[English] 日本語
Yorodumi
- PDB-7bre: The crystal structure of MLL2 in complex with ASH2L and RBBP5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bre
TitleThe crystal structure of MLL2 in complex with ASH2L and RBBP5
Components
  • Histone-lysine N-methyltransferase 2B
  • Retinoblastoma-binding protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
KeywordsPROTEIN BINDING / Histone methyltransferase / MLL2 complex / MLL2 / RBBP5 / ASH2L / histone methylation / epigenetics / non-histone substrate / P53
Function / homology
Function and homology information


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / MLL1 complex / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / Neddylation / histone binding / methylation / transcription cis-regulatory region binding / DNA damage response / positive regulation of cell population proliferation / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
KMT2B, ePHD domain / : / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus ...KMT2B, ePHD domain / : / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Retinoblastoma-binding protein 5 / Set1/Ash2 histone methyltransferase complex subunit ASH2 / Histone-lysine N-methyltransferase 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsLi, Y. / Zhao, L. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970576 China
National Natural Science Foundation of China (NSFC)31900934 China
CitationJournal: Structure / Year: 2020
Title: Crystal Structure of MLL2 Complex Guides the Identification of a Methylation Site on P53 Catalyzed by KMT2 Family Methyltransferases.
Authors: Li, Y. / Zhao, L. / Tian, X. / Peng, C. / Gong, F. / Chen, Y.
History
DepositionMar 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Set1/Ash2 histone methyltransferase complex subunit ASH2
B: Histone-lysine N-methyltransferase 2B
E: Histone-lysine N-methyltransferase 2B
D: Set1/Ash2 histone methyltransferase complex subunit ASH2
C: Retinoblastoma-binding protein 5
F: Retinoblastoma-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,67910
Polymers85,7806
Non-polymers9004
Water00
1
A: Set1/Ash2 histone methyltransferase complex subunit ASH2
B: Histone-lysine N-methyltransferase 2B
C: Retinoblastoma-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3405
Polymers42,8903
Non-polymers4502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Histone-lysine N-methyltransferase 2B
D: Set1/Ash2 histone methyltransferase complex subunit ASH2
F: Retinoblastoma-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3405
Polymers42,8903
Non-polymers4502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.075, 66.195, 83.734
Angle α, β, γ (deg.)90.000, 93.230, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein


Mass: 20597.355 Da / Num. of mol.: 2 / Fragment: UNP residues 286-402 and UNP residues 445-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH2L, ASH2L1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9UBL3
#2: Protein Histone-lysine N-methyltransferase 2B / Lysine N-methyltransferase 2B / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / Trithorax ...Lysine N-methyltransferase 2B / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / Trithorax homolog 2 / WW domain-binding protein 7 / WBP-7


Mass: 19037.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: Q9UMN6, [histone H3]-lysine4 N-trimethyltransferase
#3: Protein/peptide Retinoblastoma-binding protein 5 / RBBP-5 / Retinoblastoma-binding protein RBQ-3


Mass: 3255.321 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q15291
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
Has ligand of interestN
Sequence detailsAuthors made a construct of ASH2L (Q9UBL3-3) that delete a loop deletion from 402-445, and the loop ...Authors made a construct of ASH2L (Q9UBL3-3) that delete a loop deletion from 402-445, and the loop is replaced by a linker sequence (ISGRGS).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 21457 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.066 / Rrim(I) all: 0.173 / Χ2: 0.631 / Net I/σ(I): 3.4 / Num. measured all: 142941
