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- PDB-7jxr: Crystal Structure Human Immunodeficiency Virus-1 Matrix protein M... -

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Basic information

Entry
Database: PDB / ID: 7jxr
TitleCrystal Structure Human Immunodeficiency Virus-1 Matrix protein Mutant Q63R Crystal Form 1
ComponentsMatrix protein
KeywordsSTRUCTURAL PROTEIN / HIV-1 / gag
Function / homologyviral process / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / structural molecule activity / Gag protein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsGreen, T.J. / Eastep, G.N. / Ghanam, R.H. / Saad, J.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)9R01AI150901 United States
Other government1S10RR026478 United States
Other governmentP30 CA013148 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation.
Authors: Eastep, G.N. / Ghanam, R.H. / Green, T.J. / Saad, J.S.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein
B: Matrix protein
C: Matrix protein
D: Matrix protein
E: Matrix protein
F: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,59426
Polymers93,5556
Non-polymers3,03920
Water3,909217
1
A: Matrix protein
D: Matrix protein
E: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,29713
Polymers46,7783
Non-polymers1,51910
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix protein
C: Matrix protein
F: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,29713
Polymers46,7783
Non-polymers1,51910
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.136, 97.923, 84.817
Angle α, β, γ (deg.)90.000, 99.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 94 or resid 96 through 110))
21(chain B and (resid 7 through 94 or resid 96 through 110))
31(chain C and (resid 7 through 94 or resid 96 through 110))
41(chain D and (resid 7 through 94 or resid 96 through 110))
51(chain E and (resid 7 through 94 or resid 96 through 110))
61(chain F and (resid 7 through 94 or resid 96 through 110))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVAL(chain A and (resid 7 through 94 or resid 96 through 110))AA7 - 946 - 93
12ASPASPLYSLYS(chain A and (resid 7 through 94 or resid 96 through 110))AA96 - 11095 - 109
21VALVALVALVAL(chain B and (resid 7 through 94 or resid 96 through 110))BB7 - 946 - 93
22ASPASPLYSLYS(chain B and (resid 7 through 94 or resid 96 through 110))BB96 - 11095 - 109
31VALVALVALVAL(chain C and (resid 7 through 94 or resid 96 through 110))CC7 - 946 - 93
32ASPASPLYSLYS(chain C and (resid 7 through 94 or resid 96 through 110))CC96 - 11095 - 109
41VALVALVALVAL(chain D and (resid 7 through 94 or resid 96 through 110))DD7 - 946 - 93
42ASPASPLYSLYS(chain D and (resid 7 through 94 or resid 96 through 110))DD96 - 11095 - 109
51VALVALVALVAL(chain E and (resid 7 through 94 or resid 96 through 110))EE7 - 946 - 93
52ASPASPLYSLYS(chain E and (resid 7 through 94 or resid 96 through 110))EE96 - 11095 - 109
61VALVALVALVAL(chain F and (resid 7 through 94 or resid 96 through 110))FF7 - 946 - 93
62ASPASPLYSLYS(chain F and (resid 7 through 94 or resid 96 through 110))FF96 - 11095 - 109

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Components

#1: Protein
Matrix protein


Mass: 15592.562 Da / Num. of mol.: 6 / Mutation: Q63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): codon-plus RIL-competent cells / References: UniProt: Q6E183
#2: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: 40 % PEG 400, 0.1 M NaAcetate (pH 4.0), 0.05 M Li2SO4

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→46.21 Å / Num. obs: 61646 / % possible obs: 95.03 % / Redundancy: 2.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.048 / Rrim(I) all: 0.083 / Net I/av σ(I): 28.86 / Net I/σ(I): 28.86
Reflection shellResolution: 2.04→2.113 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6078 / CC1/2: 0.726 / Rpim(I) all: 0.298 / Rrim(I) all: 0.508

