[English] 日本語
Yorodumi
- PDB-3f9z: Structural Insights into Lysine Multiple Methylation by SET Domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f9z
TitleStructural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy
Components
  • Histone H4
  • Histone-lysine N-methyltransferase SETD8
KeywordsTRANSFERASE / methyltransferase / histone / SET / lysine / Alternative splicing / Cell cycle / Cell division / Chromatin regulator / Chromosomal protein / Coiled coil / Mitosis / Nucleus / Repressor / S-adenosyl-L-methionine / Transcription / Transcription regulation / Acetylation / DNA-binding / Methylation / Nucleosome core
Function / homology
Function and homology information


histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator ...histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / negative regulation of double-strand break repair via homologous recombination / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / regulation of signal transduction by p53 class mediator / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / cell division / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Class V SAM-dependent methyltransferases / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain ...Class V SAM-dependent methyltransferases / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Beta Complex / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H4 / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCouture, J.-F. / Dirk, L.M.A. / Brunzelle, J.S. / Houtz, R.L. / Trievel, R.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural origins for the product specificity of SET domain protein methyltransferases.
Authors: Couture, J.F. / Dirk, L.M. / Brunzelle, J.S. / Houtz, R.L. / Trievel, R.C.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD8
B: Histone-lysine N-methyltransferase SETD8
C: Histone-lysine N-methyltransferase SETD8
D: Histone-lysine N-methyltransferase SETD8
E: Histone H4
F: Histone H4
G: Histone H4
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,77312
Polymers80,2358
Non-polymers1,5384
Water10,611589
1
A: Histone-lysine N-methyltransferase SETD8
F: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4433
Polymers20,0592
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-5.2 kcal/mol
Surface area9280 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase SETD8
E: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4433
Polymers20,0592
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-5.2 kcal/mol
Surface area9740 Å2
MethodPISA
3
C: Histone-lysine N-methyltransferase SETD8
G: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4433
Polymers20,0592
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-6.2 kcal/mol
Surface area9410 Å2
MethodPISA
4
D: Histone-lysine N-methyltransferase SETD8
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4433
Polymers20,0592
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-6.5 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.990, 45.550, 94.410
Angle α, β, γ (deg.)89.37, 87.09, 90.50
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Histone-lysine N-methyltransferase SETD8 / H4-K20-HMTase SETD8 / SET domain-containing protein 8 / PR/SET domain-containing protein 07 / ...H4-K20-HMTase SETD8 / SET domain-containing protein 8 / PR/SET domain-containing protein 07 / PR/SET07 / PR-Set7 / Lysine N-methyltransferase 5A


Mass: 18774.258 Da / Num. of mol.: 4 / Fragment: SET domain: UNP residues 232-393 / Mutation: Y245F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD8, KMT5A, PRSET7, SET07, SET8 / Plasmid: pHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9NQR1, histone-lysine N-methyltransferase
#2: Protein/peptide
Histone H4 /


Mass: 1284.557 Da / Num. of mol.: 4 / Fragment: UNP residues 16-25 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to residues 16-25 of human histone H4
References: UniProt: P62805
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 90904 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.041 / Net I/σ(I): 31.1
Reflection shellResolution: 1.6→1.7 Å / Mean I/σ(I) obs: 8.4 / Rsym value: 0.173

