[English] 日本語
Yorodumi
- PDB-7wm3: hnRNP A2/B1 RRMs in complex with single-stranded DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wm3
TitlehnRNP A2/B1 RRMs in complex with single-stranded DNA
Components
  • DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
  • Heterogeneous nuclear ribonucleoproteins A2/B1
KeywordsDNA BINDING PROTEIN/DNA / homodimerization / U-shaped structured DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of telomerase RNA reverse transcriptase activity / miRNA transport / positive regulation of telomere maintenance via telomere lengthening / RNA transport / G-quadruplex DNA unwinding / primary miRNA processing / single-stranded telomeric DNA binding / N6-methyladenosine-containing RNA reader activity / G-rich strand telomeric DNA binding / miRNA binding ...positive regulation of telomerase RNA reverse transcriptase activity / miRNA transport / positive regulation of telomere maintenance via telomere lengthening / RNA transport / G-quadruplex DNA unwinding / primary miRNA processing / single-stranded telomeric DNA binding / N6-methyladenosine-containing RNA reader activity / G-rich strand telomeric DNA binding / miRNA binding / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / Cajal body / mRNA export from nucleus / pre-mRNA intronic binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / molecular condensate scaffold activity / mRNA 3'-UTR binding / spliceosomal complex / mRNA processing / nuclear matrix / mRNA splicing, via spliceosome / chromosome, telomeric region / ribonucleoprotein complex / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
hnRNP A2/B1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Heterogeneous nuclear ribonucleoproteins A2/B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsAbula, A. / Liu, Y. / Guo, H. / Li, T. / Ji, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Insight Into hnRNP A2/B1 Homodimerization and DNA Recognition.
Authors: Liu, Y. / Abula, A. / Xiao, H. / Guo, H. / Li, T. / Zheng, L. / Chen, B. / Nguyen, H.C. / Ji, X.
History
DepositionJan 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoproteins A2/B1
B: Heterogeneous nuclear ribonucleoproteins A2/B1
C: Heterogeneous nuclear ribonucleoproteins A2/B1
D: Heterogeneous nuclear ribonucleoproteins A2/B1
E: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
F: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
G: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
H: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)97,2318
Polymers97,2318
Non-polymers00
Water17,384965
1
A: Heterogeneous nuclear ribonucleoproteins A2/B1
C: Heterogeneous nuclear ribonucleoproteins A2/B1
E: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
G: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)48,6154
Polymers48,6154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heterogeneous nuclear ribonucleoproteins A2/B1
D: Heterogeneous nuclear ribonucleoproteins A2/B1
F: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
H: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)48,6154
Polymers48,6154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.190, 101.620, 111.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Heterogeneous nuclear ribonucleoproteins A2/B1 / hnRNP A2/B1


Mass: 20534.172 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 15-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA2B1, HNRPA2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22626
