[English] 日本語
Yorodumi
- PDB-3hpg: Visna virus integrase (residues 1-219) in complex with LEDGF IBD:... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hpg
TitleVisna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces
Components
  • Integrase
  • PC4 and SFRS1-interacting protein
KeywordsTRANSFERASE / PROTEIN-PROTEIN COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / MAGNESIUM / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / VIRAL NUCLEOPROTEIN / VIRION / ZINC / DNA-BINDING / HOST-VIRUS INTERACTION / TRANSCRIPTION / TRANSCRIPTION REGULATION / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / RECOMBINATION
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / exoribonuclease H / euchromatin / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / viral capsid / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / response to heat / DNA-binding transcription factor binding / DNA recombination / response to oxidative stress / DNA-directed DNA polymerase / transcription coactivator activity / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / chromatin remodeling / symbiont entry into host cell / chromatin binding / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Integrase, N-terminal zinc-binding domain / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / dUTPase-like / dUTPase / dUTPase, trimeric ...Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Integrase, N-terminal zinc-binding domain / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMaedi visna virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsHare, S. / Labeja, A. / Cherepanov, P.
CitationJournal: Plos Pathog. / Year: 2009
Title: Structural basis for functional tetramerization of lentiviral integrase
Authors: Hare, S. / Di Nunzio, F. / Labeja, A. / Wang, J. / Engelman, A. / Cherepanov, P.
History
DepositionJun 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Integrase
B: Integrase
C: Integrase
D: Integrase
E: Integrase
F: Integrase
G: PC4 and SFRS1-interacting protein
H: PC4 and SFRS1-interacting protein
I: PC4 and SFRS1-interacting protein
J: PC4 and SFRS1-interacting protein
K: PC4 and SFRS1-interacting protein
L: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,39118
Polymers216,99912
Non-polymers3926
Water00
1
A: Integrase
B: Integrase
E: Integrase
F: Integrase
G: PC4 and SFRS1-interacting protein
H: PC4 and SFRS1-interacting protein
K: PC4 and SFRS1-interacting protein
L: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,92712
Polymers144,6668
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-36 kcal/mol
Surface area21130 Å2
2
C: Integrase
D: Integrase
E: Integrase
F: Integrase
I: PC4 and SFRS1-interacting protein
J: PC4 and SFRS1-interacting protein
K: PC4 and SFRS1-interacting protein
L: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,92712
Polymers144,6668
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-36 kcal/mol
Surface area20430 Å2
3
C: Integrase
D: Integrase
I: PC4 and SFRS1-interacting protein
J: PC4 and SFRS1-interacting protein
hetero molecules

A: Integrase
B: Integrase
G: PC4 and SFRS1-interacting protein
H: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,92712
Polymers144,6668
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3200 Å2
ΔGint-38 kcal/mol
Surface area20580 Å2
Unit cell
Length a, b, c (Å)91.104, 148.904, 91.076
Angle α, β, γ (deg.)90.000, 113.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13G
23H
33I
43J
53K
63L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A, 1-43A1 - 43
211CHAIN B, 1-43B1 - 43
311CHAIN C, 1-43C1 - 43
411CHAIN D, 1-43D1 - 43
511CHAIN E, 1-43E1 - 43
611CHAIN F, 1-43F1 - 43
112CHAIN A, 60-141, 155-189, 197-212A60 - 141
122CHAIN A, 60-141, 155-189, 197-212A155 - 189
132CHAIN A, 60-141, 155-189, 197-212A197 - 212
212CHAIN B, 60-141, 155-189, 197-212B60 - 141
222CHAIN B, 60-141, 155-189, 197-212B155 - 189
232CHAIN B, 60-141, 155-189, 197-212B197 - 212
312CHAIN C, 60-141, 155-189, 197-212C60 - 141
322CHAIN C, 60-141, 155-189, 197-212C155 - 189
332CHAIN C, 60-141, 155-189, 197-212C197 - 212
412CHAIN D, 61-141, 155-189, 197-212D61 - 141
422CHAIN D, 61-141, 155-189, 197-212D155 - 189
432CHAIN D, 61-141, 155-189, 197-212D197 - 212
512CHAIN E, 60-141, 155-189, 197-212E60 - 141
522CHAIN E, 60-141, 155-189, 197-212E155 - 189
532CHAIN E, 60-141, 155-189, 197-212E197 - 212
612CHAIN F, 60-141, 155-189, 197-212F60 - 141
622CHAIN F, 60-141, 155-189, 197-212F155 - 189
632CHAIN F, 60-141, 155-189, 197-212F197 - 212
113CHAIN G, 320-423G320 - 423
213CHAIN H, 320-418H320 - 418
313CHAIN I, 320-418I320 - 418
413CHAIN J, 320-423J320 - 423
513CHAIN K, 320-426K320 - 426
613CHAIN L, 320-413L320 - 413