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZKK

1zkk


Resolution: 1.6→38.9 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.232 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25697 4612 5 %RANDOM
Rwork0.21571 ---
obs0.21776 87679 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.01 Å20.03 Å2
2--0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5422 0 104 589 6115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225622
X-RAY DIFFRACTIONr_angle_refined_deg1.61.997538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26323.478276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.173151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2581550
X-RAY DIFFRACTIONr_chiral_restr0.1120.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024186
X-RAY DIFFRACTIONr_nbd_refined0.2090.22529
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23772
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2507
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.248
X-RAY DIFFRACTIONr_mcbond_it0.9811.53451
X-RAY DIFFRACTIONr_mcangle_it1.41825322
X-RAY DIFFRACTIONr_scbond_it2.30132496
X-RAY DIFFRACTIONr_scangle_it3.2344.52216
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 334 -
Rwork0.259 6337 -
obs--100 %
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)
13.7675-3.7949-0.55599.8416-0.42795.1239-0.3209-0.6510.09550.30790.2758-0.42550.39710.43830.04510.03570.07440.00140.1950.0210.137524.1671-14.7385-11.1661
26.9161-2.07370.84833.7275-2.53533.1546-0.00540.09560.2402-0.289-0.1153-0.7269-0.03480.31440.12080.0139-0.04440.0420.06460.00570.185320.9769-1.5437-18.7326
32.4001-1.68540.15292.85720.55371.1174-0.01650.11650.1387-0.14410.0299-0.193-0.09120.0897-0.01340.0507-0.01640.01050.05570.0340.00832.8486-2.0395-26.8188
41.17470.1976-0.1115.37941.02812.24080.0181-0.02990.06890.09710.0899-0.2666-0.12640.0807-0.1080.019-0.015-0.00140.06470.02430.040612.016-3.5883-16.9548
54.4166-2.7994-1.96578.08643.0145.34760.1552-0.08050.1368-0.4884-0.02830.3165-0.96580.1472-0.12690.2172-0.06860.0010.0562-0.02440.07158.05314.2551-3.3239
63.4341.27992.52181.43071.22264.8683-0.2333-0.26690.50290.0289-0.01060.1006-0.836-0.17150.24390.12830.019-0.03360.019-0.02680.03324.53519.0755-7.7978
71.74620.51190.31170.82260.41123.1953-0.067-0.10510.1847-0.0577-0.0275-0.0872-0.37180.16220.09450.0426-0.0077-0.00470.00470.0260.01276.65114.6416-13.2733
87.02193.08254.00981.77381.87495.31810.1149-0.2408-0.06580.1503-0.0625-0.25680.03430.2189-0.05240.0212-0.0015-0.03160.0659-0.00620.025314.8939-2.5545-8.7222
91.1252-0.30460.09291.89110.71123.1233-0.0414-0.1199-0.05030.08530.0445-0.0086-0.0853-0.0879-0.0030.0188-0.00760.00230.03710.0218-0.01811.2927-5.5649-14.7132
109.74920.31491.74753.1473-2.18118.6583-0.0607-0.015-0.31440.11120.14940.3416-0.3842-0.8906-0.08870.01940.05260.01360.15720.01820.0052-10.66350.5384-10.6677
113.7465-6.0927-4.835513.48773.805421.176-0.4987-0.3664-0.62891.15110.33920.0890.25860.18860.15950.13630.1228-0.1427-0.0191-0.04370.2177-22.35837.012735.1854