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.96.30.64221200.7930.2760.70.477100
2.9-3.026.60.52421480.8690.2210.570.495100
3.02-3.156.50.40121220.920.170.4360.527100
3.15-3.3270.31621300.9540.1280.3410.543100
3.32-3.536.90.23221140.9640.0960.2510.592100
3.53-3.86.50.1721440.9780.0720.1850.643100
3.8-4.186.90.1321540.9890.0530.140.73100
4.18-4.796.80.121340.9920.0410.1090.801100
4.79-6.036.70.09421750.9920.0390.1020.682100
6.03-506.40.08122160.9970.0340.0880.80199.9

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.17refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TOJ,5F6E
Resolution: 2.803→37.833 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.25
RfactorNum. reflection% reflection
Rfree0.2646 1096 5.13 %
Rwork0.2185 --
obs0.2209 21376 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.34 Å2 / Biso mean: 52.2977 Å2 / Biso min: 13.43 Å2
Refinement stepCycle: final / Resolution: 2.803→37.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5813 0 54 0 5867
Biso mean--49.21 --
Num. residues----723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.803-2.93040.30671390.2767248799
2.9304-3.08490.30361410.26512530100
3.0849-3.2780.27641150.24692543100
3.278-3.5310.31931380.23682525100
3.531-3.8860.25831310.21272551100
3.886-4.44750.27931490.19272535100
4.4475-5.60050.20321450.18472542100
5.6005-37.830.25041380.2199256798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.9556-2.3293-0.39575.15420.16375.96070.10450.1219-0.92890.9338-0.16130.77380.5148-0.86450.20920.3126-0.03380.05380.2251-0.04240.284125.3627-7.861496.9135
24.1897-0.5321-0.54784.32661.20474.34360.10920.05820.03110.9577-0.20220.847-0.0131-0.21120.27030.34160.02450.03250.2207-0.0010.251821.66153.170697.3615
33.8581-2.1456-1.17755.43650.76931.79750.07720.0866-0.301-0.53510.0310.30480.1425-0.2673-0.07050.2120.0264-0.00940.219-0.00850.233333.1059-2.825690.7333
43.04770.69551.13590.8948-0.32222.87520.0234-0.3128-0.0519-0.90060.3770.5626-0.55920.1932-0.22680.3371-0.03980.03670.1368-0.02840.270930.514410.162792.4691
50.7868-1.5863-0.47165.38830.6381.4869-0.46240.36820.02190.92350.0259-0.47310.07490.11510.44170.20660.0519-0.01990.26560.0350.200537.3823.0427103.3456
61.94720.7874-0.54911.33430.7632.2070.16680.05360.1454-0.321-0.1455-0.55530.12760.06940.03260.3206-0.0139-0.0270.11380.04060.171741.11385.709689.0797
72.43870.0046-1.78482.8651-0.44651.4753-0.07040.29010.0712-0.145-0.010.00290.0598-0.14940.04490.3102-0.0277-0.07680.1812-0.00360.139135.52681.509387.8914
83.0099-0.91160.0914.32651.33711.8405-0.00620.39750.5207-1.0915-0.07650.3305-0.3675-0.15350.1150.69460.09410.00050.1991-0.09210.307437.8586-9.109982.8949
92.5582.68470.31052.15570.52352.3454-0.0486-0.16740.3486-0.0474-0.02440.4906-0.2765-0.6030.0950.45470.0761-0.01040.318-0.09620.57169.022215.3769129.17
101.1175-0.54520.81242.19871.364.0590.0205-0.51660.1448-0.1221-0.1266-0.0301-0.3881-0.3944-0.08330.3037-0.06330.1650.2578-0.1240.339421.67721.3815135.3392
110.81370.374-0.89671.87442.10734.75970.40960.04530.3844-0.18080.0734-0.5238-0.44140.8149-0.41870.48850.0701-0.04760.1679-0.02660.37735.460116.7381114.2215
120.7566-0.6881-0.86693.8024-2.34.1559-0.18570.4468-0.62950.0758-0.28430.1304-0.56330.01790.34530.45350.0798-0.00860.2581-0.17470.553929.112916.6366119.7736
134.9935-1.04640.1474.20221.3212.75190.0191-0.014-0.27110.0852-0.0413-0.294-0.04090.3467-0.02320.3941-0.08380.03980.23170.02010.271627.934813.4736134.0648
148.0433-1.9746-3.03150.48410.71123.6886-0.67110.5376-0.79390.1310.4025-0.35730.49950.67450.08940.64380.1426-0.16640.4648-0.00110.448128.05868.1407126.4257
153.91444.36640.36125.43042.54098.2518-0.79610.47540.38490.44420.2768-0.00150.41750.62710.43170.40970.0595-0.00150.47540.0460.902518.0971-7.7702125.3876
