[English] 日本語
Yorodumi
- PDB-5ja4: Crystal structure of human TONSL and MCM2 HBDs binding to a histo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ja4
TitleCrystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer
Components
  • DNA replication licensing factor MCM2
  • Histone H3.3
  • Histone H4
  • Tonsoku-like protein
KeywordsCHAPERONE / DNA repair and histone chaperone
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of chromosome condensation / Barr body / : / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / pericentric heterochromatin formation / inner kinetochore ...Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of chromosome condensation / Barr body / : / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / pericentric heterochromatin formation / inner kinetochore / MCM complex / muscle cell differentiation / double-strand break repair via break-induced replication / mitotic DNA replication initiation / oocyte maturation / regulation of DNA-templated DNA replication initiation / nucleosomal DNA binding / nucleus organization / nuclear replication fork / histone reader activity / replication fork processing / DNA replication origin binding / cochlea development / spermatid development / DNA replication initiation / Activation of the pre-replicative complex / single fertilization / subtelomeric heterochromatin formation / Activation of ATR in response to replication stress / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / protein localization to chromatin / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / embryo implantation / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to interleukin-4 / telomere organization / DNA helicase activity / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / 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 / Assembly of the pre-replicative complex / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / multicellular organism growth / male gonad development / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / HCMV Early Events / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / single-stranded DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP)
Similarity search - Function
: / DNA replication licensing factor MCM2-like, winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / Leucine rich repeat, ribonuclease inhibitor type / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain ...: / DNA replication licensing factor MCM2-like, winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / Leucine rich repeat, ribonuclease inhibitor type / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Leucine Rich repeat / Ankyrin repeat-containing domain / Histone, subunit A / Histone, subunit A / Tetratricopeptide repeat / TPR repeat region circular profile. / Ankyrin repeat / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich repeat / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Ankyrin repeats (3 copies) / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Leucine-rich repeat domain superfamily / Ankyrin repeat-containing domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA replication licensing factor MCM2 / Histone H4 / Histone H3.3 / Tonsoku-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.424 Å
AuthorsHuang, H. / Patel, D.
CitationJournal: Nature / Year: 2016
Title: H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex.
Authors: Saredi, G. / Huang, H. / Hammond, C.M. / Alabert, C. / Bekker-Jensen, S. / Forne, I. / Reveron-Gomez, N. / Foster, B.M. / Mlejnkova, L. / Bartke, T. / Cejka, P. / Mailand, N. / Imhof, A. / ...Authors: Saredi, G. / Huang, H. / Hammond, C.M. / Alabert, C. / Bekker-Jensen, S. / Forne, I. / Reveron-Gomez, N. / Foster, B.M. / Mlejnkova, L. / Bartke, T. / Cejka, P. / Mailand, N. / Imhof, A. / Patel, D.J. / Groth, A.
History
DepositionApr 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
D: Tonsoku-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8987
Polymers48,5184
Non-polymers3793
Water1,56787
1
A: Histone H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
D: Tonsoku-like protein
hetero molecules

A: Histone H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
D: Tonsoku-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,79514
Polymers97,0368
Non-polymers7596
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_647y+1,x-1,-z+21
Buried area24010 Å2
ΔGint-97 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.506, 139.506, 72.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

-
Protein , 4 types, 4 molecules ABCD

#1: Protein Histone H3.3


Mass: 9026.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P84243
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


Mass: 7860.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030 / Production host: Escherichia coli (E. coli) / References: UniProt: P49736, DNA helicase
#4: Protein Tonsoku-like protein / Inhibitor of kappa B-related protein / IkappaBR / NF-kappa-B inhibitor-like protein 2 / Nuclear ...Inhibitor of kappa B-related protein / IkappaBR / NF-kappa-B inhibitor-like protein 2 / Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2


Mass: 20368.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TONSL, IKBR, NFKBIL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96HA7