123.18090.4845-3.66822.4661-1.05978.08090.19470.2753-0.00160.16090.10550.4744-0.1671-0.4868-0.3002-0.00120.048-0.0050.0835-0.0110.2435-20.76114.683618.9986
132.0618-1.0453-1.78412.14861.13622.16650.02310.06580.1831-0.1380.032-0.0919-0.3146-0.0523-0.05510.05410.0195-0.02940.0280.00560.0095-2.55889.8969.308
140.14941.00130.43176.74422.62043.62510.033-0.0060.0480.1765-0.18750.1685-0.025-0.06290.15450.02140.0282-0.01840.0747-0.02560.027-10.25135.862220.5165
151.9991-1.1806-0.52514.18590.50851.4215-0.04230.1772-0.3259-0.2578-0.04060.26310.3636-0.30340.08290.1149-0.06480.00110.0895-0.04130.0436-10.7825-15.699110.0955
161.23110.5986-0.85161.3473-1.55933.3587-0.12020.1359-0.1504-0.24980.06770.02380.3436-0.21680.05250.0746-0.03090.00450.0282-0.02110.022-7.2629-12.449510.5549
174.4014-0.30910.47961.7880.27742.3787-0.07380.0943-0.0551-0.09880.03720.0581-0.109-0.24060.03660.02490.005-0.0090.01880.0043-0.0245-5.42910.87369.7083
1810.35198.2397-0.12718.6052-0.09981.28150.2563-0.32120.09620.4476-0.1970.35520.0533-0.1541-0.05930.014-0.00480.01080.01810.00080.0083-12.0611-2.522721.6155
190.5683-0.1433-0.76342.55640.51221.087-0.0406-0.05840.01470.08650.0005-0.1163-0.01860.06780.04020.00820.0049-0.03550.0118-0.0042-0.00781.01141.902218.4094
202.7471-1.3429-0.357510.63280.03164.0685-0.0806-0.08390.1916-0.1735-0.1417-0.8740.27290.49120.22230.00030.03290.03860.0680.05250.125810.0122-6.714312.4079
214.6036-0.6098-2.9250.98091.75638.5177-0.2379-0.4036-0.28590.23860.06640.24970.3803-0.04080.1715-0.02340.0460.05270.00890.08830.0287-26.847124.1862-15.657
223.15880.4974-1.2271.5064-0.33261.8454-0.0350.15370.1062-0.04120.09710.208-0.1244-0.1925-0.06220.01960.0052-0.01260.04780.02310.0333-12.381928.3322-36.603
231.40210.3315-0.06622.58960.03161.65180.0448-0.05950.13590.0447-0.08870.2167-0.0802-0.04780.0439-0.00250.0021-0.00270.04320.00660.0366-13.427127.8231-29.3633
246.6436-4.8747-0.92336.08161.02592.14970.06170.1556-0.3426-0.4015-0.03850.2120.3887-0.0446-0.02320.1686-0.0244-0.03620.0191-0.00890.0355-10.7233.3026-36.9828
251.578-0.4208-1.28632.3564-2.00293.50080.05810.2995-0.0618-0.5556-0.0377-0.21960.64090.1463-0.02030.22530.01320.05890.0311-0.02840.0575-3.22949.1225-46.6657
261.30450.1788-0.40974.8057-1.81484.6212-0.0018-0.0345-0.1246-0.03570.07520.12030.2447-0.1332-0.07340.0368-0.0072-0.01450.01440.00360.0198-11.83689.5867-31.7002
274.240.44532.31222.23220.08573.8632-0.10050.15630.0901-0.08710.02720.0163-0.0186-0.01970.07330.02810.00410.0120.01210.0078-0.0082-7.916622.778-36.5085
286.7375.5209-0.68167.9974-0.8450.99930.1659-0.26570.02540.3152-0.12010.40380.0945-0.1237-0.04590.0504-0.02550.01490.02460.01280.0286-14.589318.9854-24.0524
291.17730.9102-0.18812.5495-0.16291.41450.0113-0.05860.05760.10890.01950.08140.04570.0193-0.03080.00830.0031-0.00310.00220.0095-0.0051-8.28824.2926-27.9864
304.22190.0771-2.1456.69321.43353.5308-0.1895-0.1791-0.1739-0.05530.1482-0.90230.36210.40770.04130.030.03920.01370.0526-0.00390.20087.693615.3908-33.3088
