[English] 日本語
Yorodumi
- PDB-6xwt: drosophila melanogaster CENP-A/H4 bound to N-terminal CAL1 fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xwt
Titledrosophila melanogaster CENP-A/H4 bound to N-terminal CAL1 fragment
Components
  • Chromosome alignment defect 1
  • Histone H3-like centromeric protein cid
  • Histone H4
KeywordsCELL CYCLE / Centromere / Kinetochore / Cell Division
Function / homology
Function and homology information


HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / kinetochore organization / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / CENP-A containing chromatin assembly / kinetochore assembly / protein localization to chromosome, centromeric region / chromatin-protein adaptor activity / condensed chromosome, centromeric region / inner kinetochore / protein localization to kinetochore / mitotic metaphase chromosome alignment / nuclear chromosome / chromosome, centromeric region / CENP-A containing nucleosome / spindle assembly / chromosome segregation / kinetochore / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / chromatin organization / chromosome / protein heterodimerization activity / nucleolus / DNA binding / nucleus
Similarity search - Function
Centromere protein Scm3 / Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold ...Centromere protein Scm3 / Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Histone H4 / Histone H3-like centromeric protein cid / Chromosome alignment defect 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsJeyaprakash, A.A. / Medina-Pritchard, B. / Lazou, V. / Zou, J. / Byron, O. / Abad, M.A. / Rappsilber, J. / Heun, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust202811 United Kingdom
CitationJournal: Embo J. / Year: 2020
Title: Structural basis for centromere maintenance by Drosophila CENP-A chaperone CAL1.
Authors: Medina-Pritchard, B. / Lazou, V. / Zou, J. / Byron, O. / Abad, M.A. / Rappsilber, J. / Heun, P. / Jeyaprakash, A.A.
History
DepositionJan 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Histone H3-like centromeric protein cid
B: Histone H4
C: Histone H3-like centromeric protein cid
D: Histone H4
E: Chromosome alignment defect 1
F: Chromosome alignment defect 1


Theoretical massNumber of molelcules
Total (without water)294,2816
Polymers294,2816
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-126 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.250, 178.250, 133.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUPHEPHE(chain 'A' and (resid 47 through 54 or resid 56...AA47 - 53147 - 153
121LEULEULYSLYS(chain 'A' and (resid 47 through 54 or resid 56...AA56 - 63156 - 163
131ASPASPARGARG(chain 'A' and (resid 47 through 54 or resid 56...AA67 - 71167 - 171
141THRTHRALAALA(chain 'A' and (resid 47 through 54 or resid 56...AA73 - 79173 - 179
151GLUGLUMETMET(chain 'A' and (resid 47 through 54 or resid 56...AA82 - 115182 - 215
161ILEILECYSCYS(chain 'A' and (resid 47 through 54 or resid 56...AA118 - 119218 - 219
271LEULEUPHEPHE(chain 'C' and (resid 47 through 54 or resid 56...CC47 - 53147 - 153
281LEULEULYSLYS(chain 'C' and (resid 47 through 54 or resid 56...CC56 - 63156 - 163
291ASPASPARGARG(chain 'C' and (resid 47 through 54 or resid 56...CC67 - 71167 - 171
2101THRTHRALAALA(chain 'C' and (resid 47 through 54 or resid 56...CC73 - 79173 - 179
2111GLUGLUMETMET(chain 'C' and (resid 47 through 54 or resid 56...CC82 - 115182 - 215
2121ILEILECYSCYS(chain 'C' and (resid 47 through 54 or resid 56...CC118 - 119218 - 219
1132LYSLYSVALVAL(chain 'B' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))BB32 - 4432 - 44
1142ILEILEILEILE(chain 'B' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))BB47 - 5147 - 51
1152GLUGLUTHRTHR(chain 'B' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))BB54 - 9754 - 97
2162LYSLYSVALVAL(chain 'D' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))DD32 - 4432 - 44
2172ILEILEILEILE(chain 'D' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))DD47 - 5147 - 51
2182GLUGLUTHRTHR(chain 'D' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))DD54 - 9754 - 97
1193ARGARGALAALA(chain 'E' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))EE18 - 3018 - 30
1203GLUGLUVALVAL(chain 'E' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))EE33 - 4033 - 40
1213PHEPHEASNASN(chain 'E' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))EE43 - 4543 - 45
2223ARGARGALAALA(chain 'F' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))FF18 - 3018 - 30
2233GLUGLUVALVAL(chain 'F' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))FF33 - 4033 - 40
2243PHEPHEASNASN(chain 'F' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))FF43 - 4543 - 45

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Histone H3-like centromeric protein cid / CENP-A homolog / Centromere identifier protein


Mass: 26014.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cid, CENP-A, CG13329 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V6Q2
#2: Protein Histone H4


Mass: 11408.452 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His4r, BcDNA:RH52884, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, CG3379, Dmel_CG3379
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4KFZ9, UniProt: P84040*PLUS
#3: Protein Chromosome alignment defect 1