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Integrase / IN


Mass: 25090.455 Da / Num. of mol.: 6
Fragment: N-terminal and catalytic core domains, UNP residues 823-1039
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maedi visna virus / Strain: KV1772 / Gene: pol / Plasmid: pCDF-duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: P35956
#2: Protein
PC4 and SFRS1-interacting protein / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Dense fine speckles ...Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Dense fine speckles 70 kDa protein / DFS 70 / CLL-associated antigen KW-7


Mass: 11075.970 Da / Num. of mol.: 6 / Fragment: integrase binding domain, UNP residues 347-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DFS70, LEDGF, PSIP1, PSIP2 / Plasmid: pES / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: O75475
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9696 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9696 Å / Relative weight: 1
ReflectionResolution: 3.28→40 Å / Num. all: 34448 / Num. obs: 34296 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 65.905 Å2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 3.28→3.46 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / Num. measured obs: 19335 / Num. unique obs: 5069 / % possible all: 99.7

-
Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B4J and 1K6Y

2b4j

1k6y


Resolution: 3.28→38.672 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.82 / SU ML: 0.44 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1718 5.04 %RANDOM
Rwork0.212 ---
obs0.214 34084 99.71 %-
all-34183 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.567 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 223.84 Å2 / Biso mean: 97.809 Å2 / Biso min: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.629 Å20 Å2-7.863 Å2
2--22.529 Å20 Å2
3----16.9 Å2
Refinement stepCycle: LAST / Resolution: 3.28→38.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12786 0 6 0 12792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113004
X-RAY DIFFRACTIONf_angle_d1.26117556
X-RAY DIFFRACTIONf_chiral_restr0.0842001
X-RAY DIFFRACTIONf_plane_restr0.0052248
X-RAY DIFFRACTIONf_dihedral_angle_d18.8234803
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A319X-RAY DIFFRACTIONPOSITIONAL0.048
12B319X-RAY DIFFRACTIONPOSITIONAL0.048
13C319X-RAY DIFFRACTIONPOSITIONAL0.05
14D319X-RAY DIFFRACTIONPOSITIONAL0.052
15E319X-RAY DIFFRACTIONPOSITIONAL0.044
16F313X-RAY DIFFRACTIONPOSITIONAL0.043
21A1068X-RAY DIFFRACTIONPOSITIONAL0.07
22B1068X-RAY DIFFRACTIONPOSITIONAL0.07
23C1068X-RAY DIFFRACTIONPOSITIONAL0.071
24D1056X-RAY DIFFRACTIONPOSITIONAL0.062
25E1068X-RAY DIFFRACTIONPOSITIONAL0.059
26F1068X-RAY DIFFRACTIONPOSITIONAL0.066
31G547X-RAY DIFFRACTIONPOSITIONAL0.043
32H547X-RAY DIFFRACTIONPOSITIONAL0.043
33I540X-RAY DIFFRACTIONPOSITIONAL0.038
34J604X-RAY DIFFRACTIONPOSITIONAL0.039
35K515X-RAY DIFFRACTIONPOSITIONAL0.039
36L500X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.28-3.3760.3591460.31627112857100
3.376-3.4850.2911340.28226712805100
3.485-3.610.3051300.24327072837100
3.61-3.7540.3071340.23826912825100
3.754-3.9250.2691440.21826712815100
3.925-4.1320.231420.19527232865100
4.132-4.390.2261440.1926742818100
4.39-4.7290.2381520.16926882840100
4.729-5.2030.1921470.17627072854100
5.203-5.9540.2641300.20527322862100
5.954-7.4930.2521490.21927142863100
7.493-38.6750.2161660.1862677284398
