[English] 日本語
Yorodumi
- PDB-4wan: Crystal structure of Msl5 protein in complex with RNA at 1.8 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wan
TitleCrystal structure of Msl5 protein in complex with RNA at 1.8 A
Components
  • Branchpoint-bridging protein
  • RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
KeywordsPROTEIN BINDING/RNA / Msl5 / BBP / RNA binding / yeast pre-mRNA splicing / PROTEIN BINDING-RNA complex
Function / homology
Function and homology information


pre-mRNA branch point binding / regulation of mRNA splicing, via spliceosome / commitment complex / spliceosomal complex assembly / mRNA splicing, via spliceosome / mRNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / K Homology domain, type 1 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / K Homology domain, type 1 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / RNA / RNA (> 10) / Branchpoint-bridging protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJacewicz, A. / Smith, P. / Chico, L. / Schwer, B. / Shuman, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM52470 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM50288 United States
CitationJournal: Rna / Year: 2015
Title: Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs.
Authors: Jacewicz, A. / Chico, L. / Smith, P. / Schwer, B. / Shuman, S.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Branchpoint-bridging protein
B: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
C: Branchpoint-bridging protein
D: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
E: Branchpoint-bridging protein
F: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
G: Branchpoint-bridging protein
H: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,62119
Polymers71,6588
Non-polymers96311
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-95 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.380, 130.970, 53.370
Angle α, β, γ (deg.)90.00, 117.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / RNA chain , 2 types, 8 molecules ACEGBDFH

#1: Protein
Branchpoint-bridging protein / Mud synthetic-lethal 5 protein / Splicing factor 1 / Zinc finger protein BBP


Mass: 14455.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MSL5, BBP, SF1, YLR116W, L2949 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q12186
#2: RNA chain
RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')


Mass: 3459.138 Da / Num. of mol.: 4 / Source method: obtained synthetically

-
Non-polymers , 4 types, 488 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 2.1-2.3 M ammonium sulfate, 0.01 M magnesium acetate, 0.05 M MES
PH range: 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.072 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.8→45.61 Å / Num. obs: 59297 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.4 / % possible all: 95.4