-
Non-polymers , 3 types, 90 molecules

#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.22 Å3/Da / Density % sol: 70.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M MES pH 5.6, 7% isopropanol / PH range: 5.5-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31146 / % possible obs: 99.8 % / Redundancy: 5.5 % / Net I/σ(I): 23.1
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BNV

5bnv


Resolution: 2.424→46.513 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.43
RfactorNum. reflection% reflection
Rfree0.2461 1446 4.64 %
Rwork0.2013 --
obs0.2033 31137 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.424→46.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 24 87 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092970
X-RAY DIFFRACTIONf_angle_d1.3163997
X-RAY DIFFRACTIONf_dihedral_angle_d16.961128
X-RAY DIFFRACTIONf_chiral_restr0.048441
X-RAY DIFFRACTIONf_plane_restr0.007526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4241-2.51070.3071570.27872831X-RAY DIFFRACTION97
2.5107-2.61120.29691520.27312945X-RAY DIFFRACTION100
2.6112-2.73010.32161320.26692959X-RAY DIFFRACTION100
2.7301-2.8740.28651320.25422948X-RAY DIFFRACTION100
2.874-3.0540.29611450.23912981X-RAY DIFFRACTION100
3.054-3.28980.25221630.22662945X-RAY DIFFRACTION100
3.2898-3.62070.25621390.21392984X-RAY DIFFRACTION100
3.6207-4.14440.22441260.18363015X-RAY DIFFRACTION100
4.1444-5.22030.21631470.16293015X-RAY DIFFRACTION100
5.2203-46.52130.22121530.17393068X-RAY DIFFRACTION99
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)
12.36250.888-0.70413.305-5.16918.5525-0.13731.024-0.464-0.8115-0.754-0.38220.52181.13890.61780.61520.12720.06980.6074-0.04060.4328132.9444-63.108866.8172
22.25680.4699-0.26678.3131-0.94817.36240.4183-0.27880.08840.5260.1281-0.23690.31160.3236-0.53910.44370.10920.0060.4173-0.00210.4581127.9335-69.907283.1764
35.1108-0.29090.49299.42297.29688.0125-0.0191-0.6047-1.00991.27560.0841-0.24060.4621-1.4075-0.03050.60990.08810.11370.30520.09280.6844122.8498-78.650685.1855
42.436-0.2752-0.02098.3244-3.20782.1186-0.06950.2342-0.0245-0.41030.0540.38440.25560.04450.00920.27380.02480.01940.3685-0.05240.3565121.787-56.758771.3312
59.55541.6402-2.06722.7835-2.25764.69290.0052-0.3170.70520.38620.11690.1115-0.21930.2829-0.18050.36640.05180.03710.352-0.06250.424120.0499-44.802276.1455
63.09371.82182.27044.3363.45633.39490.5115-0.2752-0.1840.4917-0.0534-0.03530.71030.3467-0.460.8740.10230.01280.7992-0.06690.3986135.5026-59.4474103.0983
73.3563-0.648-0.28612.817-1.60256.5997-0.10160.2160.25090.0396-0.0904-0.3286-0.00120.29970.16310.2810.0330.020.3892-0.030.4316132.1132-54.225272.6362
84.16441.9098-0.49167.9084-0.28492.5476-0.0946-0.2956-0.29460.54760.02030.64110.3161-0.08730.07990.30980.11110.0910.3445-0.01420.4184118.1199-67.088981.4501
93.31360.48491.04082.5349-1.02544.2109-0.83731.25170.6888-0.55770.30111.34360.51110.59460.38640.84490.0884-0.26551.2246-0.22270.9009113.9651-66.519870.5572
106.6893-0.2832-3.18241.85540.52352.40140.28960.1861.2086-0.55310.0371-0.6271-0.94271.6652-0.40820.4629-0.1257-0.00030.84780.01460.6889137.7081-45.932367.7421