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)
12.7706-0.58930.60131.8531-0.60831.41910.0836-0.4532-0.247-0.1737-0.02710.0566-0.0109-0.0477-0.0880.5336-0.04760.01880.52480.11090.4494-3.42449.824132.7705
23.0939-0.5233-0.29590.93580.42571.52790.0299-0.0110.5756-0.3389-0.0632-0.19270.03-0.15440.01640.67270.0510.01570.2863-0.08620.604460.67546.096422.6373
34.33650.44071.28921.21170.47521.3166-0.08070.3874-0.1148-0.164-0.12830.0971-0.47520.05510.18790.69970.01760.01830.6442-0.08950.460326.542114.4044-4.2965
41.39962.74770.97030.97080.95270.0485-0.3690.21490.8214-0.37210.04780.8485-0.4015-0.02650.40340.8610.3361-0.21791.2767-0.2971.0291.35323.2858-6.4749
5-1.0553-0.06630.81283.03370.2674-0.20710.0523-0.38070.5395-0.9199-0.2609-0.20650.55360.24560.11630.71770.05760.27330.45640.17120.793-4.435140.592818.7116
6-1.67730.505-2.4158-0.07770.20930.395-0.0945-0.1578-0.6521-0.2833-0.26150.08070.1776-0.81280.00430.6944-0.031-0.19861.10870.14431.055864.19115.455520.7684
7-0.1487-0.6406-1.2624-0.0585-0.58081.125-0.27290.14430.04240.0992-0.11050.0291-0.01210.3580.30680.6684-0.1399-0.11250.772-0.04560.849850.872914.70017.573
80.1762-1.33110.69290.8151-1.09660.9461-0.5559-1.10470.29970.23390.48670.18880.4035-0.9711-0.05680.6566-0.1083-0.04071.1881-0.26051.056734.880238.752224.4858
9-1.4983-1.36680.73530.4751-0.27770.5725-0.1949-0.37370.4851-0.1009-0.2291-0.7799-0.30890.51530.17270.6058-0.12030.06270.99390.12281.01522.016518.24833.0562
100.8032-0.84850.42871.5923-0.45871.3862-0.17130.59070.18990.2284-0.046-0.3810.0706-0.03420.38270.7791-0.22840.00721.06490.12310.838719.370420.082359.9025
110.4096-0.4162-1.54751.1340.20564.6489-0.43420.6303-0.7117-0.026-0.35120.0634-0.116-1.21060.76860.8518-0.0616-0.03861.08940.00531.3647-28.6955-16.463938.6613
12-0.3216-0.27950.28413.04751.50622.8109-0.4339-0.0519-0.5702-0.04640.3595-0.07210.25551.07330.06550.84530.14760.19061.01030.18981.197388.644265.18059.7117
130.2939-0.092-0.14542.3259-0.53920.945-0.05230.1974-0.4936-0.01430.03781.05410.1914-0.39480.04080.7998-0.18560.05641.0928-0.2471.242232.290462.767340.2903
141.7667-0.5701-1.55490.54540.07522.6291-0.0831-1.0396-0.33510.22360.331-0.40110.17841.0425-0.41780.86890.0092-0.13591.2634-0.21621.037852.9287-10.3691-2.5567
150.77570.53280.11972.1781.25661.7412-0.34090.31430.0247-0.16810.15730.4415-0.08590.91030.32811.001-0.1318-0.23311.28970.18390.91834.563117.4563-32.2603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A, 50-212, chain B 50-212A50 - 212
2X-RAY DIFFRACTION1chain A, 50-212, chain B 50-212B50 - 212
3X-RAY DIFFRACTION2chain C, 50-212, chain D 50-212C50 - 212
4X-RAY DIFFRACTION2chain C, 50-212, chain D 50-212D50 - 212
5X-RAY DIFFRACTION3chain E, 50-212, chain F 50-212E50 - 212
6X-RAY DIFFRACTION3chain E, 50-212, chain F 50-212F50 - 212
7X-RAY DIFFRACTION4chain A, 4-49A4 - 49
8X-RAY DIFFRACTION5chain B, 4-49B4 - 49
9X-RAY DIFFRACTION6chain C, 4-49C4 - 49
10X-RAY DIFFRACTION7chain D, 2-49D2 - 49
11X-RAY DIFFRACTION8chain E, 2-49E2 - 49
12X-RAY DIFFRACTION9chain F, 2-49F2 - 49
13X-RAY DIFFRACTION10chain G, 348-423G348 - 423
14X-RAY DIFFRACTION11chain H, 347-418H347 - 418
15X-RAY DIFFRACTION12chain I, 348-418I348 - 418
16X-RAY DIFFRACTION13chain J, 347-423J347 - 423
17X-RAY DIFFRACTION14chain K, 347-426K347 - 426
18X-RAY DIFFRACTION15chain L, 348-413L348 - 413

+
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://pdbjlc1.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