160.1112-0.30360.42632.6078-2.31462.6529-0.3888-1.0016-1.1933-1.06560.0962-0.02190.71770.70740.35520.8320.3070.06960.84050.25890.69077.0415-20.9545132.0533
174.4821-0.5919-1.70163.34540.69024.4962-0.7566-0.8551-0.96280.1729-0.0756-0.11731.33340.67960.57260.481-0.04720.19740.94080.42890.469-4.7002-19.0806137.1048
180.91580.50780.43591.6622-0.15230.3586-0.7138-0.332-0.02210.1154-0.1192-0.25920.09590.6361-0.13580.46150.0777-0.22030.70320.07490.44768.6001-13.6799133.2369
190.14670.7223-0.05433.9568-1.09661.11730.1797-0.4929-0.24630.8003-0.01490.59050.5174-0.5489-0.37340.388-0.0255-0.09050.5320.16680.5787-10.3326-10.519113.6463
203.2579-1.52712.11261.55950.76825.0476-0.0171-0.34170.17370.35560.05880.16860.1798-0.1118-0.22040.29010.02160.02240.32610.02060.4551-5.066-7.2991119.9745
213.1943-0.3672-1.92030.7733-0.73776.3428-0.33510.102-0.3566-0.3264-0.06580.14321.4999-0.28330.1280.6666-0.0956-0.28770.38050.21020.4897-2.4127-14.1346118.4212
229.8728-1.8533-1.02077.402-5.81845.2228-0.302-0.29820.46250.14020.24380.16690.26460.6921-0.0080.3156-0.045-0.14250.45470.04050.372-3.2351-11.5407134.4527
236.55290.2818-0.52085.8352-0.3974.5924-0.2511-1.01910.6821-0.13830.2298-0.50710.3353-0.10660.08010.27450.0534-0.03880.4-0.03540.42177.0348-8.3598131.5221
248.30842.1892-5.29425.81220.84074.3230.80570.51250.7555-0.084-0.01530.3731-0.5896-0.5881-0.63880.41320.1877-0.12250.8385-0.18410.6248-8.9319-4.1817130.499
254.93390.0063-4.66978.849-0.35047.6493-0.0982-0.52630.86930.14420.57960.61870.675-0.4108-0.39380.4409-0.0772-0.16990.623-0.00310.6033-13.8582-5.5498138.134
261.00751.9585-0.79894.1091-1.10291.23990.32050.25781.38120.2103-0.5989-0.5815-0.29350.70970.44780.382-0.06260.02730.72120.1851.40890.359113.503799.4391
273.2347-0.43391.3920.3198-0.01591.20790.38441.29111.0613-0.4464-0.311-0.7752-0.3980.94980.2174-0.48770.2898-0.16070.97090.49570.90023.81534.324697.8367
281.0152-0.8850.74940.8146-0.63090.55040.02290.78141.5872-0.4613-0.3227-0.6882-0.20960.31030.2580.25560.03620.02180.48580.37990.9901-8.963513.254892.7499
292.03130.53070.81940.4727-0.65052.58520.42841.31990.4584-0.5495-0.2081-0.76040.33520.86080.01060.42660.19510.00160.75180.16550.7296-3.3526-1.637791.1806
305.25950.06282.86252.3396-2.43954.18990.0319-0.34690.59-0.1756-0.28420.06390.1612-0.42010.17270.19090.03720.05420.231-0.07970.2902-12.24751.273398.4902
315.5607-0.528-1.16323.8451.26642.08850.51630.7762-0.911-0.214-0.72320.08530.70420.96990.28940.3540.1906-0.00870.610.03340.4121-14.0072-3.222589.9726
322.54711.68351.44091.73340.56522.4271-0.41680.81231.1829-0.4338-0.4434-0.28990.03431.0452-0.04320.50190.06290.11530.62510.3640.5991-13.67610.335586.7641
334.3155-1.04210.53374.1013-0.28762.58050.33470.16451.1652-0.0205-0.6481-0.233-0.83880.26240.48810.42580.03650.02010.39450.12280.7903-22.181513.02788.5111
342.9634-0.08160.43880.940.08131.9471-0.15980.72540.7095-0.1314-0.4555-0.6119-0.02680.33690.53070.2620.02740.02030.52590.1410.5748-11.74554.899691.8541
353.07080.4755-2.13091.4014-0.71221.59250.11520.36420.2887-0.0992-0.00380.06840.1979-0.7857-0.2190.1719-0.35960.44361.510.82610.177-4.507612.89980.9021
360.21120.2735-0.17591.1990.41110.5628-0.46580.94430.6456-0.4394-0.6697-0.5901-0.82360.76570.74030.6708-0.1313-0.29090.89980.80731.2463-11.87917.807383.3985
375.1193-3.6032-5.69172.87252.8832.0001-0.1124-0.5140.36320.41510.2129-0.87271.3433-1.3734-0.03211.2691-0.0304-0.20310.59880.02190.647623.927528.853120.8116
389.7312-1.82980.8051.98031.23762.4031.001-0.08-0.31570.623-0.33290.3947-0.3716-0.6982-0.7040.4443-0.10240.13470.3142-0.10570.618221.244720.1155113.4672
392.0969-0.75521.82835.35050.90782.09480.66040.52050.6955-0.3275-0.33450.8018-1.2602-0.229-0.39190.37160.10040.01640.34810.06840.499430.09618.7223102.2417
407.9911-1.78150.84322.71583.46875.86820.50320.53451.0787-0.1322-0.0475-0.0229-1.55791.1619-0.38320.4164-0.1045-0.02290.41740.02720.705438.456316.8932103.0676