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HIW
Resolution: 2.04→46.21 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 2000 3.24 %
Rwork0.2032 59646 -
obs0.2042 61646 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.1 Å2 / Biso mean: 51.9604 Å2 / Biso min: 28.24 Å2
Refinement stepCycle: final / Resolution: 2.04→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5135 0 149 217 5501
Biso mean--59.73 53.77 -
Num. residues----635
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3146X-RAY DIFFRACTION13.431TORSIONAL
12B3146X-RAY DIFFRACTION13.431TORSIONAL
13C3146X-RAY DIFFRACTION13.431TORSIONAL
14D3146X-RAY DIFFRACTION13.431TORSIONAL
15E3146X-RAY DIFFRACTION13.431TORSIONAL
16F3146X-RAY DIFFRACTION13.431TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.090.31241330.25333970410388
2.09-2.140.29281420.24784228437095
2.14-2.210.2941340.23483991412589
2.21-2.280.25871440.22574308445295
2.28-2.360.31041470.22374396454398
2.36-2.450.23081470.21764369451698
2.45-2.560.2531450.22114319446497
2.56-2.70.25881450.21634342448796
2.7-2.870.24111440.21864289443395
2.87-3.090.2241410.21974203434494
3.09-3.40.25491400.20864174431492
3.4-3.890.21331460.19144342448896
3.89-4.90.16951440.16754313445795
4.9-46.210.26441480.20744402455096
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)
15.19031.1530.71825.4931-1.69375.49880.0309-0.41330.840.63410.07850.6064-0.81640.0542-0.05360.51950.0002-0.03310.31460.00570.41336.709624.07275.2005
23.6762-0.8319-1.50050.29260.79873.3648-0.06960.8441-0.6298-1.3272-0.13030.49410.46880.17210.0750.5534-0.02380.00110.4165-0.01370.45476.92279.40331.1967
31.40460.62480.39992.8360.44314.28950.161-0.4398-0.01630.0936-0.05590.4333-0.1424-0.533-0.00440.46440.03380.07810.28820.06710.53095.51675.236610.0754
49.4337-0.8395-3.77372.59361.05424.6836-0.6634-1.2131-1.16710.52570.2349-0.14020.60060.70860.19850.60040.08130.06980.5870.070.498916.1347.350412.9911
56.0035-2.6233-0.09576.89270.7435.8828-0.2021-0.3478-0.15890.06230.2702-0.2662-0.18110.88190.07870.49650.0403-0.02890.40380.02160.34913.167114.08498.7826
60.57661.1638-1.27712.6808-2.81763.42140.21190.02470.89150.96960.13080.0814-0.8076-0.3973-0.46040.8593-0.0061-0.07320.7354-0.08720.56558.859824.486715.1491
72.77880.24072.91224.01633.04375.008-0.3354-0.9230.48610.9289-0.2146-1.5852-1.64421.69030.39220.6092-0.0223-0.16310.7420.02410.480518.16519.878417.9133
87.6272-1.56313.80343.6133-0.62044.8668-0.175-0.59920.17920.28280.2093-0.9318-0.26030.3613-0.09640.4837-0.058-0.05260.245-0.0220.554745.802324.86838.5627
92.61060.1142-0.94674.7440.24581.77-0.3364-0.2783-0.47710.35030.2062-1.06610.40740.57230.1150.45520.0085-0.07250.3254-0.04720.66547.76778.738839.1471
104.87560.3246-2.95145.28990.88834.8494-0.54750.5676-0.7113-0.61110.28250.00930.596-0.49850.1460.4416-0.0554-0.01510.3015-0.05050.399237.02387.246831.9658
114.3784-0.47980.38866.1776-0.13953.8745-0.02740.4544-0.0639-0.06170.07170.0269-0.2636-0.63030.07120.3861-0.0195-0.04510.2318-0.04620.347840.772517.996833.6557
122.46941.18881.58042.44162.10142.3361-0.10180.6493-0.6235-1.3782-0.36080.669-0.8676-1.73230.3810.80180.0292-0.14430.6899-0.18050.627432.721618.366522.1867
135.9563-1.36730.90654.4445-1.99579.2473-0.1855-0.4345-0.7570.31280.1225-0.21290.21310.8390.07490.41540.10760.02690.426-0.03570.452657.7357-22.209333.9807
147.6802-1.3724-1.27522.52240.21974.2602-0.3607-1.3180.02270.92170.47850.21360.17510.4249-0.11310.39930.11420.03290.4451-0.00190.366445.8096-15.587842.3816
