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- PDB-4eq0: Crystal Structure of inactive single chain variant of HIV-1 Prote... -

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Basic information

Entry
Database: PDB / ID: 4eq0
TitleCrystal Structure of inactive single chain variant of HIV-1 Protease in Complex with the substrate p2-NC
Components
  • protease, tethered dimer
  • substrate p2-NC
Keywordshydrolase/hydrolase substrate / HIV-1 protease / specificity design / drug design / Protease inhibitors / AIDS / Aspartyl protease / HYDROLASE / hydrolase-hydrolase substrate complex
Function / homology
Function and homology information


viral budding via host ESCRT complex / RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal 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 ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / BETA-MERCAPTOETHANOL / PHOSPHATE ION / Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchiffer, C.A. / Mittal, S.
CitationJournal: Protein Sci. / Year: 2012
Title: Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.
Authors: Alvizo, O. / Mittal, S. / Mayo, S.L. / Schiffer, C.A.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Derived calculations
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 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 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protease, tethered dimer
P: substrate p2-NC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,77211
Polymers23,0772
Non-polymers6959
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-14 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.080, 59.181, 61.901
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

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Protein / Protein/peptide , 2 types, 2 molecules AP

#1: Protein protease, tethered dimer /


Mass: 22169.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide substrate p2-NC


Mass: 908.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to p2-NC cleavage site for HIV-1 protease.
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YP46

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Non-polymers , 6 types, 97 molecules

