[English] 日本語
Yorodumi
- PDB-3psk: Crystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3psk
TitleCrystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyces cerevisiae, Form Native Spt6 (1247-1451)
ComponentsTranscription elongation factor SPT6
KeywordsTRANSCRIPTION / Tandem SH2 Domain / Transcription Elongation / Nucleus
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / transcription antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of mRNA 3'-end processing / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation factor complex / transcription antitermination ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / transcription antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of mRNA 3'-end processing / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation factor complex / transcription antitermination / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / euchromatin / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus
Similarity search - Function
: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 ...: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / RuvA domain 2-like / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor SPT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsClose, D. / Hill, C.P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain.
Authors: Close, D. / Johnson, S.J. / Sdano, M.A. / McDonald, S.M. / Robinson, H. / Formosa, T. / Hill, C.P.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Sep 6, 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 / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription elongation factor SPT6
B: Transcription elongation factor SPT6
C: Transcription elongation factor SPT6
D: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,41416
Polymers100,2624
Non-polymers1,15312
Water5,044280
1
A: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5466
Polymers25,0651
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5466
Polymers25,0651
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1612
Polymers25,0651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1612
Polymers25,0651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Transcription elongation factor SPT6
hetero molecules

C: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7078
Polymers50,1312
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area1970 Å2
ΔGint-83 kcal/mol
Surface area21010 Å2
MethodPISA
6
A: Transcription elongation factor SPT6
hetero molecules

D: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7078
Polymers50,1312
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546x+1/2,-y-1/2,-z+11
Buried area1730 Å2
ΔGint-65 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.778, 105.176, 119.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Transcription elongation factor SPT6 / Chromatin elongation factor SPT6


Mass: 25065.430 Da / Num. of mol.: 4 / Fragment: unp residues 1247-1451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: SPT6, CRE2, SSN20, YGR116W, G6169 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23615
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Tris pH5.5 25% PEG 3350 0.2M (NH4)2SO4 , VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2008
RadiationMonochromator: Varimax confocal optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 58489 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.066 / Χ2: 0.978 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.184.30.47857521.033199.2