156.1932-1.2309-1.59056.2119-1.64993.0864-0.02410.25150.5579-0.45250.1940.9873-0.3429-0.2392-0.15640.3459-0.0032-0.03890.2731-0.0320.475540.646-11.138931.4231
164.6898-1.178-0.86467.05471.71773.1337-0.20290.03610.3213-0.6330.285-0.7156-0.39290.277-0.02160.32710.0499-0.02280.28050.00510.358648.3705-14.370232.7054
172.46953.65671.40266.17072.11274.2986-0.19871.2118-1.7642-0.31530.5578-0.63760.76290.489-0.30390.63340.0510.02050.4719-0.10040.588151.9709-24.93925.8245
183.20890.65314.00634.02970.43188.1426-0.07662.26150.5039-1.21740.45310.7927-0.15550.1326-0.2710.4952-0.0242-0.09730.57780.11290.514445.9222-16.483420.7375
195.0191-3.16131.03825.94861.19654.577-0.1841-0.0331-0.93740.13220.14120.67641.20450.1670.04970.5619-0.0353-0.01090.3535-0.00550.46433.2995-28.88126.0276
204.7448-2.6510.00722.95211.02994.64550.31970.3496-0.1498-0.7841-0.22620.5953-0.3159-1.011-0.00130.49130.0149-0.10970.44270.00310.4721-6.1277-19.59937.7904
218.84564.95-0.68456.20051.13594.0561-0.36361.32910.1967-0.47760.56410.1201-0.01490.1964-0.1520.42330.0192-0.00430.37970.05020.38288.279-15.20660.0431
225.51390.53520.17443.8919-2.57516.2053-0.18320.5698-0.5106-0.7883-0.0159-0.88830.78440.76090.16140.2990.03450.03470.2991-0.01240.466116.6154-17.6874.933
235.5912-1.5525-1.10699.4112-0.06455.1781-0.3379-0.45990.32570.97520.5557-0.838-0.39190.5999-0.22130.43940.0125-0.03790.3780.03960.480313.5661-11.605613.8167
244.35391.85890.0975.8889-1.81983.3576-0.18030.23370.49580.45290.19180.1468-0.59310.0380.04850.3750.0114-0.02170.31080.00690.35416.5335-15.503810.6653
258.8869-4.5096-0.00316.9160.58683.2729-0.5387-0.2706-1.34390.42820.29291.02411.1013-0.32880.30950.5606-0.00260.10560.37970.06360.41982.1157-26.408316.2081
262.94630.20312.51764.75230.238.50420.0677-1.34460.59650.8076-0.3415-0.7068-0.1840.13470.22930.5309-0.0446-0.00440.6018-0.00550.55835.0656-17.837321.9064
273.2347-0.63270.69416.35930.45715.3359-0.01890.1387-0.0936-0.32220.1507-0.78060.18051.0125-0.06690.35280.10850.05120.67950.00610.365239.5167-7.7841-11.6313
284.4908-2.4912-1.17766.1526-0.07765.21660.13190.3382-0.1064-0.5251-0.34720.7454-0.2348-0.45150.15230.34970.0260.02070.405-0.02970.34127.14190.5485-5.2266
294.51612.824-0.88028.7077-0.54922.31630.4849-0.65960.4371.4092-0.24490.4593-0.34260.3939-0.1610.4568-0.02320.02760.5879-0.06150.343930.0168-4.17616.3783
306.25381.1104-1.4385.08170.74485.71970.3554-0.134-0.56630.8003-0.0693-0.08560.8540.1449-0.24540.35380.03940.00510.52620.00270.25833.1555-6.6233-1.2339
311.77831.17770.67516.47262.51585.61960.05320.14460.0427-0.12220.2052-0.80280.30111.893-0.26380.41290.1056-0.06571.13840.07850.69745.7614-6.2949-3.6646
322.37080.83351.19313.93412.13531.45270.30290.12870.02651.15830.1203-1.22461.58892.5112-0.26990.59480.1949-0.06011.03140.07450.500642.9111-9.82736.0091
332.8444-0.71620.58246.8348-0.30963.42840.3258-0.24940.14870.5328-0.23810.8676-0.52950.0943-0.21510.44460.07080.07130.5446-0.01520.435516.1822-2.49760.1846
343.4469-1.49030.23745.1993-0.00446.46960.1875-0.6277-1.16360.4734-0.0149-0.06131.6587-0.0945-0.16340.57380.0607-0.0440.48030.01880.459621.2945-14.737960.3109
357.51821.1656-2.69247.8178-0.64067.90290.6026-0.55340.2180.3354-0.569-0.9523-0.85460.9906-0.03780.3704-0.0314-0.03260.47020.0010.436230.8997-1.86654.6897