315.6174-4.35880.312514.448-2.59780.73760.28950.3768-0.55580.1399-0.48440.05070.28920.2420.1949-0.04760.0537-0.06120.0107-0.06730.03724.107811.3991-59.9968
322.1597-0.6790.47851.06760.32351.95580.05070.19770.0411-0.10010.0202-0.1453-0.01180.224-0.07090.0166-0.00570.0122-0.00090.01210.02695.703423.4443-70.7853
331.7884-1.9611.88964.25810.20844.46360.17140.1399-0.2511-0.10430.0011-0.11590.20950.2133-0.17250.00970.0249-0.00790.0201-0.00940.09528.93513.6241-69.5219
340.6851-0.5475-0.69421.04661.14184.10510.0527-0.15070.14870.09480.0062-0.1193-0.35420.0948-0.0590.0583-0.0243-0.01250.0277-0.01640.04915.503133.3604-54.909
357.1726-0.94062.4384.15041.02126.0471-0.051-0.35880.3268-0.0378-0.11030.2941-0.387-0.3270.16130.15120.036-0.01610.008-0.04010.0852-6.31240.1558-56.2037
362.491-0.71061.42952.2769-1.12223.6744-0.0048-0.27360.06040.1009-0.0051-0.1296-0.20320.12860.00990.0104-0.0174-0.00380.0471-0.00780.01473.998430.4413-53.221
372.79350.3339-1.24152.8896-0.07532.46970.0323-0.0732-0.0526-0.0616-0.0936-0.1888-0.0110.07650.0613-0.00880.004-0.0236-0.01440.0114-0.0035-0.135825.4931-66.0326
385.35334.24533.09643.82633.41493.7930.2224-0.0923-0.23120.18160.0203-0.2880.23460.2586-0.24270.0110.0078-0.04380.0520.00510.075910.893321.6953-57.3644
391.5595-0.20950.56732.2420.61331.89020.0263-0.0185-0.17290.01890.0438-0.06060.18040.034-0.07010.0074-0.0028-0.0134-0.02080.01110.02750.171315.1059-66.2811
402.6319-0.0203-0.77282.57920.92217.384-0.1196-0.0029-0.07960.1023-0.00260.25250.1656-0.35870.1222-0.0023-0.0175-0.00030.05570.01250.022-13.146621.9792-55.4216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A193 - 205
2X-RAY DIFFRACTION2A206 - 215
3X-RAY DIFFRACTION3A216 - 235
4X-RAY DIFFRACTION4A236 - 248
5X-RAY DIFFRACTION5A249 - 259
6X-RAY DIFFRACTION6A260 - 277
7X-RAY DIFFRACTION7A278 - 303
8X-RAY DIFFRACTION8A304 - 318
9X-RAY DIFFRACTION9A319 - 343
10X-RAY DIFFRACTION10A344 - 352
11X-RAY DIFFRACTION11B192 - 202
12X-RAY DIFFRACTION12B203 - 216
13X-RAY DIFFRACTION13B217 - 235
14X-RAY DIFFRACTION14B236 - 245
15X-RAY DIFFRACTION15B246 - 259
16X-RAY DIFFRACTION16B260 - 288
17X-RAY DIFFRACTION17B289 - 301
18X-RAY DIFFRACTION18B302 - 321
19X-RAY DIFFRACTION19B322 - 341
20X-RAY DIFFRACTION20B342 - 352
21X-RAY DIFFRACTION21C193 - 207
22X-RAY DIFFRACTION22C208 - 230
23X-RAY DIFFRACTION23C231 - 248
24X-RAY DIFFRACTION24C249 - 260
25X-RAY DIFFRACTION25C261 - 270
26X-RAY DIFFRACTION26C271 - 288
27X-RAY DIFFRACTION27C289 - 302
28X-RAY DIFFRACTION28C303 - 313
29X-RAY DIFFRACTION29C314 - 338
30X-RAY DIFFRACTION30C339 - 352
31X-RAY DIFFRACTION31D192 - 204
32X-RAY DIFFRACTION32D205 - 232
33X-RAY DIFFRACTION33D233 - 242
34X-RAY DIFFRACTION34D243 - 256
35X-RAY DIFFRACTION35D257 - 268
36X-RAY DIFFRACTION36D269 - 288
37X-RAY DIFFRACTION37D289 - 303
38X-RAY DIFFRACTION38D304 - 321
39X-RAY DIFFRACTION39D322 - 337
40X-RAY DIFFRACTION40D338 - 352

+
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