#2: DNA chain
DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Mass: 3773.462 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 965 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM LiCl, 0.1M HEPEs pH 7.0 , 20 % (w/v) polyethylene glycol (PEG) 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.62→38.1 Å / Num. obs: 118490 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.4
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.558 / Mean I/σ(I) obs: 2 / Num. unique obs: 8688 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.10_2148refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1Q

1u1q


Resolution: 1.62→33.027 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 2000 1.69 %
Rwork0.1632 116385 -
obs0.1636 118385 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.21 Å2 / Biso mean: 33.1193 Å2 / Biso min: 11.85 Å2
Refinement stepCycle: final / Resolution: 1.62→33.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 1016 0 965 7761
Biso mean---37.63 -
Num. residues----764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157036
X-RAY DIFFRACTIONf_angle_d1.3319664
X-RAY DIFFRACTIONf_chiral_restr0.0741012
X-RAY DIFFRACTIONf_plane_restr0.0091092
X-RAY DIFFRACTIONf_dihedral_angle_d19.854028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.62-1.66050.29911410.27048231
1.6605-1.70540.28591420.2428209
1.7054-1.75560.2581410.22928264
1.7556-1.81230.23061420.22178209
1.8123-1.8770.22881410.19798241
1.877-1.95220.18511420.16988278
1.9522-2.0410.19651410.16968239
2.041-2.14860.20911430.16438271
2.1486-2.28320.18741430.16288294
2.2832-2.45940.19241420.16338303
2.4594-2.70680.17791430.16628332
2.7068-3.09830.20581440.16818382
3.0983-3.90250.16371460.14678438
3.9025-100.1491490.14058694
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)
10.0271-0.02790.02490.0201-0.02350.01410.1324-0.1372-0.0416-0.0394-0.1448-0.02830.0298-0.1772-00.16060.01560.00520.1769-0.03540.1404-12.7192-1.5219.2325
20.1021-0.02720.10490.24260.00320.2023-0.0468-0.3363-0.18770.38740.05110.05070.5332-0.04390.01640.3064-0.05250.03450.25070.05440.1861-11.1826-15.891726.1559
30.1617-0.04660.09380.0434-0.01170.04620.1564-0.134-0.1642-0.0348-0.12320.17180.1187-0.243100.2482-0.0599-0.00170.2252-0.02010.2268-14.8655-16.600216.2443
40.36190.11370.06090.15880.06140.12510.0273-0.14870.00170.1433-0.0344-0.03310.0716-0.0929-00.19010.0005-0.01440.19160.00620.1327-6.6897-7.174622.023
50.0189-0.0243-0.00130.0676-0.00920.00830.1130.1702-0.10740.1123-0.1375-0.10930.0323-0.00640.00010.14090.0019-0.01010.1929-0.01230.19620.3213-3.25778.6431
60.04620.0266-0.05040.01890.00820.10060.01770.03240.11060.0998-0.1293-0.2505-0.0969-0.0003-0.00190.1942-0.0198-0.04940.12280.02060.24499.432215.052611.0278
70.2146-0.12990.30110.9415-0.34110.46110.0613-0.37950.27940.480.0169-0.1108-0.44010.10870.1170.3274-0.0313-0.06510.2502-0.08480.24987.456513.57321.7222
80.04290.0838-0.01470.18370.15810.18420.0309-0.1390.04730.11320.0767-0.2714-0.21190.12110.00250.2128-0.0812-0.03120.1870.0180.298516.767211.895310.8264
90.09380.0955-0.01270.19130.15220.16360.0408-0.10330.09650.0882-0.0475-0.0176-0.1137-0.0394-00.17730.0059-0.03580.1656-0.00180.2012.78277.435716.0267
100.0586-0.0323-0.05260.08190.08390.0730.00610.1976-0.0458-0.1303-0.0834-0.12570.0186-0.3661-0.00050.17060.0276-0.01290.21090.00340.18675.72975.63276.2851