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.61 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3010 5.08 %RANDOM
Rwork0.175 ---
obs0.18 59249 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 627 58 477 4896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014554
X-RAY DIFFRACTIONf_angle_d1.0656270
X-RAY DIFFRACTIONf_dihedral_angle_d15.0651866
X-RAY DIFFRACTIONf_chiral_restr0.045723
X-RAY DIFFRACTIONf_plane_restr0.004716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8041-1.83520.3061410.32522606X-RAY DIFFRACTION86
1.8352-1.86860.34031470.31272663X-RAY DIFFRACTION91
1.8686-1.90460.33891330.29532858X-RAY DIFFRACTION95
1.9046-1.94340.30721340.28852814X-RAY DIFFRACTION95
1.9434-1.98570.2771410.27682847X-RAY DIFFRACTION95
1.9857-2.03190.27971390.2612781X-RAY DIFFRACTION95
2.0319-2.08270.28511460.26182849X-RAY DIFFRACTION95
2.0827-2.1390.26481490.24762878X-RAY DIFFRACTION95
2.139-2.20190.25121490.23862799X-RAY DIFFRACTION95
2.2019-2.27290.22031420.23382804X-RAY DIFFRACTION95
2.2729-2.35420.24231620.22582830X-RAY DIFFRACTION95
2.3542-2.44840.25781360.22572845X-RAY DIFFRACTION95
2.4484-2.55980.22761810.21872805X-RAY DIFFRACTION94
2.5598-2.69470.22221550.22182813X-RAY DIFFRACTION95
2.6947-2.86340.24051650.20222806X-RAY DIFFRACTION94
2.8634-3.08430.20581440.17242849X-RAY DIFFRACTION95
3.0843-3.39440.19391600.14952826X-RAY DIFFRACTION95
3.3944-3.8850.15431370.11832849X-RAY DIFFRACTION95
3.885-4.8920.13121600.09332863X-RAY DIFFRACTION95
4.892-32.74790.1751670.12472858X-RAY DIFFRACTION94
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)
18.195-7.66632.00482.2549-1.78811.85080.0738-0.3046-0.1062-0.27760.1688-0.14030.14840.2894-0.31720.1690.03710.04130.2033-0.04920.263110.41610.664316.939
27.8003-2.5866-1.81057.65182.31366.9610.3739-0.12640.31840.0691-0.20960.2817-0.3765-0.5611-0.19460.13230.00940.03870.13540.00420.1474-1.08724.66929.0797
35.7014-2.52778.00371.0851-3.15742.05350.05140.67380.0248-0.1977-0.3236-0.4165-0.00931.23440.30350.26370.01480.14260.26190.03360.294414.458620.81193.026
42.99341.48853.97611.82971.8666.41210.02390.0325-0.04980.00420.02480.04420.0852-0.0048-0.01420.12940.00550.04570.09450.03550.14243.392711.11357.2864
52.3066-8.47175.82748.1758-6.69897.663-0.5179-0.56070.51060.34280.3604-0.7982-0.4845-0.26720.21440.1852-0.01640.01970.2179-0.03520.278111.440722.671816.4096
60.04890.0112-0.00750.0014-0.00420.0030.04950.60011.1049-0.6078-0.03380.3073-0.9709-0.6049-0.06611.18990.1660.13560.2122-0.00970.49112.874137.37128.4829
76.30440.9832-2.71152.1154-1.65718.56610.36870.5180.6573-0.43030.1082-0.2567-1.22070.1405-0.37750.44570.0490.14710.24460.03530.28318.82532.2084-5.4991
84.50371.15252.39793.4997-2.58836.47980.11470.22180.6109-0.4287-0.094-0.0608-0.5217-0.35430.01520.28830.08270.10480.20180.0020.22314.74724.0121-2.1113
93.3236-0.23951.14783.9419-1.72952.6050.0404-0.1966-0.2920.2516-0.01370.1989-0.1576-0.141-0.03820.10080.01530.03170.1144-0.00450.16017.763861.002813.484
102.5953-0.57160.56112.38191.96135.16990.05410.2474-0.0583-0.0683-0.0164-0.2745-0.10820.2498-0.04970.0947-0.030.03080.10570.02350.203917.46164.368813.569
114.24441.59462.08186.63961.55225.4497-0.05540.04620.6383-0.12-0.04730.3304-0.4522-0.41650.0810.16320.02640.05640.16650.01590.20659.479271.874118.7445
121.24290.4338-0.34524.7761-5.1129.46770.0318-0.0215-0.1688-0.6481-0.1358-0.14370.6075-0.08390.11740.10490.02950.03420.1528-0.01860.22988.450960.42654.7371
133.3248-1.4662-2.97927.82335.3494.93440.2473-2.4857-2.34341.81661.24710.46241.3883-0.1534-1.36440.53760.14-0.16540.71590.24530.813610.902942.662216.6015
143.2676-1.2065-0.53245.1481-0.36439.74770.01410.0221-1.2469-0.46490.0925-0.15140.73750.1505-0.10920.2280.0060.00610.1341-0.00090.472524.085648.431515.6138
152.0102-7.6194-2.3367.4068-2.24076.93180.2243-0.3878-1.0061-0.1119-0.5253-1.49831.07280.70510.24130.5873-0.0922-0.16070.46860.22370.990331.771645.38920.9756
168.7087-4.5599-0.23033.392.69436.78540.1505-0.7105-0.74170.36040.16380.29560.93630.6189-0.34410.22030.033-0.05610.25190.06770.288321.327454.896119.2946
173.35745.2521.15489.16794.48947.61810.2257-0.03460.8566-0.2425-0.36450.681-0.3813-0.50880.19460.1539-0.04660.10850.24630.06070.4019-5.386267.91177.7751
184.62972.38971.37893.7534-0.14932.5701-0.08650.4509-0.2677-0.148-0.0790.27260.1431-0.19840.15210.1406-0.0110.01320.1681-0.0450.2511-10.672552.16216.7937
194.07271.35112.25755.81323.04988.4652-0.12380.50210.0637-0.7287-0.16781.11-0.2152-1.15260.25680.1939-0.0394-0.08380.28660.05440.449-12.805958.89020.0232