Mass: 109717.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: cal1, CAL1, Cal1, CLD2, Dmel\CG5148, CG5148, Dmel_CG5148
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VEN2

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.01M Cobalt (II) Chloride hexahydrate, 0.1M MES pH 6.5 and 1.8 M Ammonium Sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.47→100.88 Å / Num. obs: 10675 / % possible obs: 99.93 % / Redundancy: 7.6 % / Biso Wilson estimate: 137.49 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 10.46
Reflection shellResolution: 3.47→3.59 Å / Rmerge(I) obs: 1.96 / Num. unique obs: 1059

-
Processing

Software
NameVersionClassification
xia21.17.1_3660data reduction
PHENIX1.17.1_3660refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PYO

2pyo


Resolution: 3.47→100.88 Å / SU ML: 0.5757 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.7683
RfactorNum. reflection% reflection
Rfree0.2863 542 5.08 %
Rwork0.2717 --
obs0.2724 10673 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 136.62 Å2
Refinement stepCycle: LAST / Resolution: 3.47→100.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 0 0 2803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392838
X-RAY DIFFRACTIONf_angle_d0.86463811
X-RAY DIFFRACTIONf_chiral_restr0.0462440
X-RAY DIFFRACTIONf_plane_restr0.0055479
X-RAY DIFFRACTIONf_dihedral_angle_d8.0201395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.47-3.820.40141260.35412511X-RAY DIFFRACTION100
3.82-4.370.35921470.32812495X-RAY DIFFRACTION99.96
4.37-5.510.2721340.29212522X-RAY DIFFRACTION99.96
5.51-100.880.24851350.22842603X-RAY DIFFRACTION99.82
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)
13.839594375440.9562311322520.7235153471983.695644446860.649659383626.548171770290.1403343472060.2131665193880.5815011012170.2802954963170.1371791470780.214240174015-0.812658503779-0.418277163919-0.2163716370150.8857716283180.1450298411320.1775034400990.7870489348970.04454452895291.0524028363625.0175366361-22.770643395839.3651146885
28.565917701680.8402433657494.792671669936.125059799173.730614896388.570134345480.02325956081561.74709523379-0.905280812042.978191861930.4091782594210.9567153616942.008879552352.48285525496-0.236019300771.289750872610.2880815097180.2001992367851.14822683226-0.089559683892.1217431757634.5537864846-14.809157514950.5139445063
36.03558736782-1.60717422653-0.1166469293772.5957661214-0.7651199222822.472659381850.218868482771.029003918571.35908278667-2.273417360260.02715362833470.870971755234-2.597027969450.135175301247-0.1283945857211.85646471147-0.1376581852360.1328911808111.38957651058-0.0151984257161.5971515322821.4723921509-11.136704270139.0305433889
44.20215051734-1.295118436092.296929434812.871447707673.449791397436.23634657032-0.3224980914621.283510798920.2008275672330.07152795575380.946530558878-2.68888023078-0.6915911359860.926833667051-0.41406756221.104217604780.03689409387220.2212897396531.28173305259-0.2037833800911.3872381781830.4271140509-26.718447655239.0058526596
54.93531162653-0.749527189470.7794074080232.83876475633-0.295638143559.660040913180.1047886418270.385883624905-1.939553222342.1315739171-0.5189903754261.510698051592.83522512211-1.184290090160.03953900285911.36554473244-0.05998490442410.2597555303240.997105417136-0.1278861241421.1817433205924.0412574941-40.657054233439.4855856467
67.724153565375.50340303512-5.110280874836.70754493848-1.495334984635.163077947931.30960158286-0.04149727120330.6758543180634.590479628130.253479056997-2.83051223659-1.28964049343-1.94262430025-1.656683281181.622184610470.270424660579-0.1298027278961.147447120290.1598878198120.7252303924727.9868336621-30.678636139150.0840622462
78.204078614141.657638559952.224690490843.41776079517-0.8604682887299.20684145386-0.657279868794-3.182408683912.451666124751.462312631250.4016542538890.780624511524-0.4909418171090.05391381714470.1819292675561.4902416665-0.1446657054870.2414007866781.4430550886-0.3775675479041.2247835344935.2456981661-29.322153791983.191286515
83.81386619013-3.195149677810.8821399057499.038013836630.8730963134532.157503134870.2408967098280.2180971770970.0328981957286-0.0251131943932-0.357490842066-0.319712800641-0.0110110406730.4036990481890.08633863691431.2000789524-0.06861013149180.1863682039970.840678302751-0.2134961334230.87681675767137.5561622263-22.978687148670.9523277371
95.436189886211.370109296570.2491374983092.178139870291.285031465474.05863161175-0.859380993501-0.852835665995-0.3372108357910.9753546144430.607300394521.173414825620.307521065685-0.4938825068850.07588491399341.25109527968-0.03669414422470.1117999971341.29541402326-0.04442974880631.6233805600528.7528038948-14.913921626363.9728493172
