, Y. / Asada, S. / Ruthenburg, A.J. / Poirier, M.G. / Cote, J. / Yokoyama, ...Authors: Gaurav, N. / Kanai, A. / Lachance, C. / Cox, K.L. / Liu, J. / Grzybowski, A.T. / Saksouk, N. / Klein, B.J. / Komata, Y. / Asada, S. / Ruthenburg, A.J. / Poirier, M.G. / Cote, J. / Yokoyama, A. / Kutateladze, T.G.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.1,Protein Jade-1
B: Histone H3.1,Protein Jade-1
C: Histone H3.1,Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,40618
Polymers62,4243
Non-polymers98115
Water1,856103
1
A: Histone H3.1,Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1356
Polymers20,8081
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone H3.1,Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1356
Polymers20,8081
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone H3.1,Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1356
Polymers20,8081
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.160, 78.160, 222.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 7 or resid 18...
d_2ens_1(chain "B" and (resid 1 through 7 or resid 18...
d_3ens_1(chain "C" and (resid 1 through 18 or resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAALAA1 - 7
d_12ens_1ASPASPA18
d_13ens_1ASPCYSA20 - 64
d_14ens_1THRPROA66 - 79
d_15ens_1LYSTHRA81 - 88
d_16ens_1SERTHRA90 - 92
d_17ens_1TRPGLUA94 - 112
d_18ens_1METALAA114 - 171
d_19ens_1GLUSERA175 - 187
d_21ens_1ALAALAG1 - 7
d_22ens_1ASPASPG18
d_23ens_1ASPCYSG20 - 64
d_24ens_1THRPROG66 - 79
d_25ens_1LYSTHRG81 - 88
d_26ens_1SERTHRG90 - 92
d_27ens_1TRPGLUG94 - 112
d_28ens_1METALAG114 - 171
d_29ens_1GLUSERG175 - 187
d_31ens_1ALAASPM1 - 8
d_32ens_1ASPCYSM10 - 54
d_33ens_1THRPROM56 - 69
d_34ens_1LYSTHRM71 - 78
d_35ens_1SERTHRM80 - 82
d_36ens_1TRPGLUM84 - 102
d_37ens_1METALAM104 - 161
d_38ens_1GLUSERM165 - 177

NCS oper:
IDCodeMatrixVector
1given(0.00486955961082, 0.999571889033, -0.028850061408), (0.500468832975, -0.0274133464642, -0.865320435247), (-0.865740858808, -0.0102248271222, -0.500388067704)-9.73762641617, 170.941620985, 170.312148506
2given(-0.023418126049, 0.99971280532, 0.00508903239865), (-0.494389613069, -0.00715629077345, -0.869210962881), (-0.868924911521, -0.0228712566504, 0.494415213922)-25.2984977113, 169.943432368, 67.2666576969

-
Components

#1: Protein Histone H3.1,Protein Jade-1


Mass: 20808.127 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J, JADE1, KIAA1807, PHF17
Production host: Escherichia coli (E. coli) / References: UniProt: P68431, UniProt: Q6IE81
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.27819 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27819 Å / Relative weight: 1
ReflectionResolution: 2.4→49.51 Å / Num. obs: 28040 / % possible obs: 99.9 % / Redundancy: 39.8 % / Biso Wilson estimate: 46.4 Å2 / Rpim(I) all: 0.028 / Net I/σ(I): 28.2
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2849 / Rpim(I) all: 0.388