364.79411.2541-1.97013.739-0.93235.72910.0959-0.0115-0.0502-0.22-0.41060.0317-0.8050.04270.29680.46210.04410.02970.34890.0320.42126.5653.664547.6528
376.4305-1.6748-1.17656.14881.00876.04270.32710.8353-0.042-0.9134-0.36270.4202-0.3598-0.47320.01120.3430.0215-0.0190.33130.02370.318525.4214-5.180640.9975
388.16971.62890.42972.9231-1.31336.28650.23710.325-1.2185-0.5076-0.1659-0.08640.47520.5309-0.15450.31640.04520.00170.28860.00020.267923.8249-7.699148.9975
396.4925-4.9062.55933.7572-1.79655.9269-0.2571-0.86980.23631.01610.35511.4929-0.3181-1.11260.06220.39980.0216-0.03470.5256-0.01350.59511.3943-8.629153.0962
407.93051.16731.07687.2769-0.85522.40350.13651.71540.3979-1.63240.33470.94090.43830.0525-0.36440.59630.026-0.09420.58750.03460.511514.6288-12.415543.2169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 30 )A7 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 43 )A31 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 53 )A44 - 53
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 72 )A54 - 72
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 89 )A73 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 96 )A90 - 96
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 110 )A97 - 110
8X-RAY DIFFRACTION8chain 'B' and (resid 7 through 30 )B7 - 30
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 53 )B31 - 53
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 72 )B54 - 72
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 96 )B73 - 96
12X-RAY DIFFRACTION12chain 'B' and (resid 97 through 117 )B97 - 117
13X-RAY DIFFRACTION13chain 'C' and (resid 7 through 30 )C7 - 30
14X-RAY DIFFRACTION14chain 'C' and (resid 31 through 53 )C31 - 53
15X-RAY DIFFRACTION15chain 'C' and (resid 54 through 72 )C54 - 72
16X-RAY DIFFRACTION16chain 'C' and (resid 73 through 89 )C73 - 89
17X-RAY DIFFRACTION17chain 'C' and (resid 90 through 96 )C90 - 96
18X-RAY DIFFRACTION18chain 'C' and (resid 97 through 112 )C97 - 112
19X-RAY DIFFRACTION19chain 'D' and (resid 7 through 18 )D7 - 18
20X-RAY DIFFRACTION20chain 'D' and (resid 19 through 30 )D19 - 30
21X-RAY DIFFRACTION21chain 'D' and (resid 31 through 43 )D31 - 43
22X-RAY DIFFRACTION22chain 'D' and (resid 44 through 53 )D44 - 53
23X-RAY DIFFRACTION23chain 'D' and (resid 54 through 72 )D54 - 72
24X-RAY DIFFRACTION24chain 'D' and (resid 73 through 89 )D73 - 89
25X-RAY DIFFRACTION25chain 'D' and (resid 90 through 96 )D90 - 96
26X-RAY DIFFRACTION26chain 'D' and (resid 97 through 110 )D97 - 110
27X-RAY DIFFRACTION27chain 'E' and (resid 7 through 30 )E7 - 30
28X-RAY DIFFRACTION28chain 'E' and (resid 31 through 53 )E31 - 53
29X-RAY DIFFRACTION29chain 'E' and (resid 54 through 72 )E54 - 72
30X-RAY DIFFRACTION30chain 'E' and (resid 73 through 89 )E73 - 89
31X-RAY DIFFRACTION31chain 'E' and (resid 90 through 96 )E90 - 96
32X-RAY DIFFRACTION32chain 'E' and (resid 97 through 111 )E97 - 111
33X-RAY DIFFRACTION33chain 'F' and (resid 7 through 18 )F7 - 18
34X-RAY DIFFRACTION34chain 'F' and (resid 19 through 30 )F19 - 30
35X-RAY DIFFRACTION35chain 'F' and (resid 31 through 43 )F31 - 43
36X-RAY DIFFRACTION36chain 'F' and (resid 44 through 53 )F44 - 53
37X-RAY DIFFRACTION37chain 'F' and (resid 54 through 72 )F54 - 72
38X-RAY DIFFRACTION38chain 'F' and (resid 73 through 89 )F73 - 89
39X-RAY DIFFRACTION39chain 'F' and (resid 90 through 96 )F90 - 96
40X-RAY DIFFRACTION40chain 'F' and (resid 97 through 111 )F97 - 111

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