107.498353121631.66513122503-1.867173696799.01288418755-0.8010221481192.621935019940.492482200533-0.897120146675-2.028250523861.58331367338-0.0669712052506-1.277939970041.528655018081.52904137884-0.2372025851122.15915014780.22452285961-0.3433957619631.09595288213-0.09156068795071.2013452962342.8989215726-15.318507011277.4784336578
115.88686371223-2.12685651956-3.499449341899.49705548884-4.485008488178.447968057940.03363040639360.05028339713490.8065230043861.578559073950.1376306717412.43162050572-0.509747009048-0.877564364731-0.1653070102440.8312754508460.04668951690290.1019727229960.744742716257-0.02120088516290.83665694093933.2084586771-24.450502734773.4843134237
124.34032443251.666286915940.2544091804166.13980612045-0.9254003486622.652739479710.1033898693520.916662396322-2.59808550802-1.26394835118-1.0318505777-1.289252358842.782724071160.8737721857570.7183349301551.37290084075-0.2503052708610.2347316628290.8068481826660.01618333655981.1722524924436.2674230202-42.458620979372.4291343242
133.634460999133.8081519661-0.3705672214395.76574659675-3.240019077163.26510484858-1.846358909543.194471768520.88746133044-3.730718480131.681057269444.23263485071-2.08991738694-0.317668269896-0.1670520993551.5907503123-0.3817209232870.03513675172671.26840630380.1415142684571.0236885823834.3688426283-28.944757475461.9620535151
142.57235860824-0.8385552898170.8928815859746.488292862182.83808548797.505335664681.086587522830.6702721570060.0188134064976-1.594278460710.0220596567143-0.57838488408-0.2632998212891.75277030915-1.131751165091.51164978667-0.2186687986260.004833594704841.28495511065-0.05008379664351.1364256695545.7445488537-30.928926888763.0707014541
155.97259577629-0.815635481001-2.60818275044.67144100013-1.707133543071.967016187110.305733760934-0.183067390131-0.3859052580722.70907980069-0.6942076137350.0963674627922.56258522173-2.186901297320.140136216092.06870167517-0.422790403249-0.2477883820131.559915141990.1219940615891.2963683756442.1825552463-41.793937472982.1532868361
160.0776102802769-0.372583332612-0.2186188957393.998325016853.026431875182.44488896865-1.28467156326-2.860776471562.616255664410.792748280068-0.9903549154241.34741654391-1.75613553725-1.471258056091.934444773252.098680944291.279228052830.2251295275541.844370972291.012749104393.4252818597239.945967338-35.215182541891.297740739
179.787772164330.548141542009-3.13448993096.84915399028-2.676109192286.13031959021-1.037251769961.94846327037-1.287759449310.03308624257440.8599978466911.85902356933-0.0581529411286-1.86188718755-0.4627370634751.12822220143-0.08474385905490.1950499560781.17015609303-0.05803186607171.5498851122716.5944529592-29.649528766450.7127507887
187.92795304076-2.582454383573.032696852613.27879998861.366183658343.49404653737-0.370168735180.611675706528-1.00327058173-1.23793732124-0.734936379913.211327490480.6199835659611.346023810442.545278078221.661863436870.141593273269-0.1105747183311.22233823208-0.04816873386141.6351877638415.7427590507-38.765721074931.8470810316
192.992823585082.954585614521.061755890233.04464660710.746527472212.244745285650.09662554990261.753888128032.98629353206-3.597221030570.2480245792350.307164815083-0.4340433249061.724441043850.2406143339291.9489085262-0.159350871407-0.05468722608672.15905329921-0.2095204869751.5807855263720.4387020226-30.81832076221.7565397506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 120 )
3X-RAY DIFFRACTION3chain 'B' and (resid 27 through 48 )
4X-RAY DIFFRACTION4chain 'B' and (resid 49 through 76 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 92 )
6X-RAY DIFFRACTION6chain 'B' and (resid 93 through 98 )
7X-RAY DIFFRACTION7chain 'C' and (resid 47 through 63 )
8X-RAY DIFFRACTION8chain 'C' and (resid 64 through 108 )
9X-RAY DIFFRACTION9chain 'C' and (resid 109 through 120 )
10X-RAY DIFFRACTION10chain 'D' and (resid 29 through 41 )
11X-RAY DIFFRACTION11chain 'D' and (resid 42 through 76 )
12X-RAY DIFFRACTION12chain 'D' and (resid 77 through 92 )
13X-RAY DIFFRACTION13chain 'D' and (resid 93 through 99 )
14X-RAY DIFFRACTION14chain 'E' and (resid 17 through 29 )
15X-RAY DIFFRACTION15chain 'E' and (resid 30 through 40 )
16X-RAY DIFFRACTION16chain 'E' and (resid 41 through 46 )
17X-RAY DIFFRACTION17chain 'F' and (resid 17 through 29 )
18X-RAY DIFFRACTION18chain 'F' and (resid 30 through 38 )
19X-RAY DIFFRACTION19chain 'F' and (resid 39 through 47 )

+
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