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- PDB-4f73: Crystal Structure of active HIV-1 Protease in Complex with the N ... -

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Basic information

Entry
Database: PDB / ID: 4f73
TitleCrystal Structure of active HIV-1 Protease in Complex with the N terminal product of CA-p2 cleavage site
Components
  • N terminal product of substrate CA-p2
  • Protease
Keywordshydrolase/hydrolase product / HIV-1 protease / substrate complex / AIDS / product complex / Aspartyl protease / HYDROLASE / hydrolase-hydrolase product complex
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / 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 / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSchiffer, C.A. / Mittal, S. / Nalam, M.N.L.
CitationJournal: To be Published
Title: Crystal Structure of active HIV-1 Protease in Complex with the N terminal product of CA-p2 cleavage site
Authors: Mittal, S. / Nalam, M.N.L. / Schiffer, C.A.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
C: N terminal product of substrate CA-p2
D: N terminal product of substrate CA-p2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9306
Polymers22,7794
Non-polymers1512
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-36 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.788, 58.327, 61.636
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Protease


Mass: 10801.763 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide N terminal product of substrate CA-p2


Mass: 587.755 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: synthetic peptide corresponding to CA-p2 cleavage site
Source: (synth.) Human immunodeficiency virus 1
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS CRYSTALLIZED ACTIVE PROTEASE WITH 10-MER LENGTH PEPTIDE CORRESPONDING TO CA-P2 CLEAVAGE ...AUTHORS CRYSTALLIZED ACTIVE PROTEASE WITH 10-MER LENGTH PEPTIDE CORRESPONDING TO CA-P2 CLEAVAGE SITE. DURING CRYSTALLIZATION, PROTEASE CLEAVED THE 10-MER PEPTIDE TO TWO 5-MER PRODUCTS (N-TERMINAL KARVL*AEAMS C-TERMINAL, WHERE * INDICATES SITE OF HYDROLYSIS). INITIALLY N-TERMINAL PRODUCT IS MODELED IN THE STRUCTURE AS K1-A2-R3-V4-L5*. THE C-TERMINAL PRODUCT THAT SHOULD HAVE BEEN THEORETICALLY PRESENT NEXT TO N-TERMINAL PRODUCT IN THE PROTEASE ACTIVE SITE MAY HAVE PROBABLY DIFFUSED AWAY POST CLEAVAGE AND (THE DENSITY FOR IT) IS ABSENT IN THE CRYSTAL STRUCTURE. WHAT AUTHORS OBSERVED IS A PARTIAL DENSITY FOR ANOTHER N-TERMINAL PRODUCT FRAGMENT IN ITS PLACE. THIS IS BECAUSE THE CRYSTALLIZED DIMER IS NOT UNIQUELY ORIENTED IN THE CRYSTAL LATTICE. POSSIBLY DUE TO THE AVERAGING OF ELECTRON DENSITY OF ANOTHER PROTEASE DIMER WITH N-TERMINAL PRODUCT THAT IS IN THE OPPOSITE ORIENTATION AS THE FIRST LEADS TO THE OVERALL IMPRESSION OF TWO, SEPARATE N-TERMINAL PRODUCTS BEING PRESENT IN THE ACTIVE SITE OF THE CRYSTALLIZED PROTEASE DIMER. THEREFORE, ARVL*LVR IS MODELELD IN ACTIVE SITE WHICH IS NOTHING BUT TWO n-TERMINAL PEPTIDES IN OPPOSITE DIRECTIONS.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-31% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14927 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.086 / Χ2: 1.038 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.977.90.42614571.0481100
1.97-2.057.90.3114701.0651100
2.05-2.147.90.25614611.051100
2.14-2.257.90.20514611.0211100
2.25-2.397.90.1814721.031100
2.39-2.587.80.14214911.0721100
2.58-2.847.80.1114811.0051100
2.84-3.257.60.08415061.0461100
3.25-4.097.40.05715151.0231100
4.09-506.90.03616131.022199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.1652 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8725 / SU B: 6.715 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1571 / SU Rfree: 0.1501 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 754 5.1 %RANDOM