110.12560.0178-0.01540.0191-0.02330.08650.04640.0764-0.08830.0107-0.04630.07250.0486-0.079900.1673-0.01790.00110.18390.01180.1984-26.2625-8.53663.5252
120.1556-0.07230.01620.0405-0.00620.10.07580.04460.23830.19330.02650.2175-0.0817-0.3909-00.18610.03890.04590.2799-0.00650.2519-37.8572.44137.0242
130.2780.1864-0.15010.2842-0.06910.77940.06050.07870.0890.0858-0.03540.0566-0.0288-0.197300.14940.001-0.00330.18050.01560.182-30.3955-0.06833.8974
140.02610.0489-0.00860.0936-0.05380.0388-0.0140.02640.35760.0161-0.21410.1780.11820.17030.00030.1745-0.00430.00420.2610.04360.2214-18.01880.391-7.4541
150.11520.0271-0.05230.09780.05510.0940.18050.20120.0696-0.2337-0.23710.02210.08740.15380.00010.26590.0794-0.03240.30850.03770.1497-16.258-15.6741-21.5195
160.0554-0.036-0.01960.0606-0.01560.0273-0.02780.04-0.2344-0.0295-0.00710.47750.2841-0.1716-0.00190.2448-0.0335-0.06850.27070.02850.2413-26.6685-17.4715-18.6722
170.11840.16350.02230.24350.01140.02620.01140.07630.1226-0.2128-0.00730.09960.13260.1141-0.02470.24220.06470.00760.40430.06420.1312-17.6497-11.2967-28.0848
180.032-0.0245-0.00370.0847-0.05010.02640.03620.07190.00930.007-0.07340.02940.0169-0.0191-0.01230.20180.0164-0.01740.26330.03530.1575-24.5707-7.5724-13.6072
190.0102-0.01610.0050.0213-0.00460.01180.1092-0.1285-0.0478-0.03720.0017-0.00080.1433-0.1976-0.00010.26890.0212-0.03060.26710.05720.2315-17.0866-18.5118-11.6147
200.04470.01710.05260.0883-0.03550.06790.0599-0.10240.12990.0005-0.3001-0.08820.06630.4259-0.0160.1627-0.0284-0.04970.28780.05490.2478-14.4005-5.0967-14.658
210.5488-0.0481-0.16380.5721-0.31830.7252-0.05830.1305-0.0302-0.2592-0.1-0.2941-0.05170.1688-0.23860.19870.00350.09340.19480.04970.259119.5504-2.8526-15.3572
220.61110.23290.12170.96860.06120.55520.03560.0806-0.0035-0.0412-0.0332-0.12370.0183-0.07210.00410.16890.02620.02650.12230.01170.16581.4933-21.2649-5.711
230.0559-0.0187-0.06860.03740.01290.08760.04390.01440.0353-0.0130.0799-0.199-0.148-0.162500.2556-0.0017-0.03860.2646-0.01230.21544.805815.408-19.5591
240.1253-0.3014-0.01190.8298-0.00290.02960.01340.16870.0132-0.24130.0318-0.4063-0.1619-0.54820.01110.2803-0.0272-0.00170.32660.0210.162-1.153515.631-34.5954
25-0.0189-0.00570.00060.08230.04380.2142-0.06360.10280.1043-0.26840.0236-0.30770.1297-0.18570.00020.3217-0.07850.00580.2614-0.01910.20920.71875.6902-31.4441
260.02980.0426-0.05520.027-0.04350.16180.01160.0576-0.03950.2526-0.0122-0.166-0.1221-0.22150.00010.30950.0359-0.03840.21950.00210.1931.945519.9615-23.9016
270.3381-0.1164-0.14570.0370.02940.0597-0.13610.2142-0.04150.04940.0375-0.1835-0.0634-0.4535-0.02410.19680.0895-0.03840.37380.04310.0913-5.591514.8488-24.0773
280.05850.04280.00780.04680.02620.0081-0.2006-0.28650.0111-0.05570.03180.0332-0.037-0.08980.00020.2190.0599-0.01840.2618-0.00270.2258-8.928910.0259-11.9898
290.0817-0.0186-0.05450.04810.02140.0447-0.2214-0.4075-0.27610.16840.20050.1797-0.1831-0.31620.00070.28440.1355-0.02390.253-0.01120.2563-9.253824.37153.7914
300.0553-0.00330.03860.03010.03030.0552-0.1237-0.13610.4896-0.01280.1501-0.471-0.2070.0696-0.00410.2660.0374-0.04590.15740.00470.409-6.025130.8789-4.1716
310.03710.0364-0.02260.1410.05160.2174-0.007-0.0939-0.10830.03410.05160.2917-0.18390.05920.00070.27980.12180.06830.25940.07070.3143-17.2274263.3696
320.1156-0.0824-0.04370.04790.02860.03740.2017-0.0757-0.1979-0.07070.06710.2835-0.05990.14860.0040.22770.0982-0.03220.23880.02650.2588-12.900823.5866-5.9809
330.07-0.0821-0.00520.10930.03960.05810.0622-0.0650.0838-0.1739-0.1071-0.2742-0.1525-0.14380.00080.21130.0641-0.03840.2215-0.01680.2468-2.362920.9719-6.4459