2.18-2.264.30.35857311.06199
2.26-2.374.40.27557431.058199.2
2.37-2.494.40.22157811.052199.4
2.49-2.654.50.17158131.044199.6
2.65-2.854.50.12858241.008199.7
2.85-3.144.50.08958570.9611100
3.14-3.594.50.06158900.857199.9
3.59-4.524.50.04759350.826199.9
4.52-304.20.04261630.899199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.45 Å
Translation2.5 Å29.45 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PSJ

3psj


Resolution: 2.1→28.229 Å / Occupancy max: 1 / Occupancy min: 0.03 / SU ML: 0.27 / σ(F): 0 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1931 3.43 %Random
Rwork0.1841 ---
obs0.1851 56332 95.93 %-
all-58263 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.727 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso max: 179.27 Å2 / Biso mean: 50.7154 Å2 / Biso min: 19.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.3119 Å2-0 Å20 Å2
2---2.9742 Å2-0 Å2
3---4.2861 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 60 280 6784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036652
X-RAY DIFFRACTIONf_angle_d0.6878998
X-RAY DIFFRACTIONf_chiral_restr0.049946
X-RAY DIFFRACTIONf_plane_restr0.0021140
X-RAY DIFFRACTIONf_dihedral_angle_d11.7062464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.17350.26411790.22414996517589
2.1735-2.26050.2441900.20715119530992
2.2605-2.36340.26991810.20045219540093
2.3634-2.48790.26071860.20255358554495
2.4879-2.64370.23951920.19045407559996
2.6437-2.84760.22611950.1945467566297
2.8476-3.13380.24291950.1885560575598
3.1338-3.58650.2162000.18025651585199
3.5865-4.51560.17362030.157257135916100
4.5156-28.23120.19752100.18985911612199
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)
15.281.95110.08214.5086-0.87931.3633-1.00590.70550.4026-0.92540.4792-0.6677-0.1573-0.16310.45740.3406-0.0195-0.00930.3074-0.02540.398741.3392-8.642959.5431
20.30910.0448-0.20213.0456-0.08021.94560.0558-0.2519-0.04480.1336-0.1846-0.57380.25950.36830.12310.29320.00340.02770.3239-0.02310.33240.5599-8.804444.2
32.60060.1310.32580.67281.23241.8255-0.2170.03620.0932-0.23010.1171-0.1318-0.35030.12910.05170.2834-0.0432-0.02150.2567-0.0160.265333.5286-0.37444.9505
40.1674-0.2130.64990.9285-0.36331.54330.0411-0.05240.0184-0.10840.0120.15660.0109-0.1242-0.01590.2145-0.0286-0.00550.24690.00130.303628.5547-16.153146.1648
51.0191-0.85040.47761.42680.31550.50370.06990.08710.2196-0.2687-0.3141-0.1167-0.2118-0.36590.23410.27370.0666-0.03520.2782-0.04690.260118.26125.856335.2856
65.4842-1.60131.76915.1432-1.57053.62620.1406-0.08450.09870.79950.01960.3096-0.38920.2234-0.11270.4480.1702-0.02980.4622-0.0690.493810.564723.372139.4746
72.45080.5875-0.08451.7607-1.51910.74450.1131-0.33130.55680.40520.06870.238-0.1552-0.4234-0.08540.39750.12950.00070.3416-0.07830.411613.113511.831342.0905
80.0938-0.4115-0.23483.8498-0.11880.9204-0.1253-0.04830.21631.10790.19180.7316-0.5736-0.2662-0.09570.58290.27650.16270.50410.00510.5585.328715.572645.4601
90.0798-0.0153-0.12691.93040.32051.4796-0.2211-0.296-0.31750.06930.2130.7994-0.3132-0.81580.04210.26820.07480.00060.42660.01250.47599.6677-1.028540.2667
100.08430.2155-0.4280.6405-0.58153.5341-0.08770.72451.211-0.05030.01050.48490.2747-0.9725-0.13640.37890.1594-0.04390.6998-0.15710.9323-1.53256.453141.8108
110.48730.60220.55410.30760.41791.1167-0.0155-0.2588-0.0448-0.03390.0140.3622-0.210.23090.06640.3011-0.0063-0.01710.3551-0.01310.4309-1.5134-9.46497.9941
120.83450.4297-0.18390.7423-0.63020.6668-0.2160.1090.060.0570.11210.1754-0.1902-0.16490.07790.21680.0445-0.0420.2334-0.01980.30954.7239-0.963714.867