Rwork0.1674 ---
obs0.17 14809 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.4 Å2 / Biso mean: 25.3862 Å2 / Biso min: 11.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---0.04 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 10 83 1631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221646
X-RAY DIFFRACTIONr_bond_other_d0.0010.021109
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9882246
X-RAY DIFFRACTIONr_angle_other_deg0.84832731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78824.51662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01215279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7381511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
X-RAY DIFFRACTIONr_mcbond_it0.6461.51055
X-RAY DIFFRACTIONr_mcbond_other0.2011.5438
X-RAY DIFFRACTIONr_mcangle_it1.11921713
X-RAY DIFFRACTIONr_scbond_it1.833591
X-RAY DIFFRACTIONr_scangle_it2.8394.5533
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 58 -
Rwork0.17 1009 -
all-1067 -
obs--98.07 %
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)
18.88453.0818-7.31566.5263-7.12019.8758-0.0850.2156-0.0156-0.48510.0791-0.00580.411-0.17830.00590.3482-0.0989-0.03760.176-0.03760.054320.67521.7574-1.9366
213.6911.27293.49862.79180.69280.96580.10670.2458-0.4614-0.13050.0115-0.25520.06040.0542-0.11820.1546-0.0070.05630.0756-0.00550.081731.1985-2.40796.0633
37.91651.5444-0.14495.15982.2112.5425-0.2602-0.1472-0.4108-0.21130.2098-0.58710.19870.07230.05040.1520.03590.07510.05960.01620.213138.3647-4.29528.4067
45.8338-5.4743-3.78798.08486.21564.8816-0.1207-0.0234-0.22660.1748-0.00030.16840.18550.00590.1210.1493-0.00020.02690.06760.01390.064423.73082.243410.702
514.0735-12.91770.268722.1202-1.06323.3923-0.2729-0.3748-0.35660.41020.225-0.05760.1320.10510.04780.074-0.0336-0.00150.0789-0.00440.057330.8673-0.801117.6917
610.71683.6265-1.571911.06829.812911.1053-0.0998-0.1932-0.3994-0.19270.3495-0.4219-0.1620.481-0.24970.15910.0319-0.01920.24360.05960.240442.8869-1.306220.0256
722.7631-0.9744-5.82173.859-0.94726.58260.1549-1.15480.76430.2662-0.1381-0.19290.17390.5523-0.01670.1518-0.0261-0.04230.1547-0.03950.075634.88991.668128.714
83.13861.0696-0.84525.55232.51251.7399-0.10230.10550.67910.04760.02590.69690.0689-0.04260.07640.1799-0.0215-0.0060.18740.04210.19221.0657-2.090524.6377
914.862510.1556-7.10339.8402-4.23914.29390.2281-0.3422-0.07740.4646-0.2795-0.1495-0.05420.4970.05150.1087-0.0004-0.0330.16820.00450.040432.6805-1.308725.9919
101.73712.0533-0.61795.1944-6.413711.9010.2302-0.3591-0.06460.2476-0.6418-0.2676-0.06130.64770.41160.0958-0.0042-0.03160.2205-0.02450.235440.10876.569518.6142
117.7874-1.78165.642811.542-6.406919.54220.20330.7428-0.2827-0.62670.0323-0.1851-0.08940.3076-0.23550.12580.00110.07070.0886-0.0320.11436.29345.61814.5856
120.8950.14030.76475.0045-0.76572.16960.0247-0.14930.03520.2019-0.0439-0.1301-0.04190.05080.01910.02330.0050.00730.0603-0.00020.079134.2642.465817.3006
131.5523-4.4782.068313.4695-5.5213.12690.0828-0.0748-0.16360.03340.2030.42980.3539-0.076-0.28590.1823-0.02190.00720.12270.01250.155128.2495-2.442213.3172
145.44961.62821.65974.7184-0.07660.5832-0.06270.07290.0801-0.12230.0328-0.0692-0.00490.02370.02990.0604-0.00690.02020.0611-0.01190.07529.323810.203510.6211
155.43417.08265.01479.24996.24079.6303-0.2647-0.22380.2886-0.3307-0.27410.3594-0.3148-0.37410.53880.1738-0.0048-0.0250.1342-0.00160.090118.540510.49922.7858
1610.22623.81267.46714.04523.57899.3087-0.21230.35650.6234-0.5176-0.02680.4509-0.40210.03520.23910.23970.0083-0.04990.12930.01080.177720.312214.79137.5855