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.51 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2412 1371 4.9 %
Rwork0.2069 26582 -
obs0.2086 27953 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 15 103 4298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344267
X-RAY DIFFRACTIONf_angle_d0.6475759
X-RAY DIFFRACTIONf_chiral_restr0.0506641
X-RAY DIFFRACTIONf_plane_restr0.0052734
X-RAY DIFFRACTIONf_dihedral_angle_d13.45411586
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.757586061735
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.558010914085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.3211260.2722571X-RAY DIFFRACTION99.15
2.49-2.590.31251320.24812603X-RAY DIFFRACTION100
2.59-2.70.29391360.23452621X-RAY DIFFRACTION99.93
2.7-2.850.29161500.24162581X-RAY DIFFRACTION100
2.85-3.020.33651190.25712657X-RAY DIFFRACTION100
3.02-3.260.27771550.22492629X-RAY DIFFRACTION99.96
3.26-3.580.25421280.21252646X-RAY DIFFRACTION99.96
3.59-4.10.22521330.192680X-RAY DIFFRACTION100
4.1-5.170.19081420.16982707X-RAY DIFFRACTION100
5.17-49.510.2071500.1972887X-RAY DIFFRACTION99.97
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)
10.5718197447420.08886241331260.02313589610830.3217308251880.1899279327970.359885526963-0.00244906204508-0.07085137939130.162765330633-0.1999688349450.181653250606-0.261472308758-0.3158370573160.2611228038921.93455134881E-50.418769234529-0.0630831141030.07548904536030.307216991642-0.03333135090030.26047145505452.610047934356.693347754789.7131035332
20.3176485232760.0569423105612-0.07645333704230.02335238067810.05344779470.251421497659-0.198054052023-0.01936593801410.168863652243-0.1032888518490.006344328330350.0604235697969-0.424060552284-0.0477970736944-0.0001815380459030.4536899036550.0208011708983-0.01119114745260.3040204598930.01305622011440.33207579932636.967295562357.832500670386.3850343373
30.6466577563130.04829164303850.4273756519620.783004955117-0.2561815065990.3800549316710.1879504852530.329618600113-0.107911825608-0.1963338541620.003825326867980.166279044479-0.438574232636-0.4370542181670.004631772530430.3596964842830.008445948115640.00474616175730.3092250998790.04364631391720.30193648610333.020938990349.506313806685.0923754042
41.031145208960.5044987572790.3703256614060.7844711889260.06648379073580.435238998370.113928434542-0.109843652436-0.5347342471450.00920143341112-0.310810685918-0.217485113794-0.03063857769080.263747008698-0.00148603631220.258290893254-0.0268363980186-0.004526710346320.3804361173670.0686213952420.34658775204837.555312263140.700213619594.4371598478
50.0420133383682-0.06596804773720.03521187829220.0918797095568-0.03280464732020.03535495841580.06208774529680.130406646465-0.090541149241-0.62223264807-0.6450828301830.444944736119-0.349664376841-0.128709700934-0.0003144608456970.5513691500740.145184041866-0.07828119868510.524645528632-0.05401033633610.51316863855525.716072809888.4951420864117.470107153
60.07195421908090.0319182259404-0.0007214089587960.0677994712162-0.03947604594570.03529529023430.152087908313-0.2516799498150.276348728301-0.0924803853671-0.3730480693860.01847804852360.166403622263-0.16789275268-0.0003849487256520.545759769744-0.000158371797640.0827291191510.376639412026-0.03735810417750.36353623312434.346382623779.0458999428116.692924036
70.0474659435811-0.065951141084-0.04066322867690.175363765728-0.04136880204660.1206660183290.1776708611450.08739389870560.216081414985-0.298440110089-0.2786453275880.197932271431-0.21337021003-0.128551191915-4.48875718106E-50.5879403073590.02116159915150.004185236859180.398399523992-0.005466102047840.34167936465634.818776074276.4452716678104.79959104
81.13746220295-1.502381325440.9911100757562.04458248915-1.37813308420.9446838905140.1972160909920.166140855022-0.505709650114-0.5358729632820.1403706385870.659037258866-0.185750107752-0.3613313303940.0607043907690.3904900155020.01841854536970.01660778801950.334832071245-0.05914848634120.25288136443934.855584772961.9203102315108.181526288
90.1081278667830.0181298156305-0.06994441762320.103044498559-0.05421175809130.05259255108870.142925282608-0.0385669610069-0.307686351333-0.1165845193170.0683621303530.140158077970.07182751338790.130447986772-0.0001746767294860.4363059820440.01910731825330.0448619706260.2780029880190.009046819357120.24601447903641.332805391563.4215702624107.978884461