340.02440.0244-0.0120.0356-0.01130.0003-0.108-0.1568-0.36220.08030.1644-0.14440.24110.0194-0.00090.24870.0481-0.02510.20320.0350.3453-10.764914.363-2.1706
350.01670.11560.10480.24990.26730.35540.01180.02390.01580.0458-0.0790.01530.1164-0.13570.00010.16940.00760.0040.1481-0.00090.1682-7.4438-16.41887.6504
360.0513-0.02220.030.1435-0.13690.05550.0453-0.04670.35580.1991-0.01180.14620.1203-0.0651-0.00610.11850.0230.01040.15050.02620.2712-20.404410.43554.768
370.0045-0.0375-0.0150.07390.11320.3046-0.01830.02030.0995-0.10110.0149-0.1679-0.14670.141-00.1795-0.004-0.00990.16310.02730.237113.98595.7779-3.1154
380.1847-0.0786-0.07280.16960.004-0.012-0.1941-0.023-0.0847-0.26490.3599-0.2142-0.0219-0.03840.05750.2161-0.0158-0.01430.27890.08620.1517-6.5814-0.6251-24.36
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 26 )A15 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 44 )A27 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 63 )A45 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 101 )A64 - 101
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 112 )A102 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 124 )A113 - 124
7X-RAY DIFFRACTION7chain 'A' and (resid 125 through 135 )A125 - 135
8X-RAY DIFFRACTION8chain 'A' and (resid 136 through 154 )A136 - 154
9X-RAY DIFFRACTION9chain 'A' and (resid 155 through 179 )A155 - 179
10X-RAY DIFFRACTION10chain 'A' and (resid 180 through 193 )A180 - 193
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 26 )B15 - 26
12X-RAY DIFFRACTION12chain 'B' and (resid 27 through 44 )B27 - 44
13X-RAY DIFFRACTION13chain 'B' and (resid 45 through 101 )B45 - 101
14X-RAY DIFFRACTION14chain 'B' and (resid 102 through 112 )B102 - 112
15X-RAY DIFFRACTION15chain 'B' and (resid 113 through 124 )B113 - 124
16X-RAY DIFFRACTION16chain 'B' and (resid 125 through 135 )B125 - 135
17X-RAY DIFFRACTION17chain 'B' and (resid 136 through 154 )B136 - 154
18X-RAY DIFFRACTION18chain 'B' and (resid 155 through 171 )B155 - 171
19X-RAY DIFFRACTION19chain 'B' and (resid 172 through 179 )B172 - 179
20X-RAY DIFFRACTION20chain 'B' and (resid 180 through 193 )B180 - 193
21X-RAY DIFFRACTION21chain 'C' and (resid 15 through 101 )C15 - 101
22X-RAY DIFFRACTION22chain 'C' and (resid 102 through 193 )C102 - 193
23X-RAY DIFFRACTION23chain 'D' and (resid 15 through 26 )D15 - 26
24X-RAY DIFFRACTION24chain 'D' and (resid 27 through 44 )D27 - 44
25X-RAY DIFFRACTION25chain 'D' and (resid 45 through 63 )D45 - 63
26X-RAY DIFFRACTION26chain 'D' and (resid 64 through 81 )D64 - 81
27X-RAY DIFFRACTION27chain 'D' and (resid 82 through 101 )D82 - 101
28X-RAY DIFFRACTION28chain 'D' and (resid 102 through 112 )D102 - 112
29X-RAY DIFFRACTION29chain 'D' and (resid 113 through 124 )D113 - 124
30X-RAY DIFFRACTION30chain 'D' and (resid 125 through 135 )D125 - 135
31X-RAY DIFFRACTION31chain 'D' and (resid 136 through 153 )D136 - 153
32X-RAY DIFFRACTION32chain 'D' and (resid 154 through 162 )D154 - 162
33X-RAY DIFFRACTION33chain 'D' and (resid 163 through 179 )D163 - 179
34X-RAY DIFFRACTION34chain 'D' and (resid 180 through 193 )D180 - 193
35X-RAY DIFFRACTION35chain 'E' and (resid 1 through 12 )E1 - 12
36X-RAY DIFFRACTION36chain 'F' and (resid 1 through 12 )F1 - 12
37X-RAY DIFFRACTION37chain 'G' and (resid 1 through 12 )G1 - 12
38X-RAY DIFFRACTION38chain 'H' and (resid 1 through 12 )H1 - 12

+
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