412.7716-1.19494.11571.7403-2.26858.17690.60360.3141-0.2498-0.0485-0.0862-0.49810.22140.0774-0.44241.53150.5769-0.05991.13990.16080.49214.1714-20.9914118.5403
422.9239-0.3953.03947.3601-2.33863.9009-0.164-0.0782-0.0586-0.48650.1245-0.42990.46220.1661-0.08630.74750.29140.19440.2030.30870.7632.0855-13.0173110.0191
435.1359-0.94451.04214.63422.03692.29870.09820.7496-1.3716-0.11790.6425-0.18282.41060.1115-0.7720.8415-0.0245-0.21520.4609-0.0740.5123-7.0263-10.6869101.5451
445.87450.7315-2.45260.73530.4417.00490.18711.1817-0.9174-0.61680.41940.6722.1851-0.9779-0.41370.5698-0.1801-0.25220.49580.15660.8566-14.638-9.0195101.382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 285 through 294 )A285 - 294
2X-RAY DIFFRACTION2chain 'A' and (resid 295 through 313 )A295 - 313
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 335 )A314 - 335
4X-RAY DIFFRACTION4chain 'A' and (resid 336 through 347 )A336 - 347
5X-RAY DIFFRACTION5chain 'A' and (resid 348 through 362 )A348 - 362
6X-RAY DIFFRACTION6chain 'A' and (resid 363 through 451 )A363 - 451
7X-RAY DIFFRACTION7chain 'A' and (resid 452 through 493 )A452 - 493
8X-RAY DIFFRACTION8chain 'A' and (resid 494 through 503 )A494 - 503
9X-RAY DIFFRACTION9chain 'B' and (resid 2551 through 2581 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 2582 through 2606 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 2607 through 2624 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 2625 through 2646 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 2647 through 2715 )B0
14X-RAY DIFFRACTION14chain 'E' and (resid 2551 through 2558 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 2559 through 2568 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 2569 through 2581 )E0
17X-RAY DIFFRACTION17chain 'E' and (resid 2582 through 2591 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 2592 through 2606 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 2607 through 2624 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 2625 through 2636 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 2637 through 2646 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 2647 through 2658 )E0
23X-RAY DIFFRACTION23chain 'E' and (resid 2659 through 2686 )E0
24X-RAY DIFFRACTION24chain 'E' and (resid 2687 through 2698 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 2699 through 2715 )E0
26X-RAY DIFFRACTION26chain 'D' and (resid 286 through 295 )D286 - 295
27X-RAY DIFFRACTION27chain 'D' and (resid 296 through 313 )D296 - 313
28X-RAY DIFFRACTION28chain 'D' and (resid 314 through 332 )D314 - 332
29X-RAY DIFFRACTION29chain 'D' and (resid 333 through 347 )D333 - 347
30X-RAY DIFFRACTION30chain 'D' and (resid 348 through 372 )D348 - 372
31X-RAY DIFFRACTION31chain 'D' and (resid 373 through 390 )D373 - 390
32X-RAY DIFFRACTION32chain 'D' and (resid 391 through 398 )D391 - 398
33X-RAY DIFFRACTION33chain 'D' and (resid 399 through 451 )D399 - 451
34X-RAY DIFFRACTION34chain 'D' and (resid 452 through 481 )D452 - 481
35X-RAY DIFFRACTION35chain 'D' and (resid 482 through 492 )D482 - 492
36X-RAY DIFFRACTION36chain 'D' and (resid 493 through 503 )D493 - 503
37X-RAY DIFFRACTION37chain 'C' and (resid 336 through 340 )C336 - 340
38X-RAY DIFFRACTION38chain 'C' and (resid 341 through 345 )C341 - 345
39X-RAY DIFFRACTION39chain 'C' and (resid 346 through 350 )C346 - 350
40X-RAY DIFFRACTION40chain 'C' and (resid 351 through 355 )C351 - 355
41X-RAY DIFFRACTION41chain 'F' and (resid 337 through 341 )F337 - 341
42X-RAY DIFFRACTION42chain 'F' and (resid 342 through 346 )F342 - 346
43X-RAY DIFFRACTION43chain 'F' and (resid 347 through 351 )F347 - 351
44X-RAY DIFFRACTION44chain 'F' and (resid 352 through 355 )F352 - 355

+
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://pdbjlvh1.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