113.047-0.5568-1.65093.2714-2.51023.59780.15510.93241.4183-0.33740.77-0.7803-0.6745-0.1631-0.39940.56690.05110.08650.66610.01260.6429139.8599-56.294465.28
123.2222.1329-2.65542.5175-1.09192.6581-0.06081.2725-1.59690.08330.0017-1.17980.58490.6473-0.03760.35810.09510.03680.6116-0.05580.6857141.3243-67.885670.3178
134.25984.387-2.88094.5011-3.07242.2418-0.3724-0.3834-0.6613-0.2332-0.2151-1.17590.4930.30070.36680.46690.05860.10430.3378-0.0270.7123131.4197-77.915677.2497
143.8871-1.74612.67062.1852-0.84931.9335-0.1001-0.3935-0.53650.42010.1311.3845-0.1646-0.65080.07890.52530.05490.08080.5207-0.05070.8172115.5051-86.159777.4034
153.59573.47853.69883.39593.9087.85810.0301-1.0557-0.32380.3074-0.81811.4518-0.7015-1.38420.56150.62320.08510.39230.8426-0.03951.4373104.2076-70.31586.7375
163.2916-0.0452-1.19082.0374-1.94322.2422-0.2178-0.6806-0.0727-0.1065-0.60680.3292-2.7833-2.49910.4381.47350.7598-0.03911.5075-0.27960.5444126.9272-51.142295.9377
170.6164-1.3868-0.19937.8816.47327.6246-0.7089-0.02541.0319-0.772-0.64431.2911-1.3647-0.83391.26051.53630.47320.26391.4038-0.21061.25123.7836-39.048899.0843
181.0504-0.5250.52051.16020.26250.6556-0.6316-0.40150.0212-0.02720.05310.5826-1.6028-3.56940.41971.32020.53450.04942.2402-0.33850.3727126.118-54.0505104.1236
194.3519-2.08851.8664.826-3.10162.2929-0.15340.0509-0.04050.03680.68610.276-1.1445-3.0699-0.42821.34950.09820.34152.1265-0.22830.6675122.0874-47.4996110.1344
207.39441.5862-2.73692.1675-2.73313.56530.1629-1.9470.53450.131-1.21820.4036-0.6368-3.31310.82410.91990.1309-0.04841.9063-0.25820.6566130.1423-54.9079115.2981
211.3013-0.34510.33281.7237-1.46851.28430.363-0.9767-0.5937-0.0237-0.53490.3284-0.2412-1.55070.15791.3573-0.29780.28782.7201-0.6437-0.093123.9112-57.8615119.8845
227.0222-1.8886-0.6376.02022.67646.7220.73-0.03260.17160.3456-0.3254-0.60.7677-0.1914-0.41030.8171-0.16450.04571.3225-0.02630.4503139.7446-57.2892122.8161
237.90251.3027-0.78745.54741.96584.9029-0.4653-0.8710.3113-0.207-0.34310.2893-1.0326-2.11320.691.34960.1189-0.10681.5865-0.21350.492133.3886-51.7076128.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 134 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 47 )
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 92 )
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 100 )
10X-RAY DIFFRACTION10chain 'C' and (resid 68 through 76 )
11X-RAY DIFFRACTION11chain 'C' and (resid 77 through 81 )
12X-RAY DIFFRACTION12chain 'C' and (resid 82 through 87 )
13X-RAY DIFFRACTION13chain 'C' and (resid 88 through 97 )
14X-RAY DIFFRACTION14chain 'C' and (resid 98 through 106 )
15X-RAY DIFFRACTION15chain 'C' and (resid 107 through 124 )
16X-RAY DIFFRACTION16chain 'D' and (resid 521 through 541 )
17X-RAY DIFFRACTION17chain 'D' and (resid 542 through 551 )
18X-RAY DIFFRACTION18chain 'D' and (resid 552 through 574 )
19X-RAY DIFFRACTION19chain 'D' and (resid 575 through 593 )
20X-RAY DIFFRACTION20chain 'D' and (resid 594 through 616 )
21X-RAY DIFFRACTION21chain 'D' and (resid 617 through 633 )
22X-RAY DIFFRACTION22chain 'D' and (resid 634 through 650 )
23X-RAY DIFFRACTION23chain 'D' and (resid 651 through 669 )

+
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