1728.1231-0.20630.80520.34650.96383.2396-0.194-0.63950.33580.0385-0.00280.15550.006-0.08170.19680.13380.02220.02770.12220.00520.220314.313610.894113.964
1811.65347.4068-1.74513.33515.05494.66660.1955-0.08340.65970.6499-0.58861.08120.3425-0.39060.39310.20460.02670.03280.3977-0.03580.2756-0.44035.483612.3681
1918.0577-4.7001-6.11485.24992.32583.91050.0658-0.1172-0.17910.2814-0.1480.2397-0.2767-0.26420.08210.1249-0.01150.01810.1171-0.01230.14218.50927.785114.161
209.33354.5505-3.22347.3252-0.26052.0626-0.0179-0.066-0.4918-0.0239-0.0059-0.31620.2511-0.01250.02380.1133-0.0119-0.0280.09880.01520.093915.9306-2.28749.9171
2123.71880.7605-15.45365.49244.530726.94820.4027-0.7575-0.02820.2568-0.19860.361-0.5393-0.0037-0.20410.1212-0.02480.02720.08170.04060.09986.4821-0.613519.664
2214.50679.36417.909117.462611.55817.9640.1036-0.24340.6904-0.1338-0.52870.596-0.0555-0.37060.42510.16430.02-0.0250.27920.1040.2297-2.966-4.871816.6875
2339.7915-4.99814.45044.1853-2.20085.1517-0.229-0.6731-0.2819-0.18370.47250.36110.3476-0.4525-0.24350.0955-0.053-0.01730.0990.04620.11775.7975-13.560216.8243
2413.928610.20411.30947.78582.31496.1372-0.05170.1320.0854-0.07550.09730.0352-0.2330.1142-0.04560.0932-0.0245-0.02070.06610.04410.077118.9716-8.636220.0218
2511.27880.92736.76354.3015-1.414510.65670.2135-0.2917-0.11480.08970.22480.39460.4228-0.1559-0.43830.0721-0.02040.00340.06710.03660.09017.4964-10.040718.9353
2611.5061-6.60495.865910.6092-9.33848.22250.30770.1713-0.5218-0.5745-0.06570.24350.50920.0294-0.2420.1233-0.0606-0.02560.16060.05470.13920.5923-5.84258.5685
274.06550.6085-4.36550.39320.946115.38340.0603-0.22270.47920.0018-0.18430.1051-0.4611-0.02950.1240.1474-0.0348-0.06790.14860.0430.17744.88457.56254.758
281.8971-2.53844.279513.236-11.368412.91280.03430.001-0.00110.25750.18710.4831-0.1482-0.1042-0.22150.1092-0.0152-0.0180.11510.01290.1433.5257-1.38095.1613
296.3832.8373-2.04336.8446-0.21367.53820.1775-0.7345-0.09020.4026-0.1931-0.0085-0.66060.33280.01560.1158-0.01980.01630.14810.05110.09329.1335-3.456820.0745
305.6682-1.3079-6.37358.38915.869512.8650.1298-0.22660.15810.31030.11060.12380.140.1772-0.24040.0475-0.0224-0.0060.03780.01480.051912.78990.886312.1795
312.0792-0.65052.45824.7046-1.25842.9636-0.18560.02360.0518-0.29430.19690.4054-0.1347-0.0103-0.01130.1903-0.0578-0.05170.21070.04060.123210.73111.02072.3419
3232.79728.23314.15498.3569-1.59223.9872-0.40920.245-0.053-0.48410.3957-0.14480.170.1990.01350.1353-0.03720.00240.0904-0.01830.037222.83897.37310.7205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 16
3X-RAY DIFFRACTION3A17 - 22
4X-RAY DIFFRACTION4A23 - 28
5X-RAY DIFFRACTION5A29 - 35
6X-RAY DIFFRACTION6A36 - 41
7X-RAY DIFFRACTION7A42 - 46
8X-RAY DIFFRACTION8A47 - 53
9X-RAY DIFFRACTION9A54 - 58
10X-RAY DIFFRACTION10A59 - 63
11X-RAY DIFFRACTION11A64 - 69
12X-RAY DIFFRACTION12A70 - 80
13X-RAY DIFFRACTION13A81 - 86
14X-RAY DIFFRACTION14A87 - 94
15X-RAY DIFFRACTION15A95 - 99
16X-RAY DIFFRACTION16B1 - 6
17X-RAY DIFFRACTION17B7 - 12
18X-RAY DIFFRACTION18B13 - 18
19X-RAY DIFFRACTION19B19 - 24
20X-RAY DIFFRACTION20B25 - 31
21X-RAY DIFFRACTION21B32 - 35
22X-RAY DIFFRACTION22B36 - 41
23X-RAY DIFFRACTION23B42 - 46
24X-RAY DIFFRACTION24B47 - 53
25X-RAY DIFFRACTION25B54 - 58
26X-RAY DIFFRACTION26B59 - 63
27X-RAY DIFFRACTION27B64 - 69
28X-RAY DIFFRACTION28B70 - 75
29X-RAY DIFFRACTION29B76 - 81
30X-RAY DIFFRACTION30B82 - 87
31X-RAY DIFFRACTION31B88 - 94
32X-RAY DIFFRACTION32B95 - 99

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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

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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

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