100.436005753487-0.4660461903270.09526623061110.445870112324-0.1504235149170.281700137876-0.04765591285740.481000274458-0.148756608553-0.3812569029030.0642029690281-0.03275676833280.150740015888-0.1505624023940.00953270302930.3293586871080.01849936924570.07624411320250.2459849812870.01529833857820.24405819688642.694859879758.7612687879113.824836262
110.385183734365-0.126404397426-0.09069428824040.170730252692-0.1196210490440.4848110296490.177547697367-0.0798914856945-0.0100443137335-0.1001152573180.09929507548370.206692545263-0.116094819013-0.3830025027020.01715014099060.3496731878110.04503300590810.1186686353230.4022473497880.05058375168890.4098977599136.802814092660.5670898368125.109524934
120.282385177153-0.06137963710850.1257459469972.09226921069-0.461954978620.312575250454-0.0977977614926-0.1922529075580.0639451771831-0.1500124314030.0331869459544-0.820248698779-0.3074739853330.172250150259-0.03441827774280.437755073446-0.009460980135410.1305365358220.457208053416-0.02919492335780.40928925429241.212763211567.1404125497128.172725296
131.285527725290.885519623791-0.2380057047590.795386330306-0.4940574419370.63572195351-0.258434861806-0.3487471913230.8212160515160.4221662269520.051602625774-0.162414265978-0.431743100725-0.06457040207230.1231445071450.456477868140.010562047291-0.1077163645870.456683494127-0.166368719060.40327231350675.680295815979.89184641888.9861552191
140.161971860042-0.0364236561416-0.3129355559720.2311094782370.2929131649570.755989285886-0.3902893418340.1242438073650.09706382366340.214405190127-0.0694953910151-0.3237918779290.003944341193990.473030302929-0.08247637707550.405071074947-0.0342652865284-0.1536393223320.302224675803-0.02404056463980.56652911590666.391686782790.368715744983.9349090002
151.835680431521.22679869671-0.3575574905441.22854364343-0.3734033293170.447689678473-0.3402092003220.19350994041.061302377090.03222652091340.1119831908290.156233341846-0.260144211352-0.1556528089390.2703432409580.4090767994050.0951686428557-0.1735568702160.219027163596-0.1798539901810.64303378222151.780547726596.405038358180.3175565001
160.4845422743990.4224966591550.6054963570540.5517353273880.3057722339661.05600007081-0.052183410976-0.1675246247280.2363974480180.115846567345-0.1934444984880.2400382272160.212819929574-0.10817061515-0.07289354936380.281674369899-0.0366749835465-0.06020016155120.277292157525-0.03377159050450.41501417857444.243762027981.944190926676.4048002669
170.318132566671-0.02819766488190.2521761448410.2095169782180.1928233343970.41476521398-0.04448109146960.4130830490430.00165448926777-0.1540999542140.121848141535-0.5326060058030.5617028131520.4645110478890.007277040794340.482447998133-0.0210237798633-0.08842127385560.5271282563940.07426670413040.5102432419551.553168928977.914706747870.4913732425
180.2544639652030.2375536123750.2902614966460.2739441369590.3588341027030.4877620648610.00853330588207-0.1932595752460.02352692854740.247649587992-0.24069102959-0.00888151992674-0.0062440011016-0.0934852653151-0.9776751347650.394147929708-0.2469821351080.08930793554090.481237156979-0.1425888127030.29380248704859.850045725655.995881890297.7268792816
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 20 through 69 )CM20 - 6910 - 59
22chain 'C' and (resid 70 through 102 )CM70 - 10260 - 92
33chain 'C' and (resid 103 through 139 )CM103 - 13993 - 129
44chain 'C' and (resid 140 through 187 )CM140 - 187130 - 177
55chain 'A' and (resid 1 through 20 )AA1 - 201 - 20
66chain 'A' and (resid 21 through 39 )AA21 - 3921 - 39
77chain 'A' and (resid 40 through 73 )AA40 - 7340 - 73
88chain 'A' and (resid 74 through 87 )AA74 - 8774 - 87
99chain 'A' and (resid 88 through 102 )AA88 - 10288 - 102
1010chain 'A' and (resid 103 through 139 )AA103 - 139103 - 139
1111chain 'A' and (resid 140 through 170 )AA140 - 170140 - 170
1212chain 'A' and (resid 171 through 188 )AA171 - 188171 - 188
1313chain 'B' and (resid 1 through 20 )BG1 - 201 - 20
1414chain 'B' and (resid 21 through 64 )BG21 - 6421 - 64
1515chain 'B' and (resid 65 through 122 )BG65 - 12265 - 122
1616chain 'B' and (resid 123 through 171 )BG123 - 171123 - 171
1717chain 'B' and (resid 174 through 187 )BG174 - 187174 - 187
1818chain 'C' and (resid 1 through 19 )CM1 - 191 - 9

+
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