131.02060.9080.64952.28340.31560.8934-0.27950.10050.1575-0.19710.3464-0.1714-0.29560.47380.01720.32640.006-0.05680.2885-0.00520.242511.361.777713.9763
141.8298-0.49930.52950.0567-0.18491.491-0.06660.1865-0.21050.08440.14190.06580.33060.0023-0.06140.29210.0098-0.01670.2288-0.01460.34669.4392-17.88810.1741
151.21381.71731.46473.25911.80571.70890.3303-0.10670.00560.6173-0.25370.19980.4511-0.0231-0.11060.3317-0.0019-0.03980.2713-0.00290.29216.3359-7.339522.5751
162.5030.02950.2112.5070.56180.20710.0282-0.62610.28570.56020.09580.1679-0.15-0.26370.03130.3203-0.0847-0.01590.43290.03580.266725.714511.916623.2107
171.32070.7769-0.34282.61820.4560.6432-0.11010.27350.1082-0.48140.1535-0.2716-0.2164-0.0756-0.08280.3495-0.0444-0.02470.3232-0.00830.365734.436521.501320.1149
180.91430.5558-0.83962.63590.02560.45340.1007-0.0137-0.001-0.410.0026-0.4566-0.26350.0977-0.08340.3533-0.0405-0.00280.31650.05890.35631.516211.523715.0984
190.8334-0.115-0.99422.24190.0142.05570.0183-0.07950.0209-0.1468-0.1152-0.5214-0.12550.54230.12120.22690.0298-0.02420.32040.04340.3430.7235-2.229918.3227
200.26290.6716-0.4531.9655-0.21134.3376-0.9155-0.74111.37550.45190.0539-1.22890.730.90710.91420.27030.05630.05050.5510.13630.753342.57423.380116.9799
211.40740.0652-0.41040.99950.70492.5259-0.24080.4458-0.1402-0.287-0.06990.2956-0.1585-0.64190.23640.34230.0528-0.00630.4269-0.05410.383128.871-35.1291-0.1357
220.18740.269-0.04011.19761.26510.907-0.0023-0.1129-0.02870.2413-0.0823-0.00190.09360.12030.02520.33170.0799-0.01110.2611-0.01730.337939.1448-34.91197.7846
230.66661.06681.39383.2921.7264.19310.43150.3469-0.13330.0985-0.38460.63370.6759-0.80970.06090.42250.05990.03870.4426-0.06020.486422.1806-34.66937.9048
243.85450.4610.61660.76230.04740.19980.3422-0.6217-0.37630.227-0.14140.15120.3152-0.0996-0.12310.35930.081-0.02280.30170.01230.287137.2181-30.884113.3063
252.07390.54821.22450.48021.14544.08710.08660.0494-0.8960.118-0.25550.73990.7394-0.34490.13660.3630.0482-0.00810.3278-0.09830.51516.3171-28.03632.8345
262.7097-0.17680.5230.63030.23291.1390.06590.35840.39530.0297-0.11180.0486-0.11060.15090.0170.28850.05530.01740.27510.03380.312931.0627-19.50058.5246
271.3682-1.14490.30282.136-2.24394.51550.12920.02820.1107-0.1269-0.4638-0.32620.370.80860.23050.2718-0.00060.00380.3875-0.00780.395250.3896-24.007828.2859
282.10860.2285-2.57487.62722.59964.4741-0.0831-0.00060.59630.24030.8711-1.8074-0.57990.2498-0.76430.3458-0.0909-0.03560.5222-0.18380.496353.6016-16.3737.8294
291.2721-0.06911.19371.02010.37651.98290.1269-0.3018-0.1268-0.04540.0364-0.18510.2143-0.1141-0.13190.26560.0445-0.04170.3222-0.0040.276340.9493-22.597430.9265
301.1477-1.24210.28911.8375-0.78310.7084-0.058-0.14130.01490.41930.0635-0.0872-0.18190.1237-0.02010.35580.0447-0.0240.32630.00830.377735.9624-12.083123.8789
310.4045-0.0035-0.87481.9057-0.69621.79760.0405-0.0115-0.3242-0.267-0.0270.16330.04440.45070.07990.2714-0.10690.0230.2979-0.02890.39563.9591-35.023755.4777
320.9318-0.5022-1.25212.48220.00473.11890.0253-0.1585-0.3691-0.4573-0.01970.18310.12110.597-0.06910.3374-0.0579-0.00430.2986-0.0310.511711.9341-32.494551.9126
330.5162-1.03880.1011.90090.27451.4964-0.13840.2447-0.0824-0.01280.14290.3070.03740.33350.01570.3168-0.0892-0.11140.27930.0160.54320.1196-30.056546.4258
340.4690.4176-1.15374.1876-3.52514.3323-0.1995-0.3467-0.8844-0.0113-0.7725-1.00230.40280.3410.73310.3518-0.08540.060.36640.07740.68721.8428-28.747356.3053