200.16530.97831.0655.73146.19396.6847-0.2020.6810.4951-0.9617-0.82890.5516-0.248-1.09271.04411.1304-0.1008-0.36660.50870.02221.2344-16.85862.7322-6.8002
215.6379-1.5569-0.27147.04680.73264.06630.09520.28880.2898-0.27050.06560.1156-0.2190.0808-0.17550.0923-0.02020.05340.17890.03670.2284-5.986660.10029.867
224.98251.00321.31024.10590.28214.4255-0.0017-0.1214-0.83420.2702-0.27680.26940.6026-0.59380.23840.2592-0.09240.08570.2325-0.07290.4912-16.667439.75739.954
239.68381.27980.97670.89121.42499.0267-0.34390.8728-0.4502-0.6266-0.13840.70551.1415-0.39810.33080.2296-0.11210.04080.3517-0.05780.4298-16.999645.86193.7697
243.92261.6335-2.03767.5363-1.33375.5084-0.0975-0.0418-0.0108-0.04690.3563-0.6073-0.20210.4373-0.24260.14980.00740.02440.2144-0.06610.19115.686424.920227.358
252.274-0.08250.65485.91215.30575.73360.009-0.12760.13320.6909-0.28310.52570.4375-0.26870.25790.28760.01630.13780.24120.00630.2169-4.297922.499135.1857
267.03313.14534.95167.19810.66913.89510.3151-0.58610.40580.3662-0.553-0.0752-0.0747-0.23750.18730.48350.1489-0.140.6938-0.09170.333412.384823.438834.7541
271.10462.5906-0.3257.4393-1.16220.20960.4885-0.0156-0.6006-0.0798-0.1732-0.04730.7853-0.6208-0.31960.9595-0.1495-0.12010.9267-0.52260.87818.059920.509942.7123
280.1886-1.0907-0.63045.55323.3382.0171-0.6367-2.0866-0.26892.09831.2024-0.64891.38580.796-0.47050.73020.3862-0.11291.1248-0.42730.667412.80517.302734.0681
293.84121.4575-0.79972.8324-1.60592.8785-0.25020.0926-0.06960.20080.24760.26210.0228-0.3580.0070.23050.03580.10370.2322-0.03370.1743-2.667220.485124.9409
306.5088-4.1976-1.05026.5716-5.11088.8184-0.1776-0.38031.49210.89791.0259-2.2225-1.05152.8656-0.76620.6413-0.0804-0.13930.663-0.26720.6492-0.955541.930125.1372
313.55430.6477-0.70146.7351.28026.83420.2549-0.23450.4673-0.48490.23540.2875-1.4056-0.3378-0.33940.43290.02210.12590.2045-0.04530.3269-5.148138.630337.9405
321.99948.8824-4.27738.33-0.90732.0054-0.04890.42660.89691.24210.54571.4227-2.0617-0.8687-0.35220.88730.29180.41250.66630.25770.6415-5.224346.199743.9697
336.4258-4.4446-1.00935.8494.5059.4301-0.1841-0.50510.50710.43780.31530.0668-0.44160.2105-0.16720.22720.04530.05450.3176-0.07770.24511.235433.096339.0692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 145 THROUGH 153 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 154 THROUGH 170 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 171 THROUGH 183 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 184 THROUGH 223 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 224 THROUGH 242 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 243 THROUGH 249 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 250 THROUGH 268 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 3 THROUGH 10 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 145 THROUGH 170 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 171 THROUGH 203 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 204 THROUGH 215 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 216 THROUGH 242 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 243 THROUGH 249 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 250 THROUGH 262 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 263 THROUGH 269 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 2 THROUGH 10 )
17X-RAY DIFFRACTION17CHAIN 'E' AND (RESID 146 THROUGH 153 )
18X-RAY DIFFRACTION18CHAIN 'E' AND (RESID 154 THROUGH 183 )
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 184 THROUGH 200 )
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESID 201 THROUGH 210 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 211 THROUGH 243 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 244 THROUGH 267 )
23X-RAY DIFFRACTION23CHAIN 'F' AND (RESID 2 THROUGH 10 )
24X-RAY DIFFRACTION24CHAIN 'G' AND (RESID 147 THROUGH 170 )
25X-RAY DIFFRACTION25CHAIN 'G' AND (RESID 171 THROUGH 190 )
26X-RAY DIFFRACTION26CHAIN 'G' AND (RESID 191 THROUGH 195 )
27X-RAY DIFFRACTION27CHAIN 'G' AND (RESID 196 THROUGH 206 )
28X-RAY DIFFRACTION28CHAIN 'G' AND (RESID 207 THROUGH 215 )
29X-RAY DIFFRACTION29CHAIN 'G' AND (RESID 216 THROUGH 243 )
30X-RAY DIFFRACTION30CHAIN 'G' AND (RESID 244 THROUGH 249 )
31X-RAY DIFFRACTION31CHAIN 'G' AND (RESID 250 THROUGH 263 )
32X-RAY DIFFRACTION32CHAIN 'G' AND (RESID 264 THROUGH 268 )
33X-RAY DIFFRACTION33CHAIN 'H' AND (RESID 3 THROUGH 10 )

+
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://pdbjlvh1.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