#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% 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: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 21064 / % possible obs: 99.1 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.765.20.481195.2
1.76-1.835.80.354199.6
1.83-1.9160.2391100
1.91-2.0260.151100
2.02-2.1460.1071100
2.14-2.3160.0781100
2.31-2.545.90.0591100
2.54-2.915.90.048199.8
2.91-3.665.70.041199.4
3.66-505.40.02196.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.78 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.573 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1378 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26401 1080 5.1 %RANDOM
Rwork0.21269 ---
obs0.21525 19947 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.436 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2---0.03 Å20 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 43 88 1674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191641
X-RAY DIFFRACTIONr_bond_other_d0.0040.021110
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9952225
X-RAY DIFFRACTIONr_angle_other_deg2.18532731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44124.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73815274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.208159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211770
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02295
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 68 -
Rwork0.278 1254 -
obs--92.77 %
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)
12.4735-1.88993.06611.5166-2.31023.8255-0.2090.05480.32290.0971-0.1221-0.4251-0.2679-0.0220.33110.4416-0.00190.00080.39780.07580.55515.838615.240923.2879
28.6385-1.69170.1890.35270.13391.5734-0.07340.11490.34460.01010.0385-0.071-0.22940.17830.03490.369-0.03490.02890.40320.0160.493615.94259.046316.5827
325.981-1.330829.32950.1081-1.449233.83261.05490.83021.2169-0.0582-0.7478-0.18791.64250.856-0.30710.1671-0.08620.28420.73510.35051.903323.60797.730214.2383
41.4281-1.4721-0.18824.2196-1.06690.62140.06730.07360.11430.047-0.0431-0.1612-0.011-0.0183-0.02420.42990.0093-0.02130.4151-0.00230.40759.32481.851219.4849
55.34511.1985-5.49930.61390.048110.66260.01420.0569-0.1091-0.01820.1545-0.10320.17050.1722-0.16870.42150.00290.01680.41160.00780.446217.2447-2.806914.3348
613.4761-4.48123.39886.9384-3.34531.75820.02060.26380.10130.5765-0.1019-0.2064-0.23310.08120.08120.36170.0007-0.01220.4819-0.04740.369828.2743-4.668713.9382
715.6022.17644.47231.5291-0.04032.506-0.0368-0.0991-0.66020.19190.1773-0.28360.1834-0.0944-0.14050.41050.0409-0.02950.3686-0.00660.463218.6456-13.432414.3038
84.24-1.5921-0.5313.8865-1.91221.433-0.03210.1377-0.10730.0878-0.021-0.0575-0.049-0.10940.05310.40850.01130.00380.4328-0.00440.40375.7936-9.516111.2906
95.71952.50583.84751.91192.90224.4884-0.05440.1628-0.18790.05130.2457-0.24190.18840.2334-0.19130.3881-0.00330.03790.4177-0.05350.540920.9624-9.978914.085
105.4283-3.51693.577928.3652-3.28472.3955-0.24110.0943-0.20440.76290.3916-0.5012-0.18130.0538-0.15050.3460.02910.04070.4292-0.06740.473925.04310.204923.2034
110.49870.0513-1.21483.126-0.75793.12830.0314-0.16510.0656-0.06120.1181-0.0651-0.08420.2493-0.14950.35170.0142-0.02140.4422-0.04150.454620.88076.76526.047
122.85971.68272.83741.80184.02199.75690.00580.13090.0294-0.04890.0956-0.1176-0.1618-0.0164-0.10140.36140.0536-0.01070.4019-0.03550.531318.7777-5.484215.1024
132.1362-1.0301-1.90531.2962-0.2373.46820.09350.17980.0401-0.1094-0.1758-0.22460.1-0.04340.08230.41890.02370.00020.4327-0.00630.449112.43910.615516.1525
143.03342.09191.34312.20950.15751.37750.0663-0.03-0.13110.08430.0455-0.12040.0249-0.0969-0.11190.38470.018-0.04990.4252-0.00060.441915.17310.131426.9738
157.4303-3.35580.69561.5355-0.20350.8192-0.1329-0.19480.0480.09590.0903-0.0321-0.0194-0.07740.04250.41750.0151-0.02810.4245-0.01760.39066.20727.544229.6448
161.2905-0.9986-0.33511.48940.83771.3357-0.0206-0.1818-0.01860.2610.0096-0.01730.1455-0.0380.01110.45890.0044-0.01820.46110.02070.34665.01132.552732.5926
174.652-0.62680.91042.8598-0.06530.1837-0.0151-0.15780.01760.115-0.03310.12780.0163-0.02370.04820.4178-0.00540.03410.42010.00650.3703-7.4724-1.943624.8742
1814.66770.8769-3.57482.1488-0.56070.9524-0.35890.1141-0.358-0.00980.16750.07430.0985-0.0110.19140.42-0.01960.05360.4203-0.00030.4617-9.8872-4.512322.9514
191.55780.2883-0.06681.1819-1.04332.68870.01210.0482-0.01570.021-0.0213-0.0797-0.00980.01440.00910.41840.00310.00790.41990.01420.3832.02424.014618.0106
205.26636.69520.386510.28210.62380.1141-0.09150.0952-0.0377-0.3551-0.0110.03030.02570.02210.10250.42470.00820.00850.4119-0.00560.4102-6.8296-2.552513.4585
213.21153.4508-3.86866.9396-4.56864.71510.03290.29340.13580.09990.19970.90310.0108-0.3308-0.23260.35530.007-0.01310.4315-0.03530.4684-17.3376-1.09179.6589
228.7767-1.79661.32310.7394-0.25881.7723-0.15080.09110.2784-0.2068-0.0012-0.1965-0.15070.05210.1520.4090.02590.05040.41760.03590.3935-1.46-0.77832.8157
231.6441-1.9322-2.31625.81222.42243.32580.04390.2161-0.0131-0.3375-0.1928-0.03240.0175-0.26260.1490.41370.02150.00510.45810.01530.3874-8.1471-2.21374.6467
241.6194-0.1396-0.97352.86213.98195.92250.11010.1041-0.0094-0.0383-0.24540.1285-0.1251-0.35320.13530.36520.0314-0.02290.4426-0.0170.4212-14.9866.175512.815
256.9247-1.93045.70694.61491.70887.3817-0.1113-0.2645-0.03920.07160.1780.0122-0.0992-0.1084-0.06670.4273-0.02450.03710.4423-0.00950.3653-10.21955.916726.8321
260.9428-0.5673-1.73791.81331.08855.84780.03740.10950.0287-0.0051-0.10780.1332-0.135-0.07860.07040.39920.0083-0.00850.4067-0.01250.4128-11.69518.169317.0592
273.2776-1.33251.49523.34690.31210.9994-0.02880.1615-0.064-0.01150.03720.00220.02070.0397-0.00840.4346-0.00570.02890.4501-0.02220.3564-4.8886-5.060410.8252
280.2430.9256-0.06864.4132-1.39941.4938-0.01370.00570.0013-0.1389-0.0359-0.07120.07180.02870.04960.42130.0060.01510.41980.0040.3947-2.07432.936117.2585
291.5002-1.09380.28731.15970.63552.9705-0.03760.01750.04680.0691-0.0376-0.0668-0.0359-0.02080.07510.42080.00470.00410.4060.00680.406-4.902810.55421.6328
305.2054-0.29494.86930.0468-0.28394.5654-0.0280.00740.2298-0.0501-0.1092-0.02590.01640.03110.13730.42490.0201-0.02110.3936-0.00770.46456.745410.720627.3808
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 15
3X-RAY DIFFRACTION3A16 - 21
4X-RAY DIFFRACTION4A22 - 29
5X-RAY DIFFRACTION5A30 - 35
6X-RAY DIFFRACTION6A36 - 41
7X-RAY DIFFRACTION7A42 - 47
8X-RAY DIFFRACTION8A48 - 54
9X-RAY DIFFRACTION9A55 - 60
10X-RAY DIFFRACTION10A61 - 65
11X-RAY DIFFRACTION11A66 - 72
12X-RAY DIFFRACTION12A73 - 79
13X-RAY DIFFRACTION13A80 - 87
14X-RAY DIFFRACTION14A88 - 92
15X-RAY DIFFRACTION15A93 - 99
16X-RAY DIFFRACTION16A101 - 107
17X-RAY DIFFRACTION17A108 - 117
18X-RAY DIFFRACTION18A118 - 123
19X-RAY DIFFRACTION19A124 - 129
20X-RAY DIFFRACTION20A130 - 135
21X-RAY DIFFRACTION21A136 - 142
22X-RAY DIFFRACTION22A143 - 153
23X-RAY DIFFRACTION23A154 - 158
24X-RAY DIFFRACTION24A159 - 163
25X-RAY DIFFRACTION25A164 - 169
26X-RAY DIFFRACTION26A170 - 175
27X-RAY DIFFRACTION27A176 - 181
28X-RAY DIFFRACTION28A182 - 188
29X-RAY DIFFRACTION29A189 - 194
30X-RAY DIFFRACTION30A195 - 199

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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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