351.54540.1347-0.14230.371-0.17390.5393-0.00120.22050.4126-0.2238-0.0963-0.1091-0.10320.1996-0.07360.2559-0.10160.03240.3026-0.08270.435212.9322-19.847453.7425
361.7886-1.0840.61070.9932-0.90173.2797-0.096-0.02470.4514-0.1052-0.07970.0382-0.043-0.67340.22290.3712-0.08590.08390.3499-0.0420.504-6.6863-17.38845.4021
372.383-0.23640.0860.6969-0.56122.0620.07640.22281.04230.13860.20490.1508-0.1414-0.9714-0.38970.3453-0.08950.00010.62030.16730.5205-16.0094-25.477929.0244
380.1057-0.02210.71181.21960.1352.64790.01950.4542-0.0861-0.23760.52160.21240.0080.1925-0.50920.3228-0.1183-0.080.37230.06040.5872-6.7772-20.169429.4046
392.03060.72231.44351.6815-0.36181.4775-0.40750.47580.72730.40290.16320.0478-0.86960.21820.23960.3174-0.1476-0.05320.42470.04220.606-0.1474-11.253338.5731
405.53772.9853.38785.8127-0.33513.41050.55881.05970.13281.51110.89580.07230.0838-0.1544-0.82020.60180.01410.08440.4690.08220.3974-6.2742-7.799528.3191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1242:1251)A1242 - 1251
2X-RAY DIFFRACTION2(chain A and resid 1252:1264)A1252 - 1264
3X-RAY DIFFRACTION3(chain A and resid 1265:1306)A1265 - 1306
4X-RAY DIFFRACTION4(chain A and resid 1307:1340)A1307 - 1340
5X-RAY DIFFRACTION5(chain A and resid 1341:1361)A1341 - 1361
6X-RAY DIFFRACTION6(chain A and resid 1362:1375)A1362 - 1375
7X-RAY DIFFRACTION7(chain A and resid 1376:1394)A1376 - 1394
8X-RAY DIFFRACTION8(chain A and resid 1395:1410)A1395 - 1410
9X-RAY DIFFRACTION9(chain A and resid 1411:1433)A1411 - 1433
10X-RAY DIFFRACTION10(chain A and resid 1434:1440)A1434 - 1440
11X-RAY DIFFRACTION11(chain B and resid 1242:1258)B1242 - 1258
12X-RAY DIFFRACTION12(chain B and resid 1259:1298)B1259 - 1298
13X-RAY DIFFRACTION13(chain B and resid 1299:1307)B1299 - 1307
14X-RAY DIFFRACTION14(chain B and resid 1308:1329)B1308 - 1329
15X-RAY DIFFRACTION15(chain B and resid 1330:1350)B1330 - 1350
16X-RAY DIFFRACTION16(chain B and resid 1351:1361)B1351 - 1361
17X-RAY DIFFRACTION17(chain B and resid 1362:1378)B1362 - 1378
18X-RAY DIFFRACTION18(chain B and resid 1379:1408)B1379 - 1408
19X-RAY DIFFRACTION19(chain B and resid 1409:1433)B1409 - 1433
20X-RAY DIFFRACTION20(chain B and resid 1434:1440)B1434 - 1440
21X-RAY DIFFRACTION21(chain C and resid 1252:1264)C1252 - 1264
22X-RAY DIFFRACTION22(chain C and resid 1265:1280)C1265 - 1280
23X-RAY DIFFRACTION23(chain C and resid 1281:1292)C1281 - 1292
24X-RAY DIFFRACTION24(chain C and resid 1293:1305)C1293 - 1305
25X-RAY DIFFRACTION25(chain C and resid 1306:1322)C1306 - 1322
26X-RAY DIFFRACTION26(chain C and resid 1323:1350)C1323 - 1350
27X-RAY DIFFRACTION27(chain C and resid 1351:1371)C1351 - 1371
28X-RAY DIFFRACTION28(chain C and resid 1372:1381)C1372 - 1381
29X-RAY DIFFRACTION29(chain C and resid 1382:1411)C1382 - 1411
30X-RAY DIFFRACTION30(chain C and resid 1412:1436)C1412 - 1436
31X-RAY DIFFRACTION31(chain D and resid 1252:1276)D1252 - 1276
32X-RAY DIFFRACTION32(chain D and resid 1277:1292)D1277 - 1292
33X-RAY DIFFRACTION33(chain D and resid 1293:1305)D1293 - 1305
34X-RAY DIFFRACTION34(chain D and resid 1306:1319)D1306 - 1319
35X-RAY DIFFRACTION35(chain D and resid 1320:1340)D1320 - 1340
36X-RAY DIFFRACTION36(chain D and resid 1341:1356)D1341 - 1356
37X-RAY DIFFRACTION37(chain D and resid 1357:1373)D1357 - 1373
38X-RAY DIFFRACTION38(chain D and resid 1379:1410)D1379 - 1410
39X-RAY DIFFRACTION39(chain D and resid 1411:1433)D1411 - 1433
40X-RAY DIFFRACTION40(chain D and resid 1434:1438)D1434 - 1438

+
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